Patent Publication Number: US-2004044181-A1

Title: Novel nucleic acids and polypeptides

Description:
1. TECHNICAL FIELD  
       [0001] The present invention provides novel polynucleotides and proteins encoded by such polo nucleotides, along with uses for these polynucleotides and proteins, for example in therapeutic, diagnostic and research methods.  
       2. BACKGROUND  
       [0002] Technology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, circulating soluble factors, chemokines, and interleukins) has matured rapidly over the past decade. The now routine hybridization cloning and expression cloning techniques clone novel polynucleotides “directly” in the sense that they rely on information directly related to the discovered protein (i.e., partial DNA/amino acid sequence of the protein in the case of hybridization cloning; activity of the protein in the case of expression cloning). More recent “indirect” cloning techniques such as signal sequence cloning, which isolates DNA sequences based on the presence of a now well-recognized secretory leader sequence motif, as well as various PCR-based or low stringency hybridization-based cloning techniques, have advanced the state of the art by making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity, for example, by virtue of their secreted nature in the case of leader sequence cloning, by virtue of their cell or tissue source in the case of PCR-based techniques, or by virtue of structural similarity to other genes of known biological activity.  
       [0003] Identified polynucleotide and polypeptide sequences have numerous applications in, for example, diagnostics, forensics, gene mapping; identification of mutations responsible for genetic disorders or other traits, to assess biodiversity, and to produce many other types of data and products dependent on DNA and amino acid sequences.  
       3. SUMMARY OF THE INVENTION  
       [0004] The compositions of the present invention include novel isolated polypeptides, novel isolated polynucleotides encoding such polypeptides, including recombinant DNA molecules, cloned genes or degenerate variants thereof, especially naturally occurring variants such as allelic variants, antisense polynucleotide molecules, and antibodies that specifically recognize one or more epitopes present on such polypeptides, as well as hybridomas producing such antibodies.  
       [0005] The compositions of the present invention additionally include vectors, including expression vectors, containing the polynucleotides of the invention, cells genetically engineered to contain such polynucleotides and cells genetically engineered to express such polynucleotides.  
       [0006] The present invention relates to a collection or library of at least one novel nucleic acid sequence assembled from expressed sequence tags (ESTs) isolated mainly by sequencing by hybridization (SBH), and in some cases, sequences obtained from one or more public databases. The invention relates also to the proteins encoded by such polynucleotides, along with therapeutic, diagnostic and research utilities for these polynucleotides and proteins. These nucleic acid sequences are designated as SEQ ID NO: 1-245. The polypeptides sequences are designated SEQ ID NO: 246-490. The nucleic acids and polypeptides are provided in the Sequence Listing. In the nucleic acids provided in the Sequence Listing, A is adenosine; C is cytosine; G is guanine; T is thymine; and N is unknown or any of the four bases.  
       [0007] The nucleic acid sequences of the present invention also include, nucleic acid sequences that hybridize to the complement of SEQ ID NO: 1-245 under stringent hybridization conditions; nucleic acid sequences which are allelic variants or species homologues of any of the nucleic acid sequences recited above, or nucleic acid sequences that encode a peptide comprising a specific domain or truncation of the peptides encoded by SEQ ID NO: 1-245. A polynucleotide comprising a nucleotide sequence having at least 90% identity to an identifying sequence of SEQ ID NO: 1-245 or a degenerate variant or fragment thereof. The identifying sequence can be 100 base pairs in length.  
       [0008] The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-245. The sequence information can be a segment of any one of SEQ ID NO: 1-245 that uniquely identifies or represents the sequence information of SEQ ID NO: 1-245.  
       [0009] A collection as used in this application can be a collection of only one polynucleotide. The collection of sequence information or identifying information of each sequence can be provided on a nucleic acid array. In one embodiment, segments of sequence information are provided on a nucleic acid array to detect the polynucleotide that contains the segment. The array can be designed to detect full-match or mismatch to the polynucleotide that contains the segment. The collection can also be provided in a computer-readable format.  
       [0010] This invention also includes the reverse or direct complement of any of the nucleic acid sequences recited above; cloning or expression vectors containing the nucleic acid sequences; and host cells or organisms transformed with these expression vectors. Nucleic acid sequences (or their reverse or direct complements) according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology, such as use as hybridization probes, use as primers for PCR, use in an array, use in computer-readable media, use in sequencing full-length genes, use for chromosome and gene mapping, use in the recombinant production of protein, and use in the generation of anti-sense DNA or RNA, their chemical analogs and the like.  
       [0011] In a preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-245 or novel segments or parts of the nucleic acids of the invention are used as primers in expression assays that are well known in the art. In a particularly preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-245 or novel segments or parts of the nucleic acids provided herein are used in diagnostics for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.  
       [0012] The isolated polynucleotides of the invention include, but are not limited to, a polynucleotide comprising any one of the nucleotide sequences set forth in SEQ ID NO: 1-245; a polynucleotide comprising any of the full length protein coding sequences of SEQ ID NO: 1-245; and a polynucleotide comprising any of the nucleotide sequences of the mature protein coding sequences of SEQ ID NO: 1-245. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent hybridization conditions to (a) the complement of any one of the nucleotide sequences set forth in SEQ ID NO: 1-245; (b) a nucleotide sequence encoding any one of the amino acid sequences set forth in the Sequence Listing; (c) a polynucleotide which is an allelic variant of any polynucleotides recited above; (d) a polynucleotide which encodes a species homolog (e.g. orthologs) of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of any of the polypeptides comprising an amino acid sequence set forth in the Sequence Listing.  
       [0013] The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising any of the amino acid sequences set forth in SEQ ID NO: 246-490; or the corresponding full length or mature protein. Polypeptides of the invention also include polypeptides with biological activity that are encoded by (a) any of the polynucleotides having a nucleotide sequence set forth in SEQ ID NO: 1-245; or (b) polynucleotides that hybridize to the complement of the polynucleotides of (a) under stringent hybridization conditions. Biologically or immunologically active variants of any of the polypeptide sequences in the Sequence Listing, and “substantial equivalents” thereof (e.g., with at least about 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99% amino acid sequence identity) that preferably retain biological activity are also contemplated. The polypeptides of the invention may be wholly or partially chemically synthesized but are preferably produced by recombinant means using the genetically engineered cells (e.g. host cells) of the invention.  
       [0014] The invention also provides compositions comprising a polypeptide of the invention. Polypeptide compositions of the invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.  
       [0015] The invention also provides host cells transformed or transfected with a polynucleotide of the invention.  
       [0016] The invention also relates to methods for producing a polypeptide of the invention comprising growing a culture of the host cells of the invention in a suitable culture medium under conditions permitting expression of the desired polypeptide, and purifying the polypeptide from the culture or from the host cells. Preferred embodiments include those in which the protein produced by such process is a mature form of the protein.  
       [0017] Polynucleotides according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology. These techniques include use as hybridization probes, use as oligomers, or primers, for PCR, use for chromosome and gene mapping, use in the recombinant production of protein, and use in generation of anti-sense DNA or RNA, their chemical analogs and the like. For example, when the expression of an mRNA is largely restricted to a particular cell or tissue type, polynucleotides of the invention can be used as hybridization probes to detect the presence of the particular cell or tissue mRNA in a sample using, e.g., in situ hybridization.  
       [0018] In other exemplary embodiments, the polynucleotides are used in diagnostics as expressed sequence tags for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.  
       [0019] The polypeptides according to the invention can be used in a variety of conventional procedures and methods that are currently applied to other proteins. For example, a polypeptide of the invention can be used to generate an antibody that specifically binds the polypeptide. Such antibodies, particularly monoclonal antibodies, are useful for detecting or quantitating the polypeptide in tissue. The polypeptides of the invention can also be used as molecular weight markers, and as a food supplement.  
       [0020] Methods are also provided for preventing, treating, or ameliorating a medical condition which comprises the step of administering to a mammalian subject a therapeutically effective amount of a composition comprising a polypeptide of the present invention and a pharmaceutically acceptable carrier.  
       [0021] In particular, the polypeptides and polynucleotides of the invention can be utilized, for example, in methods for the prevention and/or treatment of disorders involving aberrant protein expression or biological activity.  
       [0022] The present invention further relates to methods for detecting the presence of the polynucleotides or polypeptides of the invention in a sample. Such methods can, for example, be utilized as part of prognostic and diagnostic evaluation of disorders as recited herein and for the identification of subjects exhibiting a predisposition to such conditions. The invention provides a method for detecting the polynucleotides of the invention in a sample, comprising contacting the sample with a compound that binds to and forms a complex with the polynucleotide of interest for a period sufficient to form the complex and under conditions sufficient to form a complex and detecting the complex such that if a complex is detected, the polynucleotide of interest is detected. The invention also provides a method for detecting the polypeptides of the invention in a sample comprising contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to form the complex and detecting the formation of the complex such that if a complex is formed, the polypeptide is detected.  
       [0023] The invention also provides kits comprising polynucleotide probes and/or monoclonal antibodies, and optionally quantitative standards, for carrying out methods of the invention. Furthermore, the invention provides methods for evaluating the efficacy of drugs, and monitoring the progress of patients, involved in clinical trials for the treatment of disorders as recited above.  
       [0024] The invention also provides methods for the identification of compounds that modulate (i.e., increase or decrease) the expression or activity of the polynucleotides and/or polypeptides of the invention. Such methods can be utilized, for example, for the identification of compounds that can ameliorate symptoms of disorders as recited herein. Such methods can include, but are not limited to, assays for identifying compounds and other substances that interact with (e.g., bind to) the polypeptides of the invention. The invention provides a method for identifying a compound that binds to the polypeptides of the invention comprising contacting the compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a reporter gene sequence in the cell; and detecting the complex by detecting the reporter gene sequence expression such that if expression of the reporter gene is detected the compound the binds to a polypeptide of the invention is identified.  
       [0025] The methods of the invention also provide methods for treatment which involve the administration of the polynucleotides or polypeptides of the invention to individuals exhibiting symptoms or tendencies. In addition, the invention encompasses methods for treating diseases or disorders as recited herein comprising administering compounds and other substances that modulate the overall activity of the target genie products. Compounds and other substances can effect such modulation either on the level of target gene/protein expression or target protein activity.  
       [0026] The polypeptides of the present invention and the polynucleotides encoding them are also useful for the same functions known to one of skill in the art as the polypeptides and polynucleotides to which they have homology (set forth in Table 2); for which they have a signature region (as set forth in Table 3); or for which they have homology to a gene family (as set forth in Table 4). If no homology is set forth for a sequence, then the polypeptides and polynucleotides of the present invention are useful for a variety of applications, as described herein, including use in arrays for detection.  
       4. DETAILED DESCRIPTION OF THE INVENTION  
       [0027] 4.1 Definitions  
       [0028] It must be noted that as used herein and in the appended claims, the singular forms a “an” and “the” include plural references unless the context clearly dictates otherwise.  
       [0029] The term “active” refers to those forms of the polypeptide which retain the biologic and/or immunologic activities of any naturally occurring polypeptide. According to the invention, the terms “biologically active” or “biological activity” refer to a protein or peptide having structural, regulatory or biochemical functions of a naturally occurring molecule. Likewise “immunologically active” or “immunological activity” refers to the capability of the natural, recombinant or synthetic polypeptide to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.  
       [0030] The term “activated cells” as used in this application are those cells which are engaged in extracellular or intracellular membrane trafficking, including the export of secretory or enzymatic molecules as part of a normal or disease process.  
       [0031] The terms “complementary” or “complementarity” refer to the natural binding of polynucleotides by base pairing. For example, the sequence 5′-AGT-3′ binds to the complementary sequence 3′-TCA-5′. Complementarity between two single-stranded molecules may be “partial” such that only some of the nucleic acids bind or it may be “complete” such that total complementarity exists between the single stranded molecules. The degree of complementarity between the nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands.  
       [0032] The term “embryonic stem cells (ES)” refers to a cell that can give rise to many differentiated cell types in an embryo or an adult, including the germ cells. The term “germ line stem cells (GSCs)” refers to stem cells derived from primordial stem cells that provide a steady and continuous source of germ cells for the production of gametes. The term “primordial germ cells (PGCs)” refers to a small population of cells set aside from other cell lineages particularly from the yolk sac, mesenteries, or gonadal ridges during embryogenesis that have the potential to differentiate into germ cells and other cells. PGCs are the source from which GSCs and ES cells are derived. The PGCs, the GSCs and the ES cells are capable of self-renewal. Thus these cells not only populate the germ line and give rise to a plurality of terminally differentiated cells that comprise the adult specialized organs, but are able to regenerate themselves.  
       [0033] The term “expression modulating fragment,” EMF, means a series of nucleotides which modulates the expression of an operably linked ORF or another EMF.  
       [0034] As used herein, a sequence is said to “modulate the expression of an operably linked sequence” when the expression of the sequence is altered by the presence of the EMF. EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are nucleic acid fragments which induce the expression of an operably linked ORF in response to a specific regulatory factor or physiological event.  
       [0035] The terms “nucleotide sequence” or “nucleic acid” or “polynucleotide” or “oligonculeotide” are used interchangeably and refer to a heteropolymer of nucleotides or the sequence of these nucleotides. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA) or to any DNA-like or RNA-like material. In the sequences herein A is adenine, C is cytosine, T is thymine, G is guanine and N is A, C, G or T (U). It is contemplated that where the polynucleotide is RNA, the T (thymine) in the sequences provided herein is substituted with U (uracil). Generally, nucleic acid segments provided by this invention may be assembled from fragments of the genome and short oligonucleotide linkers, or from a series of oligonucleotides, or from individual nucleotides, to provide a synthetic nucleic acid which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon, or a eukaryotic gene.  
       [0036] The terms “oligonucleotide fragment” or a “polynucleotide fragment”. “portion,” or “segment” or “probe” or “primer” are used interchangeably and refer to a sequence of nucleotide residues which are at least about 5 nucleotides, more preferably at least about 7 nucleotides, more preferably at least about 9 nucleotides, more preferably at least about 11 nucleotides and most preferably at least about 17 nucleotides. The fragment is preferably less than about 500 nucleotides, preferably less than about 200 nucleotides, more preferably less than about 100 nucleotides, more preferably less than about 50 nucleotides and most preferably less than 30 nucleotides. Preferably the probe is from about 6 nucleotides to about 200 nucleotides, preferably from about 15 to about 50 nucleotides, more preferably from about 17 to 30 nucleotides and most preferably from about 20 to 25 nucleotides. Preferably the fragments can be used in polymerase chain reaction (PCR), various hybridization procedures or microarray procedures to identify or amplify identical or related parts of mRNA or DNA molecules. A fragment or segment may uniquely identify each polynucleotide sequence of the present invention. Preferably the fragment comprises a sequence substantially similar to any one of SEQ ID NO: 1-245.  
       [0037] Probes may, for example, be used to determine whether specific mRNA molecules are present in a cell or tissue or to isolate similar nucleic acid sequences from chromosomal DNA as described by Walsh et al. (Walsh, P. S. et al., 1992, PCR Methods Appl 1:241-250). They may be labeled by nick translation, Klenow fill-in reaction, PCR, or other methods well known in the art. Probes of the present invention, their preparation and/or labeling are elaborated in Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY; or Ausubel, F. M. et al., 1989, Current Protocols in Molecular Biology, John Wiley &amp; Sons. New York N.Y. both of which are incorporated herein by reference in their entirety.  
       [0038] The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-245. The sequence information can be a segment of any one of SEQ ID NO: 1-245 that uniquely identifies or represents the sequence information of that sequence of SEQ ID NO: 1-245. One such segment can be a twenty-mer nucleic acid sequence because the probability that a twenty-mer is fully matched in the human genome is 1 in 300. In the human genome, there are three billion base pairs in one set of chromosomes. Because 4 20  possible twenty-mers exist, there are 300 times more twenty-mers than there are base pairs in a set of human chromosomes. Using the same analysis, the probability for a seventeen-mer to be fully matched in the human genome is approximately 1 in 5. When these segments are used in arrays for expression studies, fifteen-mer segments can be used. The probability that the fifteen-mer is fully matched in the expressed sequences is also approximately one in five because expressed sequences comprise less than approximately 5% of the entire genome sequence.  
       [0039] Similarly, when using sequence information for detecting a single mismatch, a segment can be a twenty-five mer. The probability that the twenty-five mer would appear in a human genome with a single mismatch is calculated by multiplying the probability for a full match (1÷4 25 ) times the increased probability for mismatch at each nucleotide position (3×25). The probability that an eighteen mer with a single mismatch can be detected in an array for expression studies is approximately one in five. The probability that a twenty-mer with a single mismatch can be detected in a human genome is approximately one in five.  
       [0040] The term “open reading frame,” ORF, means a series of nucleotide triplets coding for amino acids without any termination codons and is a sequence translatable into protein.  
       [0041] The terms “operably linked” or “operably associated” refer to functionally related nucleic acid sequences. For example, a promoter is operably associated or operably linked with a coding sequence if the promoter controls the transcription of the coding sequence. While operably linked nucleic acid sequences can be contiguous and in the same reading frame, certain genetic elements e.g. repressor genes are not contiguously linked to the coding sequence but still control transcription/translation of the coding sequence.  
       [0042] The term “pluripotent” refers to the capability of a cell to differentiate into a number of differentiated cell types that are present in an adult organism. A pluripotent cell is restricted in its differentiation capability in comparison to a totipotent cell.  
       [0043] The terms “polypeptide” or “peptide” or “amino acid sequence” refer to an oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and to naturally occurring or synthetic molecules. A polypeptide “fragment,” “portion,” or “segment” is a stretch of amino acid residues of at least about 5 amino acids, preferably at least about 7 amino acids, more preferably at least about 9 amino acids and most preferably at least about 17 or more amino acids. The peptide preferably is not greater than about 500 amino acids, more preferably less than 200 amino acids more preferably less than 150 amino acids and most preferably less than 100 amino acids. Preferably the peptide is from about 5 to about 200 amino acids. To be active, any polypeptide must have sufficient length to display biological and/or immunological activity.  
       [0044] The term “naturally occurring polypeptide” refers to polypeptides produced by cells that have not been genetically engineered and specifically contemplates various polypeptides arising from post-translational modifications of the polypeptide including, but not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation.  
       [0045] The term “translated protein coding portion” means a sequence which encodes for the full length protein which may include any leader sequence or any processing sequence.  
       [0046] The term “mature protein coding sequence” means a sequence which encodes a peptide or protein without a signal or leader sequence. The “mature protein portion” means that portion of the protein which does not include a signal or leader sequence. The peptide may have been produced by processing in the cell which removes any leader/signal sequence. The mature protein portion may or may not include an initial methionine residue. The methionine residue may be removed from the protein during processing in the cell. The peptide may be produced synthetically or the protein may have been produced using a polynucleotide only encoding for the mature protein coding sequence.  
       [0047] The term “derivative” refers to polypeptides chemically modified by such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which do not normally occur in human proteins.  
       [0048] The term “variant” (or “analog”) refers to any polypeptide differing from naturally occurring polypeptides by amino acid insertions, deletions, and substitutions, created using, e g., recombinant DNA techniques. Guidance in determining which amino acid residues may be replaced, added or deleted without abolishing activities of interest, may be found by comparing the sequence of the particular polypeptide with that of homologous peptides and minimizing the number of amino acid sequence changes made in regions of high homology (conserved regions) or by replacing amino acids with consensus sequence.  
       [0049] Alternatively, recombinant variants encoding these same or similar polypeptides may be synthesized or selected by making use of the “redundancy” in the genetic code. Various codon substitutions, such as the silent changes which produce various restriction sites, may be introduced to optimize cloning into a plasmid or viral vector or expression in a particular prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may be reflected in the polypeptide or domains of other peptides added to the polypeptide to modify the properties of any part of the polypeptide, to change characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate.  
       [0050] Preferably, amino acid “substitutions” are the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, i.e., conservative amino acid replacements. “Conservative” amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved. For example, nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include aspartic acid and glutamic acid. “Insertions” or “deletions” are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids. The variation allowed may be experimentally determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity.  
       [0051] Alternatively, where alteration of function is desired, insertions, deletions or non-conservative alterations can be engineered to produce altered polypeptides. Such alterations can, for example, alter one or more of the biological functions or biochemical characteristics of the polypeptides of the invention. For example, such alterations may change polypeptide characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate. Further, such alterations can be selected so as to generate polypeptides that are better suited for expression, scale up and the like in the host cells chosen for expression. For example, cysteine residues can be deleted or substituted with another amino acid residue in order to eliminate disulfide bridges.  
       [0052] The terms “purified” or “substantially purified” as used herein denotes that the indicated nucleic acid or polypeptide is present in the substantial absence of other biological macromolecules, e.g., polynucleotides, proteins, and the like. In one embodiment, the polynucleotide or polypeptide is purified such that it constitutes at least 95% by weight, more preferably at least 99% by weight, of the indicated biological macromolecules present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 1000 daltons, can be present).  
       [0053] The term “isolated” as used herein refers to a nucleic acid or polypeptide separated from at least one other component (e.g., nucleic acid or polypeptide) present with the nucleic acid or polypeptide in its natural source. In one embodiment, the nucleic acid or polypeptide is found in the presence of (if anything) only a solvent, buffer, ion, or other component normally present in a solution of the same. The terms “isolated” and “purified” do not encompass nucleic acids or polypeptides present in their natural source.  
       [0054] The term “recombinant,” when used herein to refer to a polypeptide or protein, means that a polypeptide or protein is derived from recombinant (e.g., microbial, insect, or mammalian) expression systems. “Microbial” refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, “recombinant microbial” defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g.,  E. coli  will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will have a glycosylation pattern in general different from those expressed in mammalian cells.  
       [0055] The term “recombinant expression vehicle or vector” refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. An expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate transcription initiation and termination sequences. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an amino terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.  
       [0056] The term “recombinant expression system” means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extrachromosomally. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed. This term also means host cells which have stably integrated a recombinant genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. Recombinant expression systems as defined herein will express polypeptides or proteins endogenous to the cell upon induction of the regulatory elements linked to the endogenous DNA segment or gene to be expressed. The cells can be prokaryotic or eukaryotic.  
       [0057] The term “secreted” includes a protein that is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence when it is expressed in a suitable host cell. “Secreted” proteins include without limitation proteins secreted wholly (e.g., soluble proteins) or partially (e.g., receptors) from the cell in which they are expressed. “Secreted” proteins also include without limitation proteins that are transported across the membrane of the endoplasmic reticulum. “Secreted” proteins are also intended to include proteins containing non-typical signal sequences (e.g. Interleukin-1 Beta, see Krasney, P. A. and Young, P. R. (1992) Cytokine 4(2): 134-143) and factors released from damaged cells (e.g. Interleukin-1 Receptor Antagonist, see Arend, W. P. et. al. (1998) Annu. Rev. Immunol. 16:27-55)  
       [0058] Where desired, an expression vector may be designed to contain a “signal or leader sequence” which will direct the polypeptide through the membrane of a cell. Such a sequence may be naturally present on the polypeptides of the present invention or provided from heterologous protein sources by recombinant DNA techniques.  
       [0059] The term “stringent” is used to refer to conditions that are commonly understood in the art as stringent. Stringent conditions can include highly stringent conditions (i.e., hybridization to filter-bound DNA in 0.5 M NaHPO 4 . 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C. and washing in 0. 1×SSC/0.1% SDS at 68° C.), and moderately stringent conditions (i.e., washing in 0.2×SSC/0.1% SDS at 42° C.). Other exemplary hybridization conditions are described herein in the examples.  
       [0060] In instances of hybridization of deoxyoligonucleotides, additional exemplary stringent hybridization conditions include washing in 6×SSC/0.05% sodium pyrophosphate at 37° C. (for 14-base oligonucleotides), 48° C. (for 17-base oligos), 55° C. (for 20-base oligonucleotides), and 60° C. (for 23-base oligonucleotides).  
       [0061] As used herein, “substantially equivalent” can refer both to nucleotide and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between the reference and subject sequences. Typically, such a substantially equivalent sequence varies from one of those listed herein by no more than about 35% (i.e., the number of individual residue substitutions, additions, and/or deletions in a substantially equivalent sequence, as compared to the corresponding reference sequence, divided by the total number of residues in the substantially equivalent sequence is about 0.35 or less). Such a sequence is said to have 65% sequence identity to the listed sequence. In one embodiment, a substantially equivalent, e.g., mutant, sequence of the invention varies from a listed sequence by no more than 30% (70% sequence identity); in a variation of this embodiment, by no more than 25% (75% sequence identity); and in a further variation of this embodiment, by no more than 20% (80% sequence identity) and in a further variation of this embodiment, by no more than 10% (90% sequence identity) and in a further variation of this embodiment, by no more that 5% (95% sequence identity). Substantially equivalent, e.g., mutant, amino acid sequences according to the invention preferably have at least 80% sequence identity with a listed amino acid sequence, more preferably at least 85% sequence identity, more preferably at least 90% sequence identity, more preferably at least 95% identity, more preferably at least 98% identity, and most preferably at least 99% identity. Substantially equivalent nucleotide sequences of the invention can have lower percent sequence identities, taking into account, for example, the redundancy or degeneracy of the genetic code. Preferably, nucleotide sequence has at least about 65% identity, more preferably at least about 75% identity, more preferably at least about 80% sequence identity, more preferably at least about 85% sequence identity, more preferably at least about 90% sequence identity, and most preferably at least about 95% identity, more preferably at least about 98% sequence identity, and most preferably at least about 99% sequence identity. For the purposes of the present invention, sequences having substantially equivalent biological activity and substantially equivalent expression characteristics are considered substantially equivalent. For the purposes of determining equivalence, truncation of the mature sequence (e.g. via a mutation which creates a spurious stop codon) should be disregarded. Sequence identity may be determined, e.g. using the Jotun Hein method (Hein. J. (1990) Methods Enzymol. 183 :626-645). Identity between sequences can also be determined by other methods known in the art, e.g. by varying hybridization conditions.  
       [0062] The term “totipotent” refers to the capability of a cell to differentiate into all of the cell types of an adult organism.  
       [0063] The term “transformation” means introducing DNA into a suitable host cell so that the DNA is replicable, either as an extrachromosomal element, or by chromosomal integration. The term “transfection” refers to the taking up of an expression vector by a suitable host cell, whether or not any coding sequences are in fact expressed. The term “infection” refers to the introduction of nucleic acids into a suitable host cell by use of a virus or viral vector.  
       [0064] As used herein, an “uptake modulating fragment,” UMF, means a series of nucleotides which mediate the uptake of a linked DNA fragment into a cell. UMFs can be readily identified using known UMFs as a target sequence or target motif with the computer-based systems described below. The presence and activity of a UMF can be confirmed by attaching the suspected UMF to a marker sequence. The resulting nucleic acid molecule is then incubated with an appropriate host under appropriate conditions and the uptake of the marker sequence is determined. As described above, a UMF will increase the frequency of uptake of a linked marker sequence.  
       [0065] Each of the above terms is meant to encompass all that is described for each, unless the context dictates otherwise.  
       [0066] 4.2 Nucleic Acids of the Invention  
       [0067] Nucleotide sequences of the invention are set forth in the Sequence Listing.  
       [0068] The isolated polynucleotides of the invention include a polynucleotide comprising the nucleotide sequences of SEQ ID NO: 1-245; a polynucleotide encoding any one of the peptide sequences of SEQ ID NO: 246-490; and a polynucleotide comprising the nucleotide sequence encoding the mature protein coding sequence of the polypeptides of any one of SEQ ID NO: 246-490. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent conditions to (a) the complement of any of the nucleotides sequences of SEQ ID NO: 1-245; (b) nucleotide sequences encoding any one of the amino acid sequences set forth in the Sequence Listing as SEQ ID NO: 246-490; (c) a polynucleotide which is an allelic variant of any polynucleotide recited above: (d) a polynucleotide which encodes a species homolog of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of the polypeptides of SEQ ID NO: 246-490. Domains of interest may depend on the nature of the encoded polypeptide; e.g. domains in receptor-like polypeptides include ligand-binding, extracellular, transmembrane, or cytoplasmic domains, or combinations thereof; domains in immunoglobulin-like proteins include the variable immunoglobulin-like domains; domains in enzyme-like polypeptides include catalytic and substrate binding domains; and domains in ligand polypeptides include receptor-binding domains.  
       [0069] The polynucleotides of the invention include naturally occurring or wholly or partially synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA. The polynucleotides may include all of the coding region of the cDNA or may represent a portion of the coding region of the cDNA.  
       [0070] The present invention also provides genes corresponding to the cDNA sequences disclosed herein. The corresponding genes can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include the preparation of probes or primers from the disclosed sequence information for identification and/or amplification of genes in appropriate genomic libraries or other sources of genomic materials. Further 5′ and 3′ sequence can be obtained using methods known in the art. For example, full length cDNA or genomic DNA that corresponds to any of the polynucleotides of SEQ ID NO: 1-245 can be obtained by screening appropriate cDNA or genomic DNA libraries under suitable hybridization conditions using any of the polynucleotides of SEQ ID NO: 1-245 or a portion thereof as a probe. Alternatively, the polynucleotides of SEQ ID NO: 1-245 may be used as the basis for suitable primer(s) that allow identification and/or amplification of genes in appropriate genomic DNA or cDNA libraries.  
       [0071] The nucleic acid sequences of the invention can be assembled from ESTs and sequences (including cDNA and genomic sequences) obtained from one or more public databases, such as dbEST, gbpri, and UniGene. The EST sequences can provide identifying sequence information, representative fragment or segment information, or novel segment information for the full-length gene.  
       [0072] The polynucleotides of the invention also provide polynucleotides including nucleotide sequences that are substantially equivalent to the polynucleotides recited above. Polynucleotides according to the invention can have, e.g., at least about 65%, at least about 70%, at least about 75%, at least about 80%, 81%, 82%, 83%, 84%, more typically at least about 85%, 86%, 87%, 88%, 89%, more typically at least about 90%, 91%, 92%, 93%, 94%, and even more typically at least about 95%, 96%, 97%, 98%, 99%, sequence identity to a polynucleotide recited above.  
       [0073] Included within the scope of the nucleic acid sequences of the invention are nucleic acid sequence fragments that hybridize under stringent conditions to any of the nucleotide sequences of SEQ ID NO: 1-245, or complements thereof, which fragment is greater than about 5 nucleotides, preferably 7 nucleotides, more preferably greater than 9 nucleotides and most preferably greater than 17 nucleotides. Fragments of, e.g. 15, 17, or 20 nucleotides or more that are selective for (i.e. specifically hybridize to) any one of the polynucleotides of the invention are contemplated. Probes capable of specifically hybridizing to a polynucleotide can differentiate polynucleotide sequences of the invention from other polynucleotide sequences in the same family of genes or can differentiate human genes from genes of other species, and are preferably based on unique nucleotide sequences.  
       [0074] The sequences falling within the scope of the present invention are not limited to these specific sequences, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequence provided in SEQ ID NO: 1-245, a representative fragment thereof, or a nucleotide sequence at least 90% identical, preferably 95% identical, to SEQ ID NO: 1-245 with a sequence from another isolate of the same species. Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another codon that encodes the same amino acid is expressly contemplated.  
       [0075] The nearest neighbor or homology result for the nucleic acids of the present invention, including SEQ ID NO: 1-245, can be obtained by searching a database using an algorithm or a program. Preferably, a BLAST which stands for Basic Local Alignment Search Tool is used to search for local sequence alignments (Altshul, S. F. J Mol. Evol. 36 290-300 (1993) and Altschul S. F. et al. J. Mol. Biol. 21:403-410 (1990)). Alternatively a FASTA version 3 search against Genpept, using Fastxy algorithm.  
       [0076] Species homologs (or orthologs) of the disclosed polynucleotides and proteins are also provided by the present invention. Species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from the desired species.  
       [0077] The invention also encompasses allelic variants of the disclosed polynucleotides or proteins; that is, naturally-occurring alternative forms of the isolated polynucleotide which also encode proteins which are identical, homologous or related to that encoded by the polynucleotides.  
       [0078] The nucleic acid sequences of the invention are further directed to sequences which encode variants of the described nucleic acids. These amino acid sequence variants may be prepared by methods known in the art by introducing appropriate nucleotide changes into a native or variant polynucleotide. There are two variables in the construction of amino acid sequence variants: the location of the mutation and the nature of the mutation. Nucleic acids encoding the amino acid sequence variants are preferably constructed by mutating the polynucleotide to encode an amino acid sequence that does not occur in nature. These nucleic acid alterations can be made at sites that differ in the nucleic acids from different species (variable positions) or in highly conserved regions (constant regions). Sites at such locations will typically be modified in series, e.g. by substituting first with conservative choices (e.g., hydrophobic amino acid to a different hydrophobic amino acid) and then with more distant choices (e.g., hydrophobic amino acid to a charged amino acid), and then deletions or insertions may be made at the target site. Amino acid sequence deletions generally range from about 1 to 30 residues, preferably about 1 to 10 residues, and are typically contiguous. Amino acid insertions include amino- and/or carboxyl-terminal fusions ranging in length from one to one hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Intrasequence insertions may range generally from about 1 to 10 amino residues, preferably from 1 to 5 residues. Examples of terminal insertions include the heterologous signal sequences necessary for secretion or for intracellular targeting in different host cells and sequences such as FLAG or poly-histidine sequences useful for purifying the expressed protein.  
       [0079] In a preferred method, polynucleotides encoding the novel amino acid sequences are changed via site-directed mutagenesis. This method uses oligonucleotide sequences to alter a polynucleotide to encode the desired amino acid variant, as well as sufficient adjacent nucleotides on both sides of the changed amino acid to form a stable duplex on either side of the site of being changed. In general, the techniques of site-directed mutagenesis are well known to those of skill in the art and this technique is exemplified by publications such as, Edelman et al.,  DNA  2:183 (1983). A versatile and efficient method for producing site-specific changes in a polynucleotide sequence was published by Zoller and Smith,  Nucleic Acids Res.  10:6487-6500 (1982). PCR may also be used to create amino acid sequence variants of the novel nucleic acids. When small amounts of template DNA are used as starting material, primer(s) that differs slightly in sequence from the corresponding region in the template DNA can generate the desired amino acid variant. PCR amplification results in a population of product DNA fragments that differ from the polynucleotide template encoding the polypeptide at the position specified by the primer. The product DNA fragments replace the corresponding region in the plasmid and this gives a polynucleotide encoding the desired amino acid variant.  
       [0080] A further technique for generating amino acid variants is the cassette mutagenesis technique described in Wells et al. Gene 34:315 (1985); and other mutagenesis techniques well known in the art, such as, for example, the techniques in Sambrook et al. supra, and Current  Protocols in Molecular Biology.  Ausubel et al. Due to the inherent degeneracy of the genetic code, other DNA sequences Which encode substantially the same or a functionally equivalent amino acid sequence may be used in the practice of the invention for the cloning and expression of these novel nucleic acids. Such DNA sequences include those which are capable of hybridizing to the appropriate novel nucleic acid sequence under stringent conditions.  
       [0081] Polynucleotides encoding preferred polypeptide truncations of the invention can be used to generate polynucleotides encoding chimeric or fusion proteins comprising one or more domains of the invention and heterologous protein sequences.  
       [0082] The polynucleotides of the invention additionally include the complement of any of the polynucleotides recited above. The polynucleotide can be DNA (genomic, cDNA, amplified, or synthetic) or RNA. Methods and algorithms for obtaining such polynucleotides are well known to those of skill in the art and can include, for example, methods for determining hybridization conditions that can routinely isolate polynucleotides of the desired sequence identities.  
       [0083] In accordance with the invention, polynucleotide sequences comprising the mature protein coding sequences corresponding to any one of SEQ ID NO: 1-245, or functional equivalents thereof, may be used to generate recombinant DNA molecules that direct the expression of that nucleic acid, or a functional equivalent thereof, in appropriate host cells. Also included are the cDNA inserts of any of the clones identified herein.  
       [0084] A polynucleotide according to the invention can be joined to any of a variety of other nucleotide sequences by well-established recombinant DNA techniques (see Sambrook J et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY). Useful nucleotide sequences for joining to polynucleotides include an assortment of vectors, e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like, that are well known in the art. Accordingly, the invention also provides a vector including a polynucleotide of the invention and a host cell containing the polynucleotide. In general, the vector contains an origin of replication functional in at least one organism, convenient restriction endonuclease sites, and a selectable marker for the host cell. Vectors according to the invention include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. A host cell according to the invention can be a prokaryotic or eukaryotic cell and can be a unicellular organism or part of a multicellular organism.  
       [0085] The present invention further provides recombinant constructs comprising a nucleic acid having any of the nucleotide sequences of SEQ ID NO: 1-245 or a fragment thereof or any other polynucleotides of the invention. In one embodiment, the recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a nucleic acid having any of the nucleotide sequences of SEQ ID NO: 1-245 or a fragment thereof is inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector ma! further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Bacterial: pBs, phagescript. PsiX174, pBluescript SK, pBs KS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia). Eukaryotic: pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia).  
       [0086] The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in Kaufman et al.,  Nucleic Acids Res.  19, 4485-4490 (1991), in order to produce the protein recombinantly. Many suitable expression control sequences are known in the art. General methods of expressing recombinant proteins are also known and are exemplified in R. Kaufman,  Methods in Enzymology  185, 537-566 (1990). As defined herein “operably linked” means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.  
       [0087] Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lac, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-1. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of  E. coli  and  S. cerevisiae  TRPI gene, and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), a-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an amino terminal identification peptide imparting desired characteristics, e.g. stabilization or simplified purification of expressed recombinant product. Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together With suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include  E. coli, Bacillus subtilis, Salmonella typhimurium  and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.  
       [0088] As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced or derepressed by appropriate means (e.g. temperature shift or chemical induction) and cells are cultured for an additional period. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.  
       [0089] Polynucleotides of the invention can also be used to induce immune responses. For example, as described in Fan et al.,  Nat. Biotech.  17:870-872 (1999), incorporated herein by reference, nucleic acid sequences encoding a polypeptide may be used to generate antibodies against the encoded polypeptide following topical administration of naked plasmid DNA or following injection, and preferably intramuscular injection of the DNA. The nucleic acid sequences are preferably inserted in a recombinant expression vector and may be in the form of naked DNA.  
       [0090] 4.3 Antisense Nucleic Acids  
       [0091] Another aspect of the invention pertains to isolated antisense nucleic acid molecules that are hybridizable to or complementary to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1-245, or fragments, analogs or derivatives thereof. An “antisense” nucleic acid comprises a nucleotide sequence that is complementary to a “sense” nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, 50, 100, 250 or 500 nucleotides or an entire coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a protein of any of SEQ ID NO: 246-490 or antisense nucleic acids complementary to a nucleic acid sequence of SEQ ID NO: 1-245 are additionally provided.  
       [0092] In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence of the invention. The term “coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence of the invention. The term “noncoding region” refers to 5′ and 3′ sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).  
       [0093] Given the coding strand sequences encoding a nucleic acid disclosed herein (e.g., SEQ ID NO: 1-245), antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of an mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or noncoding region of a mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of a mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the (D physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.  
       [0094] Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine. 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).  
       [0095] The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein according to the invention to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of antisense molecules, vector constructs in which the anti sense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.  
       [0096] In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier el al. (1987)  Nucleic Acids Res  15: 6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987)  Nucleic Acids Res  15: 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987)  FEBS Lett  215: 327-330).  
       [0097] 4.4 Ribozymes and PNA Moieties  
       [0098] In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g. hammerhead ribozymes (described in Haselhoff and Gerlach (1988)  Nature  334:585-591)) can be used to catalytically cleave a mRNA transcripts to thereby inhibit translation of a mRNA. A ribozyme having specificity for a nucleic acid of the invention can be designed based upon the nucleotide sequence of a DNA disclosed herein (i.e. SEQ ID NO: 1-245). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an mRNA of SEQ ID NO: 1-245 (see, e.g., Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, polynucleotides of the invention can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.  
       [0099] Alternatively, gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region (e.g., promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See generally, Helene. (1991)  Anticancer Drug Des.  6: 569-84; Helene, et al. (1992)  Ann. N.Y. Acad Sci.  660:27-36; and Maher (1992)  Bioassays  14: 807-15.  
       [0100] In various embodiments, the nucleic acids of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al. (1996)  Bioorg Med Chem  4: 5-23). As used herein, the terms “peptide nucleic acids” or “PNAs” refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al. (1996) above; Perry-O&#39;Keefe el al. (1996)  PNAS  93: 14670-675.  
       [0101] PNAs of the invention can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication. PNAs of the invention can also be used, e.g., in the analysis of single base pair mutations in a gene by, e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., S1 nucleases (Hyrup B. (1996) above); or as probes or primers for DNA sequence and hybridization (Hyrup et al. (1996), above; Perry-O&#39;Keefe (1996), above).  
       [0102] In another embodiment. PNAs of the invention can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example. PNA-DNA chimeras can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996) above). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996) above and Finn et al. (1996)  Nucl Acids Res  24: 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 5′-(4-methoxytrityl)amino-5′-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5′ end of DNA (Mag et al. (1989)  Nucl Acid Res  17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5′ PNA segment and a 3′ DNA segment (Finn et al. (1996) above). Alternatively, chimeric molecules can be synthesized with a 5′ DNA segment and a 3′ PNA segment. See, Petersen et al. (1975)  Bioorg Med Chem Lett  5: 1119-11124.  
       [0103] In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., 1989 , Proc. Natl. Acad. Sci. U.S.A.  86:6553-6556; Lemaitre et al., 1987 , Proc. Natl. Acad. Sci.  84:648-652; PCT Publication No. WO88/09810) or the blood-brain barrier (see, e.g., PCT Publication No. WO89/10134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al., 1988,  BioTechniques  6:958-976) or intercalating agents. (See, e.g., Zon, 1988 , Pharm. Res.  5: 539-549). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, etc.  
       [0104] 4.5 Hosts  
       [0105] The present invention further provides host cells genetically engineered to contain the polynucleotides of the invention. For example, such host cells may contain nucleic acids of the invention introduced into the host cell using known transformation, transfection or infection methods. The present invention still further provides host cells genetically engineered to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell.  
       [0106] Knowledge of nucleic acid sequences allows for modification of cells to permit, or increase, expression of endogenous polypeptide. Cells can be modified (e.g. by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the polypeptide at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the encoding sequences. See, for example, PCT International Publication No. WO94/12650, PCT International Publication No. WO92/20808, and PCT International Publication No. WO91/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.  
       [0107] The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the recombinant construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, or electroporation (Davis, L. et al.,  Basic Methods in Molecular Biology  (1986)). The host cells containing one of the polynucleotides of the invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.  
       [0108] Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, Cv-1 cell, COS cells, 293 cells, and Sf9 cells, as well as prokaryotic host such as  E. coli  and  B. subtilis.  The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level. Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., in Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference.  
       [0109] Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described by Gluzman, Cell 23:175 (1981). Other cell lines capable of expressing a compatible vector are, for example, the C127, monkey COS cells, Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells, human Colo205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from in vitro culture of primary tissue, primary explants, HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements. Recombinant polypeptides and proteins produced in bacterial culture are usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents.  
       [0110] Alternatively, it may be possible to produce the protein in lower eukaryotes such as yeast or insects or in prokaryotes such as bacteria. Potentially suitable yeast strains include  Saccharomyces cerevisiae, Schizosaccharomyces pombe , Kluyveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. Potentially suitable bacterial strains include  Escherichia coli, Bacillus subtilis, Salmonella typhimurium,  or any bacterial strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by phosphorylation or glycosylation of the appropriate sites, in order to obtain the functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.  
       [0111] In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene&#39;s existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequence include polyadenylation signals, mRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.  
       [0112] The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurring elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the host cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this purpose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.  
       [0113] The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Pat. No. 5,272,071 to Chappel; U.S. Pat. No. 5,578,461 to Sherwin et al.; International Application No. PCT/US92/09627 (WO93/09222) by Selden et al.; and International Application No. PCT/US90/06436 (WO91/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.  
       [0114] 4.6 Polypeptides of the Invention  
       [0115] The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising: the amino acid sequences set forth as any one of SEQ ID NO: 246-490 or an amino acid sequence encoded by any one of the nucleotide sequences SEQ ID NO: 1-245 or the corresponding full length or mature protein. Polypeptides of the invention also include polypeptides preferably with biological or immunological activity that are encoded by: (a) a polynucleotide having and one of the nucleotide sequences set forth in SEQ ID NO: 1-245 or (b) polynucleotides encoding any one of the amino acid sequences set forth as SEQ ID NO: 246-490 or (c) polynucleotides that hybridize to the complement of the polynucleotides of either (a) or (b) under stringent hybridization conditions. The invention also provides biologically active or immunologically active variants of any of the amino acid sequences set forth as SEQ ID NO: 246-490 or the corresponding full length or mature protein; and “substantial equivalents” thereof (e.g., with at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, 86%, 87%, 88%, 89%, at least about 90%, 91%, 92%, 93%, 94%, typically at least about 95%, 96%, 97%, more typically at least about 98%, or most typically at least about 99% amino acid identity) that retain biological activity. Polypeptides encoded by allelic variants may have a similar, increased, or decreased activity compared to polypeptides comprising SEQ ID NO: 246-490.  
       [0116] Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H. U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in R. S. McDowell, et al., J. Amer. Chem. Soc. 114, 9245-9253 (1992), both of which are incorporated herein by reference. Such fragments may be fused to carrier molecules such as immunoglobulins for many purposes, including increasing the valency of protein binding sites.  
       [0117] The present invention also provides both full-length and mature forms (for example, without a signal sequence or precursor sequence) of the disclosed proteins. The protein coding sequence is identified in the sequence listing by translation of the disclosed nucleotide sequences. The mature form of such protein may be obtained by expression of a full-length polynucleotide in a suitable mammalian cell or other host cell. The sequence of the mature form of the protein is also determinable from the amino acid sequence of the full-length form. Where proteins of the present invention are membrane bound, soluble forms of the proteins are also provided. In such forms, part or all of the regions causing the proteins to be membrane bound are deleted so that the proteins are fully secreted from the cell in which they are expressed.  
       [0118] Protein compositions of the present invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.  
       [0119] The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By “degenerate variant” is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g. an ORF) by nucleotide sequence but, due to the degeneracy of the genetic code, encode an identical polypeptide sequence. Preferred nucleic acid fragments of the present invention are the ORFs that encode proteins.  
       [0120] A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. This technique is particularly useful in producing small peptides and fragments of larger polypeptides. Fragments are useful, for example, in generating antibodies against the native polypeptide. Thus, they may be employed as biologically active or immunological substitutes for natural, purified proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.  
       [0121] The polypeptides and proteins of the present invention can alternatively be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. One skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.  
       [0122] The invention also relates to methods for producing a polypeptide comprising growing a culture of host cells of the invention in a suitable culture medium, and purifying the protein from the cells or the culture in which the cells are grown. For example, the methods of the invention include a process for producing a polypeptide in which a host cell containing a suitable expression vector that includes a polynucleotide of the invention is cultured under conditions that allow expression of the encoded polypeptide. The polypeptide can be recovered from the culture, conveniently from the culture medium, or from a lysate prepared from the host cells and further purified. Preferred embodiments include those in which the protein produced by such process is a full length or mature form of the protein.  
       [0123] In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily follow known methods for isolating polypeptides and proteins in order to obtain one of the isolated polypeptides or proteins of the present invention. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography. See, e.g. Scopes.  Protein Purification. Principles and Practice,  Springer-Verlag (1994): Sambrook, et al. in  Molecular Cloning: A Laboratory Manual;  Ausubel et al.,  Current Protocols in Molecular Biology.  Polypeptide fragments that retain biological/immunological activity include fragments comprising greater than about 100 amino acids, or greater than about 200 amino acids, and fragments that encode specific protein domains.  
       [0124] The purified polypeptides can be used in in vitro binding assays which are well known in the art to identify molecules which bind to the polypeptides. These molecules include but are not limited to, for e.g., small molecules, molecules from combinatorial libraries, antibodies or other proteins. The molecules identified in the binding assay are then tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.  
       [0125] In addition, the peptides of the invention or molecules capable of binding to the peptides may be complexed with toxins, e.g., ricin or cholera, or with other compounds that are toxic to cells. The toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for SEQ ID NO: 246-490.  
       [0126] The protein of the invention may also be expressed as a product of transgenic animals, e.g., as a component of the milk of transgenic cows, goats, pigs, or sheep which are characterized by somatic or germ cells containing a nucleotide sequence encoding the protein.  
       [0127] The proteins provided herein also include proteins characterized by amino acid sequences similar to those of purified proteins but into which modification are naturally provided or deliberately engineered. For example, modifications, in the peptide or DNA sequence, can be made by those skilled in the art using known techniques. Modifications of interest in the protein sequences may include the alteration, substitution., replacement, insertion or deletion of a selected amino acid residue in the coding sequence. For example, one or more of the cysteine residues may be deleted or replaced with another amino acid to alter the conformation of the molecule. Techniques for such alteration, substitution, replacement, insertion or deletion are well known to those skilled in the art (see, e.g., U.S. Pat. No. 4,518,584). Preferably, such alteration, substitution, replacement, insertion or deletion retains the desired activity of the protein. Regions of the protein that are important for the protein function can be determined by various methods known in the art including the alanine-scanning method which involved systematic substitution of single or strings of amino acids with alanine, followed by testing the resulting alanine-containing variant for biological activity. This type of analysis determines the importance of the substituted amino acid(s) in biological activity. Regions of the protein that are important for protein function may be determined by the eMATRIX program.  
       [0128] Other fragments and derivatives of the sequences of proteins which would be expected to retain protein activity in whole or in part and are useful for screening or other immunological methodologies may also be easily made by those skilled in the art given the disclosures herein. Such modifications are encompassed by the present invention.  
       [0129] The protein may also be produced by operably linking the isolated polynucleotide of the invention to suitable control sequences in one or more insect expression vectors, and employing an insect expression system. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, Calif., U.S.A. (the MaxBat™ kit), and such methods are well known in the art, as described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987), incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is “transformed.” 
       [0130] The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i.e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-toyopearl™ or Cibacrom blue 3GA Sepharose™; one or more steps involving hydrophobic interaction chromatography using such resins as phenyl ether, butyl ether, or propyl ether; or immunoaffinity chromatography.  
       [0131] Alternatively, the protein of the invention may also be expressed in a form which will facilitate purification. For example, it may be expressed as a fusion protein, such as those of maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin (TRX), or as a His tag. Kits for expression and purification of such fusion proteins are commercially available from New England BioLab (Beverly, Mass.), Pharmacia (Piscataway, N.J.) and Invitrogen, respectively. The protein can also be tagged with an epitope and subsequently purified by using a specific antibody directed to such epitope. One such epitope (“FLAG®”) is commercially available from Kodak (New Haven, Conn.).  
       [0132] Finally, one or more reverse-phase high performance liquid chromatography (RP-HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having pendant methyl or other aliphatic groups, can be employed to further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance With the present invention as an “isolated protein.” 
       [0133] The polypeptides of the invention include analogs (variants). This embraces fragments, as well as peptides in which one or more amino acids has been deleted, inserted, or substituted. Also, analogs of the polypeptides of the invention embrace fusions of the polypeptides or modifications of the polypeptides of the invention, wherein the polypeptide or analog is fused to another moiety or moieties, e.g., targeting moiety or another therapeutic agent. Such analogs may exhibit improved properties such as activity and/or stability. Examples of moieties which may be fused to the polypeptide or an analog include, for example, targeting moieties which provide for the delivery of polypeptide to pancreatic cells, e.g., antibodies to pancreatic cells, antibodies to immune cells such as T-cells, monocytes, dendritic cells, granulocytes, etc., as well as receptor and ligands expressed on pancreatic or immune cells. Other moieties which may be fused to the polypeptide include therapeutic agents which are used for treatment, for example, immunosuppressive drugs such as cyclosporin, SK506, azathioprine, CD3 antibodies and steroids. Also, polypeptides may be fused to immune modulators, and other cytokines such as alpha or beta interferon.  
       [0134] 4.6.1 Determining Polypeptide and Polynucleotide Identity and Similarity  
       [0135] Preferred identity and/or similarity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in computer programs including, but are not limited to, the GCG program package, including GAP (Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics Computer Group, University of Wisconsin, Madison, Wis.). BLASTP, BLASTN, BLASTX, FASTA (Altschul, S. F. et al., J. Molec. Biol. 215:403-410 (1990). PSI-BLAST (Altschul S. F. et al., Nucleic Acids Res, vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix software (Wu et al., J. Comp. Biol., Vol. 6, pp. 219-235 (1999), herein incorporated by reference), eMotif software (Nevill-Manning et al, ISMB-97, Vol. 4, pp. 202-209, herein incorporated by reference), pFam software (Sonnhammer et al., Nucleic Acids Res. Vol. 26(1), pp. 320-322 (1998), herein incorporated by reference) and the Kyte-Doolittle hydrophobocity prediction algorithm (J. Mol Biol, 157, pp. 105-31 (1982), incorporated herein by reference). The BLAST programs are publicly available from the National Center for Biotechnology Information (NCBI) and other sources (BLAST Manual, Altschul. S., et al. NCB NLM NIH Bethesda. MD 20894; Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990).  
       [0136] 4.7 Chimeric and Fusion Proteins  
       [0137] The invention also provides chimeric or fusion proteins. As used herein, a “chimeric protein” or “fusion protein” comprises a polypeptide of the invention operatively linked to another polypeptide. Within a fusion protein the polypeptide according to the invention can correspond to all or a portion of a protein according to the invention. In one embodiment, a fusion protein comprises at least one biologically active portion of a protein according to the invention. In another embodiment, a fusion protein comprises at least two biologically active portions of a protein according to the invention. Within the fusion protein, the term “operatively linked” is intended to indicate that the polypeptide according to the invention and the other polypeptide are fused in-frame to each other. The polypeptide can be fused to the N-terminus or C-terminus.  
       [0138] For example, in one embodiment a fusion protein comprises a polypeptide according to the invention operably linked to the extracellular domain of a second protein. In another embodiment, the fusion protein is a GST-fusion protein in which the polypeptide sequences of the invention are fused to the C-terminus of the GST (i.e., glutathione S-transferase) sequences.  
       [0139] In another embodiment, the fusion protein is an immunoglobulin fusion protein in which the polypeptide sequences according to the invention comprise one or more domains fused to sequences derived from a member of the immunoglobulin protein family. The immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand and a protein of the invention on the surface of a cell, to thereby suppress signal transduction in vivo. The immunoglobulin fusion proteins can be used to affect the bioavailability of a cognate ligand. Inhibition of the ligand/protein interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, e.g., cancer as well as modulating (e.g., promoting or inhibiting) cell survival. Moreover, the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies in a subject, to purify ligands, and in screening assays to identify molecules that inhibit the interaction of a polypeptide of the invention with a ligand.  
       [0140] A chimeric or fusion protein of the invention can b, produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, e.g., by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Ausubel et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley &amp; Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of the invention can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protein of the invention.  
       [0141] 4.8 Gene Therapy  
       [0142] Mutations in the polynucleotides of the invention may result in loss of normal function of the encoded protein. The invention thus provides gene therapy to restore normal activity of the polypeptides of the invention; or to treat disease states involving polypeptides of the invention. Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments). See, for example, Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 (1998). For additional reviews of gene therapy technology see Friedmann, Science, 244: 1275-1281(1989); Verma, Scientific American: 68-84 (1990); and Miller, Nature, 357: 455-460 (1992). Introduction of any one of the nucleotides of the present invention or a gene encoding the polypeptides of the present invention can also be accomplished with extrachromosomal substrates (transient expression) or artificial chromosomes (stable expression). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic purposes. Alternatively, it is contemplated that in other human disease states, preventing the expression of or inhibiting the activity of polypeptides of the invention will be useful in treating the disease states. It is contemplated that antisense therapy or gene therapy could be applied to negatively regulate the expression of polypeptides of the invention.  
       [0143] Other methods inhibiting expression of a protein include the introduction of antisense molecules to the nucleic acids of the present invention, their complements, or their translated RNA sequences, by methods known in the art. Further, the polypeptides of the present invention can be inhibited by using targeted deletion methods, or the insertion of a negative regulatory element such as a silencer, which is tissue specific.  
       [0144] The present invention still further provides cells genetically engineered in vivo to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell. These methods can be used to increase or decrease the expression of the polynucleotides of the present invention.  
       [0145] Knowledge of DNA sequences provided by the invention allows for modification of cells to permit, increase, or decrease, expression of endogenous polypeptide. Cells can be modified (e.g., by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the protein at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the desired protein encoding sequences. See, for example, PCT International Publication No. WO 94/12650, PCT International Publication No. WO 92/20808, and PCT International Publication No. WO 91/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the desired protein coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.  
       [0146] In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene&#39;s existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequences include polyadenylation signals, MRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.  
       [0147] The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurring elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this purpose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.  
       [0148] The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Pat. No. 5,272,071 to Chappel; U.S. Pat. No. 5,578,461 to Sherwin et al.; International Application No. PCT/US92/09627 (WO93/09222) by Selden et al.; and International Application No. PCT/US90/06436 (WO91/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.  
       [0149] 4.9 Transgenic Animals  
       [0150] In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals. Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as “knockout” animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Pat. No. 5,557,032, incorporated herein by reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Pat. No. 5,489,743 and PCT Publication No. WO94/28122, incorporated herein by reference.  
       [0151] Transgenic animals can be prepared wherein all or part of a promoter of the polynucleotides of the invention is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.  
       [0152] The polynucleotides of the present invention also make possible the development, through, e.g., homologous recombination or knock out strategies, of animals that fail to express polypeptides of the invention or that express a variant polypeptide. Such animals are useful as models for studying the in vivo activities of polypeptide as well as for studying modulators of the polypeptides of the invention.  
       [0153] In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals. Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as “knockout” animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Pat. No. 5,557,032, incorporated herein by reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Pat. No. 5,489,743 and PCT Publication No. WO94/28122, incorporated herein by reference.  
       [0154] Transgenic animals can be prepared wherein all or part of the polynucleotides of the invention promoter is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.  
       [0155] 4.10 Uses and Biological Activity  
       [0156] The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified herein. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA). The mechanism underlying the particular condition or pathology will dictate whether the polypeptides of the invention, the polynucleotides of the invention or modulators (activators or inhibitors) thereof would be beneficial to the subject in need of treatment. Thus, “therapeutic compositions of the invention” include compositions comprising isolated polynucleotides (including recombinant DNA molecules, cloned genes and degenerate variants thereof) or polypeptides of the invention (including full length protein, mature protein and truncations or domains thereof), or compounds and other substances that modulate the overall activity of the target gene products, either at the level of target gene/protein expression or target protein activity. Such modulators include polypeptides, analogs, (variants), including fragments and fusion proteins, antibodies and other binding proteins; chemical compounds that directly or indirectly activate or inhibit the polypeptides of the invention (identified, e.g., via drug screening assays as described herein); antisense polynucleotides and polynucleotides suitable for triple helix formation; and in particular antibodies or other binding partners that specifically recognize one or more epitopes of the polypeptides of the invention.  
       [0157] The polypeptides of the present invention may likewise be involved in cellular activation or in one of the other physiological pathways described herein.  
       [0158] 4.10.1 Research Uses and Utilities  
       [0159] The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on gels; as chromosome markers or tags (when labeled) to identify chromosomes or to map related gene positions; to compare with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA sequences; as a source of information to derive PCR primers for genetic fingerprinting; as a probe to “subtract-out” known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a “gene chip” or other support, including for examination of expression patterns; to raise anti-protein antibodies using DNA immunization techniques; and as an antigen to raise anti-DNA antibodies or elicit another immune response. Where the polynucleotide encodes a protein which binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction), the polynucleotide can also be used in interaction trap assays (such as, for example, that described in Gyuris et al. Cell 75:791-803 (1993)) to identify polynucleotides encoding the other protein with which binding occurs or to identify inhibitors of the binding interaction.  
       [0160] The polypeptides provided by the present invention can similarly be used in assays to determine biological activity, including in a panel of multiple proteins for high-throughput screening; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its receptor) in biological fluids; as markers for tissues in which the corresponding polypeptide is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands. Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.  
       [0161] Any or all of these research utilities are capable of being developed into reagent grade or kit format for commercialization as research products.  
       [0162] Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation “Molecular Cloning: A Laboratory Manual”, 2d ed. Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and “Methods in Enzymology: Guide to Molecular Cloning Techniques”, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.  
       [0163] 4.10.2 Nutritional Uses  
       [0164] Polynucleotides and polypeptides of the present invention can also be used as nutritional sources or supplements. Such uses include without limitation use as a protein or amino acid supplement, use as a carbon source, use as a nitrogen source and use as a source of carbohydrate. In such cases the polypeptide or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the polypeptide or polynucleotide of the invention can be added to the medium in or on which the microorganism is cultured.  
       [0165] 4.10.3 Cytokine and Cell Proliferation/Differentiation Activity  
       [0166] A polypeptide of the present invention may exhibit activity relating to cytokine, cell proliferation (either inducing or inhibiting) or cell differentiation (either inducing or inhibiting) activity or may induce production of other cytokines in certain cell populations. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Many protein factors discovered to date, including all known cytokines, have exhibited activity in one or more factor-dependent cell proliferation assays, and hence the assays serve as a convenient confirmation of cytokine activity. The activity of therapeutic compositions of the present invention is evidenced by any one of a number of routine factor dependent cell proliferation assays for cell lines including, without limitation, 32D, DA2, DAIG, T10, B9, B9/11, BaF3, MC9/G, M+(preB M+), 2E8, RB5, DA1, 123, T1165, HT2, CTLL2, TF-1, Mo7e, CMK, HUVEC, and Caco. Therapeutic compositions of the invention can be used in the following:  
       [0167] Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Bertagnolli et al., J. Immunol. 145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992; Bowman et al., I. Immunol. 152:1756-1761, 1994.  
       [0168] Assays for cytokine production and/or proliferation of spleen cells, lymph node cells or thymocytes include, without limitation, those described in: Polyclonal T cell stimulation, Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, John Wiley and Sons, Toronto. 1994.  
       [0169] Assays for proliferation and differentiation of hematopoietic and lymphopoietic cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Wiley and Sons, Toronto. 1991; deVries et al., J. Exp. Med. 173:1205-1211, 1991. Moreau et al., Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983; Measurement of mouse and human interleukin 6—Nordan, R. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.6.1-6.6.5, John Wiley and Sons. Toronto. 1991, Smith et al., Proc. Natl. Aced. Sci. U.S.A. 83:1857-1861, 1986; Measurement of human Interleukin 11—Bennett, F., Giannotti, J., Clark, S. C. and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto. 1991; Measurement of mouse and human Interleukin 9—Ciarletta, A., Giannotti, J., Clark. S. C. and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.13.1. John Wiley and Sons. Toronto. 1991.  
       [0170] Assays for T-cell clone responses to antigens (which will identify, among others, proteins that affect APC-T cell interactions as well as direct T-cell effects by measuring proliferation and cytokine production) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W Strober. Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors; Chapter 7, Immunologic studies in Humans); Weinberger et al., Proc. Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J. Immun. 11:405-411, 1981; Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512. 1988.  
       [0171] 4.10.4 Stem Cell Growth Factor Activity  
       [0172] A polypeptide of the present invention may exhibit stem cell growth factor activity and be involved in the proliferation, differentiation and survival of pluripotent and totipotent stem cells including primordial germ cells, embryonic stem cells, hematopoietic stem cells and/or germ line stem cells. Administration of the polypeptide of the invention to stem cells in vivo or ex vivo is expected to maintain and expand cell populations in a totipotential or pluripotential state which would be useful for re-engineering damaged or diseased tissues, transplantation, manufacture of bio-pharmaceuticals and the development of bio-sensors. The ability to produce large quantities of human cells has important working applications for the production of human proteins which currently must be obtained from non-human sources or donors, implantation of cells to treat diseases such as Parkinson&#39;s, Alzheimer&#39;s and other neurodegenerative diseases; tissues for grafting such as bone marrow, skin, cartilage, tendons, bone, muscle (including cardiac muscle), blood vessels, cornea, neural cells, gastrointestinal cells and others; and organs for transplantation such as kidney, liver, pancreas (including islet cells), heart and lung.  
       [0173] It is contemplated that multiple different exogenous growth factors and/or cytokines may be administered in combination with the polypeptide of the invention to achieve the desired effect, including any of the growth factors listed herein, other stem cell maintenance factors, and specifically including stem cell factor (SCF), leukemia inhibitory factor (LIF), Flt-3 ligand (Flt-3L), any of the interleukins, recombinant soluble IL-6 receptor fused to IL-6, macrophage inflammatory protein 1-alpha (MIP-1-alpha), G-CSF, GM-CSF, thrombopoietin (TPO), platelet factor 4 (PF-4), platelet-derived growth factor (PDGF), neural growth factors and basic fibroblast growth factor (bFGF).  
       [0174] Since totipotent stem cells can give rise to virtually any mature cell type, expansion of these cells in culture will facilitate the production of large quantities of mature cells. Techniques for culturing stem cells are known in the art and administration of polypeptides of the invention, optionally with other growth factors and/or cytokines, is expected to enhance the survival and proliferation of the stem cell populations. This can be accomplished by direct administration of the polypeptide of the invention to the culture medium. Alternatively, stroma cells transfected with a polynucleotide that encodes for the polypeptide of the invention can be used as a feeder layer for the stem cell populations in culture or in vivo. Stromal support cells for feeder layers may include embryonic bone marrow fibroblasts, bone marrow stromal cells, fetal liver cells, or cultured embryonic fibroblasts (see U.S. Pat. No. 5,690,926).  
       [0175] Stem cells themselves can be transfected with a polynucleotide of the invention to induce autocrine expression of the polypeptide of the invention. This will allow for generation of undifferentiated totipotential/pluripotential stem cell lines that are useful as is or that can then be differentiated into the desired mature cell types. These stable cell lines can also serve as a source of undifferentiated totipotential/pluripotential mRNA to create cDNA libraries and templates for polymerase chain reaction experiments. These studies would allow for the isolation and identification of differentially expressed genes in stem cell populations that regulate stem cell proliferation and/or maintenance.  
       [0176] Expansion and maintenance of totipotent stem cell populations will be useful in the treatment of many pathological conditions. For example, polypeptides of the present invention may be used to manipulate stem cells in culture to give rise to neuroepithelial cells that can be used to augment or replace cells damaged by illness, autoimmune disease, accidental damage or genetic disorders. The polypeptide of the invention may be useful for inducing the proliferation of neural cells and for the regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders which involve degeneration, death or trauma to neural cells or nerve tissue. In addition, the expanded stem cell populations can also be genetically altered for gene therapy purposes and to decrease host rejection of replacement tissues after grafting or implantation.  
       [0177] Expression of the polypeptide of the invention and its effect on stem cells can also be manipulated to achieve controlled differentiation of the stem cells into more differentiated cell types. A broadly applicable method of obtaining pure populations of a specific differentiated cell type from undifferentiated stem cell populations involves the use of a cell-type specific promoter driving a selectable marker. The selectable marker allows only cells of the desired type to survive. For example, stem cells can be induced to differentiate into cardiomyocytes (Wobus et al. Differentiation, 48: 173-182, (1991); Klug et al., J. Clin. Invest. 98(1): 216-224, (1998)) or skeletal muscle cells (Browder, L. W. In:  Principles of Tissue Engineering eds.  Lanza et al., Academic Press (1997)). Alternatively, directed differentiation of stem cells can be accomplished by culturing the stem cells in the presence of a differentiation factor such as retinoic acid and an antagonist of the polypeptide of the invention which would inhibit the effects of endogenous stem cell factor activity and allow differentiation to proceed.  
       [0178] In vitro cultures of stem cells can be used to determine if the polypeptide of the invention exhibits stem cell growth factor activity. Stem cells are isolated from any one of various cell sources (including hematopoietic stem cells and embryonic stem cells) and cultured on a feeder layer, as described by Thompson et al. Proc. Natl. Acad. Sci, U.S.A., 92: 7844-7848 (1995), in the presence of the polypeptide of the invention alone or in combination with other growth factors or cytokines. The ability of the polypeptide of the invention to induce stem cells proliferation is determined by colony formation on semi-solid support e.g. as described by Bernstein et al., Blood, 77: 2316-2321 (1991).  
       [0179] 4.10.5 Hematopoiesis Regulating Activity  
       [0180] A polypeptide of the present invention may be involved in regulation of hematopoiesis and, consequently, in the treatment of myeloid or lymphoid cell disorders. Even marginal biological activity in support of colony forming cells or of factor-dependent cell lines indicates involvement in regulating hematopoiesis, e.g. in supporting the growth and proliferation of erythroid progenitor cells alone or in combination with other cytokines, thereby indicating utility, for example, in treating various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocytes and monocytes/macrophages (i.e., traditional CSF activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in supporting the growth and proliferation of megakaryocytes and consequently of platelets thereby allowing prevention or treatment of various platelet disorders such as thrombocytopenia, and generally for use in place of or complimentary to platelet transfusions; and/or in supporting the growth and proliferation of hematopoietic stem cells which are capable of maturing to any and all of the above-mentioned hematopoietic cells and therefore find therapeutic utility in various stem cell disorders (such as those usually treated with transplantation, including, without limitation, aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in repopulating the stem cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo (i.e., in conjunction with bone marrow transplantation or with peripheral progenitor cell transplantation (homologous or heterologous)) as normal cells or genetically manipulated for gene therapy.  
       [0181] Therapeutic compositions of the invention can be used in the following:  
       [0182] Suitable assays for proliferation and differentiation of various hematopoietic lines are cited above.  
       [0183] Assays for embryonic stem cell differentiation (which will identify, among others, proteins that influence embryonic differentiation hematopoiesis) include, without limitation, those described in: Johansson et al. Cellular Biology 15:141-151. 1995: Keller et al., Molecular and Cellular Biology 13:473-486. 1993: McClanahan et al. Blood 81:2903-2915, 1993.  
       [0184] Assays for stem cell survival and differentiation (which will identify, among others, proteins that regulate lympho-hematopoiesis) include, without limitation, those described in: Methylcellulose colony forming assays. Freshney, M. G. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 265-268, Wiley-Liss, Inc., New York, N.Y. 1994; Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911. 1992; Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, I. K. and Briddell, R. A. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 23-39, Wiley-Liss, Inc., New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994; Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 1-21, Wiley-Liss, Inc., New York, N.Y. 1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M. and Allen, T. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 163-179, Wiley-Liss, Inc., New York, N.Y. 1994; Long term culture initiating cell assay, Sutherland, H. J. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 139-162, Wiley-Liss, Inc., New York, N.Y. 1994.  
       [0185] 4.10.6 Tissue Growth Activity  
       [0186] A polypeptide of the present invention also may be involved in bone, cartilage, tendon, ligament and/or nerve tissue growth or regeneration, as well as in wound healing and tissue repair and replacement, and in healing of burns, incisions and ulcers.  
       [0187] A polypeptide of the present invention which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals. Compositions of a polypeptide, antibody, binding partner, or other modulator of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogenic agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.  
       [0188] A polypeptide of this invention may also be involved in attracting bone-forming cells, stimulating growth of bone-forming cells, or inducing differentiation of progenitors of bone-forming cells. Treatment of osteoporosis, osteoarthritis, bone degenerative disorders, or periodontal disease, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes may also be possible using the composition of the invention.  
       [0189] Another category of tissue regeneration activity that may involve the polypeptide of the present invention is tendon/ligament formation. Induction of tendon/ligament-like tissue or other tissue formation in circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament-like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tendon/ligament-like tissue formation induced by a composition of the present invention contributes to the repair of congenital, trauma induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions of the present invention may provide environment to attract tendon- or ligament-forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon- or ligament-forming cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions of the invention may also be useful in the treatment of tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.  
       [0190] The compositions of the present invention may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders, which involve degeneration, death or trauma to neural cells or nerve tissue. More specifically, a G composition may be used in the treatment of diseases of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer&#39;s, Parkinson&#39;s disease, Huntington&#39;s disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions which may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma and cerebrovascular diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a composition of the invention.  
       [0191] Compositions of the invention may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with vascular insufficiency, surgical and traumatic wounds, and the like.  
       [0192] Compositions of the present invention may also be involved in the generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation of fibrotic scarring may allow normal tissue to regenerate. A polypeptide of the present invention may also exhibit angiogenic activity.  
       [0193] A composition of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.  
       [0194] A composition of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.  
       [0195] Therapeutic compositions of the invention can be used in the following:  
       [0196] Assays for tissue generation activity include, without limitation, those described in: International Patent Publication No. WO95/16035 (bone, cartilage, tendon); International Patent Publication No. WO95/05846 (nerve, neuronal); International Patent Publication No. WO91/07491 (skin, endothelium).  
       [0197] Assays for wound healing activity include, without limitation, those described in: Winter, Epidermal Wound Healing, pps. 71-112 (Maibach, H. I. and Rovee, D. T., eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J. Invest. Dermatol 71:382-84 (1978).  
       [0198] 4.10.7 Immune Stimulating or Suppressing Activity  
       [0199] A polypeptide of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A polynucleotide of the invention can encode a polypeptide exhibiting such activities. A protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., in regulating (up or down) growth and proliferation of T and/or B lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations. These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania spp, malaria spp, and various fungal infections such as candidiasis. Of course, in this regard, proteins of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e. in the treatment of cancer.  
       [0200] Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation. Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft-versus-host disease and autoimmune inflammatory eye disease. Such a protein (or antagonists thereof, including antibodies) of the present invention may also to be useful in the treatment of allergic reactions and conditions (e.g., anaphylaxis, serum sickness, drug reactions, food allergies, insect venom allergies, mastocytosis, allergic rhinitis, hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic dermatitis, allergic contact dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic conjunctivitis, atopic keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary conjunctivitis and contact allergies), such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein (or antagonists thereof) of the present invention. The therapeutic effects of the polypeptides or antagonists thereof on allergic reactions can be evaluated by in vivo animals models such as the cumulative contact enhancement test (Lastbom et al., Toxicology 125: 59-66, 1998), skin prick test (Hoffmann et al., Allergy 54: 446-54. 1999), guinea pig skin sensitization test (Vohr et al., Arch. Toxocol. 73: 501-9), and murine local lymph node assay (Kimber et al., J. Toxicol. Environ. Health 53: 563-79).  
       [0201] Using the proteins of the invention it may also be possible to modulate immune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T cell responses or by inducing specific tolerance in T cells, or both. Immunosuppression of T cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T cells to the suppressive agent. Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased. Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.  
       [0202] Down regulating or preventing one or more antigen functions (including without limitation B lymphocyte antigen functions (such as, for example, B7)), e.g., preventing high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft-versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation. Typically, in tissue transplants, rejection of the transplant is initiated through its recognition as foreign by T cells, followed by an immune reaction that destroys the transplant. The administration of a therapeutic composition of the invention may prevent cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, a lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking reagents may avoid the necessity of repeated administration of these blocking reagents. To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.  
       [0203] The efficacy of particular therapeutic compositions in preventing organ transplant rejection or GVHD can be assessed using animal models that are predictive of efficacy in humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA41 g fusion proteins in vivo as described in Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl. Acad. Sci USA, 89:11102-11105 (1992). In addition, murine models of GVHD (see Paul ed., Fundamental Immunology, Raven Press. New York, 1989, pp. 846-847) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.  
       [0204] Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases. Preventing the activation of autoreactive T cells may reduce or eliminate disease symptoms. Administration of reagents which block stimulation of T cells can be used to inhibit T cell activation and prevent production of autoantibodies or T cell-derived cytokines which may be involved in the disease process. Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from the disease. The efficacy of blocking reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include murine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, murine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB rats, and murine experimental myasthenia gravis (see Paul ed., Fundamental Immunology. Raven Press, New York, 1989, pp. 840-856).  
       [0205] Upregulation of an antigen function (e.g. a B lymphocyte antigen function), as a means of up regulating immune responses, may also be useful in therapy. Upregulation of immune responses may be in the form of enhancing an existing immune response or eliciting an initial immune response. For example, enhancing an immune response may be useful in cases of viral infection, including systemic viral diseases such as influenza, the common cold, and encephalitis.  
       [0206] Alternatively, anti-viral immune responses may be enhanced in an infected patient by removing T cells from the patient, costimulating the T cells in vitro with viral antigen-pulsed APCs either expressing a peptide of the present invention or together with a stimulatory form of a soluble peptide of the present invention and reintroducing the in vitro activated T cells into the patient. Another method of enhancing anti-viral immune responses would be to isolate infected cells from a patient, transfect them with a nucleic acid encoding a protein of the present invention as described herein such that the cells express all or a portion of the protein on their surface, and reintroduce the transfected cells into the patient. The infected cells would now be capable of delivering a costimulatory signal to, and thereby activate, T cells in vivo.  
       [0207] A polypeptide of the present invention may provide the necessary stimulation signal to T cells to induce a T cell mediated immune response against the transfected tumor cells. In addition, tumor cells which lack MHC class I or MHC class II molecules, or which fail to reexpress sufficient mounts of MHC class I or MHC class II molecules, can be transfected with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain truncated portion) of an MHC class I alpha chain protein and P2 microglobulin protein or an MHC class II alpha chain protein and an MHC class II beta chain protein to thereby express MHC class I or MHC class II proteins on the cell surface. Expression of the appropriate class I or class II MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7-3) induces a T cell mediated immune response against the transfected tumor cell. Optionally, a gene encoding an antisense construct which blocks expression of an MHC class II associated protein, such as the invariant chain, can also be cotransfected with a DNA encoding a peptide having the activity of a B lymphocyte antigen to promote presentation of tumor associated antigens and induce tumor specific immunity. Thus, the induction of a T cell mediated immune response in a human subject may be sufficient to overcome tumor-specific tolerance in the subject.  
       [0208] The activity of a protein of the invention may, among other means, be measured by the following methods:  
       [0209] Suitable assays for thymocyte or splenocyte cytotoxicity include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3. In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7. Immunologic studies in Humans); Herrmann et al. Proc. Natl. Acad. Sci. USA 78:2488-2492. 1981; Herrmann et al. J. Immunol. 128:1968-1974. 1982: Handa et al., J. Immunol. 135:1564-1572, 1985: Takai et al., I. Immunol. 137:3494-3500. 1986: Takai et al., J. Immunol. 140:508-512, 1988; Bowman et al. J. Virology 61:1992-1998: Bertagnolli et al., Cellular Immunology 133:327-341, 1991: Brown et al., J. Immunol. 153:3079-3092, 1994.  
       [0210] Assays for T-cell-dependent immunoglobulin responses and isotype switching (which will identify, among others, proteins that modulate T-cell dependent antibody responses and that affect Th1/Th2 profiles) include, without limitation, those described in: Maliszewski, J. Immunol. 144:3028-3033, 1990; and Assays for B cell function: In vitro antibody production, Mond, J. J. and Brunswick, M. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto. 1994.  
       [0211] Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Th1 and CTL responses) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512, 1988; Bertagnolli et al., J. Immunol. 149:3778-3783, 1992.  
       [0212] Dendritic cell-dependent assays (which will identify, among others, proteins expressed by dendritic cells that activate naive T-cells) include, without limitation, those described in: Guery et al., J. Immunol. 134:536-544, 1995; Inaba et al., Journal of Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079, 1995; Porgador et al., Journal of Experimental Medicine 182:255-260, 1995; Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-1264, 1989; Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and Inaba et al., Journal of Experimental Medicine 172:631-640, 1990.  
       [0213] Assays for lymphocyte survival/apoptosis (which will identify, among others, proteins that prevent apoptosis after superantigen induction and proteins that regulate lymphocyte homeostasis) include, without limitation, those described in: Darzynkiewicz et al., Cytometry 13:795-808, 1992; Gorczyca et al., Leukemia 7:659-670. 1993; Gorczyca et al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991: Zacharchuk, Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897. 1993; Gorczyca et al., International Journal of Oncology 1:639-648, 1992.  
       [0214] Assays for proteins that influence early steps of T-cell commitment and development include, without limitation, those described in: Antica et al. Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122. 1994; Galy et al. Blood 85:2770-2778, 1995; Toki et al. Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.  
       [0215] 4.10.8 Activin/Inhibin Activity  
       [0216] A polypeptide of the present invention may also exhibit activin- or inhibin-related activities. A polynucleotide of the invention may encode a polypeptide exhibiting such characteristics. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the present invention, alone or in heterodimers with a member of the inhibin family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the polypeptide of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH from cells of the anterior pituitary. See, for example, U.S. Pat. No. 4,798,885. A polypeptide of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as, but not limited to, cows, sheep and pigs.  
       [0217] The activity of a polypeptide of the invention may, among other means, be measured by the following methods.  
       [0218] Assays for activin/inhibin activity include, without limitation, those described in: Vale et al., Endocrinology 91:562-572, 1972; Ling et al. Nature 321:779-782, 1986; Vale et al., Nature 321:776-779, 1986; Mason et al., Nature 318:659-663, 1985; Forage et al., Proc. Natl. Acad. Sci. USA 83:3091-3095, 1986.  
       [0219] 4.10.9 Chemotactic/Chemokinetic Activity  
       [0220] A polypeptide of the present invention may be involved in chemotactic or chemokinetic activity for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Chemotactic and chemokinetic receptor activation can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic compositions (e.g. proteins, antibodies, binding partners, or modulators of the invention) provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.  
       [0221] A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell population. Preferably, the protein or peptide has the ability to directly stimulate directed movement of cells. Whether a particular protein has chemotactic activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.  
       [0222] Therapeutic compositions of the invention can be used in the following:  
       [0223] Assays for chemotactic activity (which will identify proteins that induce or prevent chemotaxis) consist of assays that measure the ability of a protein to induce the migration of cells across a membrane as well as the ability of a protein to induce the adhesion of one cell population to another cell population. Suitable assays for movement and adhesion include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Marguiles, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 6.12, Measurement of alpha and beta Chemokines 6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995; Lind et al. APMIS 103:140-146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et al. J. of Immunol. 152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768, 1994.  
       [0224] 4.10.10 Hemostatic and Thrombolytic Activity  
       [0225] A polypeptide of the invention may also be involved in hemostasis or thrombolysis or thrombosis. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Compositions may be useful in treatment of various coagulation disorders (including hereditary disorders, such as hemophilias) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A composition of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).  
       [0226] Therapeutic compositions of the invention can be used in the following:  
       [0227] Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al. J. Clin. Pharmacol. 26:131-140, 1986; Burdick et al., Thrombosis Res. 45:413-419, 1987; Humphrey et al. Fibrinolysis 5:71-79 (1991); Schaub, Prostaglandins 35:467-474. 1988.  
       [0228] 4.10.11 Cancer Diagnosis and Therapy  
       [0229] Polypeptides of the invention may be involved in cancer cell generation, proliferation or metastasis. Detection of the presence or amount of polynucleotides or polypeptides of the invention may be useful for the diagnosis and/or prognosis of one or more types of cancer. For example, the presence or increased expression of a polynucleotide/polypeptide of the invention may indicate a hereditary risk of cancer, a precancerous condition, or an ongoing malignancy. Conversely, a defect in the gene or absence of the polypeptide may be associated with a cancer condition. Identification of single nucleotide polymorphisms associated with cancer or a predisposition to cancer may also be useful for diagnosis or prognosis.  
       [0230] Cancer treatments promote tumor regression by inhibiting tumor cell proliferation, inhibiting angiogenesis (growth of new blood vessels that is necessary to support tumor growth) and/or prohibiting metastasis by reducing tumor cell motility or invasiveness. Therapeutic compositions of the invention may be effective in adult and pediatric oncology including in solid phase tumors/malignancies, locally advanced tumors, human soft tissue sarcomas, metastatic cancer, including lymphatic metastases, blood cell malignancies including multiple myeloma, acute and chronic leukemias, and lymphomas, head and neck cancers including mouth cancer, larynx cancer and thyroid cancer, lung cancers including small cell carcinoma and non-small cell cancers, breast cancers including small cell carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal cancer, stomach cancer, colon cancer, colorectal cancer and polyps associated with colorectal neoplasia, pancreatic cancers, liver cancer, urologic cancers including bladder cancer and prostate cancer, malignancies of the female genital tract including ovarian carcinoma, uterine (including endometrial) cancers, and solid tumor in the ovarian follicle, kidney cancers including renal cell carcinoma, brain cancers including intrinsic brain tumors, neuroblastoma, astrocytic brain tumors, gliomas, metastatic tumor cell invasion in the central nervous system, bone cancers including osteomas, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma and Karposi&#39;s sarcoma.  
       [0231] Polypeptides, polynucleotides, or modulators of polypeptides of the invention (including inhibitors and stimulators of the biological activity of the polypeptide of the invention) may be administered to treat cancer. Therapeutic compositions can be administered in therapeutically effective dosages alone or in combination with adjuvant cancer therapy such as surgery, chemotherapy, radiotherapy, thermotherapy, and laser therapy, and may provide a beneficial effect, e.g. reducing tumor size, slowing rate of tumor growth, inhibiting metastasis, or otherwise improving overall clinical condition, without necessarily eradicating the cancer.  
       [0232] The composition can also be administered in therapeutically effective amounts as a portion of an anti-cancer cocktail. An anti-cancer cocktail is a mixture of the polypeptide or modulator of the invention with one or more anti-cancer drugs in addition to a pharmaceutically acceptable carrier for delivery. The use of anti-cancer cocktails as a cancer treatment is routine. Anti-cancer drugs that are well known in the art and can be used as a treatment in combination with the polypeptide or modulator of the invention include: Actinomycin D, Aminoglutethimide. Asparaginase, Bleomycin, Busulfan, Carboplatin, Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine HCl (Cytosine arabinoside), Dacarbazine, Dactinomycin, Daunorubicin HCl, Doxorubicin HCl, Estramustine phosphate sodium, Etoposide (V16-213), Floxuridine, 5-Fluorouracil (5-Fu), Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a, Interferon Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine, Mechlorethamine HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX), Mitomycin, Mitoxantrone HCl, Octreotide, Plicamycin, Procarbazine HCl, Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Vincristine sulfate, Amsacrine, Azacitidine, Hexamethylmelamine, Interleukin-2, Mitoguazone, Pentostatin, Semustine, Teniposide, and Vindesine sulfate.  
       [0233] In addition, therapeutic compositions of the invention may be used for prophylactic treatment of cancer. There are hereditary conditions and/or environmental situations (e.g. exposure to carcinogens) known in the art that predispose an individual to developing cancers. Under these circumstances, it may be beneficial to treat these individuals with therapeutically effective doses of the polypeptide of the invention to reduce the risk of developing cancers.  
       [0234] In vitro models can be used to determine the effective doses of the polypeptide of the invention as a potential cancer treatment. These in vitro models include proliferation assays of cultured tumor cells, growth of cultured tumor cells in soft agar (see Freshney, (1987) Culture of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, N.Y. Ch 18 and Ch 21), tumor systems in nude mice as described in Giovanella et al., J. Natl. Can. Inst., 52: 921-30 (1974), mobility and invasive potential of tumor cells in Boyden Chamber assays as described in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and angiogenesis assays such as induction of vascularization of the chick chorioallantoic membrane or induction of vascular endothelial cell migration as described in Ribatta et al., Intl. J. Dev. Biol., 40: 1189-97 (1999) and Li et al., Clin. Exp. Metastasis, 17:423-9 (1999), respectively. Suitable tumor cells lines are available, e.g. from American Type Tissue Culture Collection catalogs.  
       [0235] 4.10.12 Receptor/Ligand Activity  
       [0236] A polypeptide of the present invention may also demonstrate activity as receptor, receptor ligand or inhibitor or agonist of receptor/ligand interactions. A polynucleotide of the invention can encode a polypeptide exhibiting such characteristics. Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selecting, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of cellular and humoral immune responses. Receptors and ligands are also useful for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.  
       [0237] The activity of a polypeptide of the invention may, among other means, be measured by the following methods:  
       [0238] Suitable assays for receptor-ligand activity include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1-7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987; Bierer et al., J. Exp. Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160 1989; Stoltenborg et al., J. Immunol. Methods 175:59-68, 1994; Stitt et al. Cell 80:661-670, 1995.  
       [0239] By way of example, the polypeptides of the invention may be used as a receptor for a ligand(s) thereby transmitting the biological activity of that ligand(s). Ligands may be identified through binding assays, affinity chromatography, dihybrid screening assays, BIAcore assays, gel overlay assays, or other methods known in the art.  
       [0240] Studies characterizing drugs or proteins as agonist or antagonist or partial agonists or a partial antagonist require the use of other proteins as competing ligands. The polypeptides of the present invention or ligand(s) thereof may be labeled by being coupled to radioisotopes, colorimetric molecules or a toxin molecules by conventional methods. (“Guide to Protein Purification” Murray P. Deutscher (ed) Methods in Enzymology Vol. 182 (1990) Academic Press, Inc. San Diego). Examples of radioisotopes include, but are not limited to, tritium and carbon-14. Examples of colorimetric molecules include, but are not limited to, fluorescent molecules such as fluorescamine, or rhodamine or other colorimetric molecules. Examples of toxins include, but are not limited, to ricin.  
       [0241] 4.10.13 Drug Screening  
       [0242] This invention is particularly useful for screening chemical compounds by using the novel polypeptides or binding fragments thereof in any of a variety of drug screening techniques. The polypeptides or fragments employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or a fragment thereof. Drugs are screened against such transformed cells in competitive binding assays. Such cells, either in viable or fixed form, can be used for standard binding assays. One may measure, for example, the formation of complexes between polypeptides of the invention or fragments and the agent being tested or examine the diminution in complex formation between the novel polypeptides and an appropriate cell line, which are well known in the art.  
       [0243] Sources for test compounds that may be screened for ability to bind to or modulate (i.e., increase or decrease) the activity of polypeptides of the invention include (1) inorganic and organic chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of either random or mimetic peptides, oligonucleotides or organic molecules.  
       [0244] Chemical libraries may be readily synthesized or purchased from a number of commercial sources, and may include structural analogs of known compounds or compounds that are identified as “hits” or “leads” via natural product screening.  
       [0245] The sources of natural product libraries are microorganisms (including bacteria and fungi), animals, plants or other vegetation, or marine organisms, and libraries of mixtures for screening may be created by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of the organisms themselves. Natural product libraries include polyketides, non-ribosomal peptides, and (non-naturally occurring) variants thereof. For a review, see  Science  282:63-68 (1998).  
       [0246] Combinatorial libraries are composed of large numbers of peptides, oligonucleotides or organic compounds and can be readily prepared by traditional automated synthesis methods, PCR, cloning or proprietary synthetic methods. Of particular interest are peptide and oligonucleotide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers,  Curr. Opin. Biotechnol.  8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al.,  Mol. Biotechnol,  9(3):205-23 (1998): Hruby et al.,  Curr Opin Chem Biol,  1(1): 14-19 (1997); Dorner et al.,  Bioorg Med Chem.  4(5):709-15 (1996) (alkylated dipeptides).  
       [0247] Identification of modulators through use of the various libraries described herein permits modification of the candidate “hit” (or “lead”) to optimize the capacity of the “hit” to bind a polypeptide of the invention. The molecules identified in the binding assay are then tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.  
       [0248] The binding molecules thus identified man be complexed with toxins, e.g. ricin or cholera, or with other compounds that are toxic to cells such as radioisotopes. The toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for a polypeptide of the invention. Alternatively, the binding molecules may be complexed with imaging agents for targeting and imaging purposes.  
       [0249] 4.10.14 Assay for Receptor Activity  
       [0250] The invention also provides methods to detect specific binding of a polypeptide e.g. a ligand or a receptor. The art provides numerous assays particularly useful for identifying previously unknown binding partners for receptor polypeptides of the invention. For example, expression cloning using mammalian or bacterial cells, or dihybrid screening assays can be used to identify polynucleotides encoding binding partners. As another example, affinity chromatography with the appropriate immobilized polypeptide of the invention can be used to isolate polypeptides that recognize and bind polypeptides of the invention. There are a number of different libraries used for the identification of compounds, and in particular small molecules, that modulate (i.e. increase or decrease) biological activity of a polypeptide of the invention. Ligands for receptor polypeptides of the invention can also be identified by adding exogenous ligands, or cocktails of ligands to two cells populations that are genetically identical except for the expression of the receptor of the invention: one cell population expresses the receptor of the invention whereas the other does not. The response of the two cell populations to the addition of ligands(s) are then compared. Alternatively, an expression library can be co-expressed with the polypeptide of the invention in cells and assayed for an autocrine response to identify potential ligand(s). As still another example. BIAcore assays, gel overlay assays, or other methods known in the art can be used to identify binding partner polypeptides, including, (1) organic and inorganic chemical libraries. (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules.  
       [0251] The role of downstream intracellular signaling molecules in the signaling cascade of the polypeptide of the invention can be determined. For example, a chimeric protein in which the cytoplasmic domain of the polypeptide of the invention is fused to the extracellular portion of a protein, whose ligand has been identified, is produced in a host cell. The cell is then incubated with the ligand specific for the extracellular portion of the chimeric protein, thereby activating the chimeric receptor. Known downstream proteins involved in intracellular signaling can then be assayed for expected modifications i.e. phosphorylation. Other methods known to those in the art can also be used to identify signaling molecules involved in receptor activity.  
       [0252] 4.10.15 Anti-Inflammatory Activity  
       [0253] Compositions of the present invention may also exhibit anti-inflammatory activity. The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inflammatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Compositions with such activities can be used to treat inflammatory conditions including chronic or acute conditions), including without limitation intimation associated with infection (such as septic shock, sepsis or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn&#39;s disease or resulting from over production of cytokines such as TNF or IL-1. Compositions of the invention may also be useful to treat anaphylaxis and hypersensitivity to an antigenic substance or material. Compositions of this invention may be utilized to prevent or treat conditions such as, but not limited to, sepsis, acute pancreatitis, endotoxin shock, cytokine induced shock, rheumatoid arthritis, chronic inflammatory arthritis, pancreatic cell damage from diabetes mellitus type 1, graft versus host disease, inflammatory bowel disease, inflamation associated with pulmonary disease, other autoimmune disease or inflammatory disease, an antiproliferative agent such as for acute or chronic mylegenous leukemia or in the prevention of premature labor secondary to intrauterine infections.  
       [0254] 4.10.16 Leukemias  
       [0255] Leukemias and related disorders may be treated or prevented by administration of a therapeutic that promotes or inhibits function of the polynucleotides and/or polypeptides of the invention. Such leukemias and related disorders include but are not limited to acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic, promyelocytic, myelomonocytic, monocytic, erythroleukemia, chronic leukemia, chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia (for a review of such disorders, see Fishman et al. 1985. Medicine. 2d Ed., J. B. Lippincott Co., Philadelphia).  
       [0256] 4.10.17 Nervous System Disorders  
       [0257] Nervous system disorders, involving cell types which can be tested for efficacy of intervention with compounds that modulate the activity of the polynucleotides and/or polypeptides of the invention, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to nervous system injuries, and diseases or disorders which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated in a patient (including human and non-human mammalian patients) according to the invention include but are not limited to the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems:  
       [0258] (i) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries;  
       [0259] (ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia;  
       [0260] (iii) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster or herpes simplex virus or with Lyme disease, tuberculosis, syphilis;  
       [0261] (iv) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson&#39;s disease, Alzheimer&#39;s disease, Huntington&#39;s chorea, or amyotrophic lateral sclerosis;  
       [0262] (v) lesions associated with nutritional diseases or disorders, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration;  
       [0263] (vi) neurological lesions associated with systemic diseases including but not limited to diabetes (diabetic neuropathy, Bell&#39;s palsy), systemic lupus erythematosus, carcinoma, or sarcoidosis;  
       [0264] (vii) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and  
       [0265] (viii) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including but not limited to multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multi focal leukoencephalopathy, and central pontine myelinolysis.  
       [0266] Therapeutics which are useful according to the invention for treatment of a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, therapeutics which elicit any of the following effects may be useful according to the invention:  
       [0267] (i) increased survival time of neurons in culture;  
       [0268] (ii) increased sprouting of neurons in culture or in vivo;  
       [0269] (iii) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or  
       [0270] (iv) decreased symptoms of neuron dysfunction in vivo.  
       [0271] Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may be measured by the method set forth in Arakawa et al. (1990, J. Neurosci. 10:3507-3515); increased sprouting of neurons may be detected by methods set forth in Pestronk et al. (1980, Exp. Neurol. 70:65-82) or Brown et al. (1981, Ann. Rev. Neurosci. 4:17-42); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.  
       [0272] In specific embodiments, motor neuron disorders that may be treated according to the invention include but are not limited to disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).  
       [0273] 4.10.18 Other Activities  
       [0274] A polypeptide of the invention may also exhibit one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites; effecting (suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair color, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ or body part size or shape (such as, for example, breast augmentation or diminution, change in bone form or shape); effecting biorhythms or circadian cycles or rhythms; effecting the fertility of male or female subjects: effecting the metabolism, catabolism, anabolism, processing, utilization, storage or elimination of dietary fat, lipid, protein, carbohydrate, vitamins, minerals, co-factors or other nutritional factors or component(s); effecting behavioral characteristics, including, without limitation, appetite, libido, stress, cognition (including cognitive disorders), depression (including depressive disorders) and violent behaviors; providing analgesic effects or other pain reducing effects; promoting differentiation and growth of embryonic stem cells in lineages other than hematopoietic lineages; hormonal or endocrine activity; in the case of enzymes, correcting deficiencies of the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.  
       [0275] 4.10.19 Identification of Polymorphisms  
       [0276] The demonstration of polymorphisms makes possible the identification of such polymorphisms in human subjects and the pharmacogenetic use of this information for diagnosis and treatment. Such polymorphisms may be associated with, e.g., differential predisposition or susceptibility to various disease states (such as disorders involving inflammation or immune response) or a differential response to drug administration, and this genetic information can be used to tailor preventive or therapeutic treatment appropriately. For example, the existence of a polymorphism associated with a predisposition to inflammation or autoimmune disease makes possible the diagnosis of this condition in humans by identifying the presence of the polymorphism.  
       [0277] Polymorphisms can be identified in a variety of ways known in the art which all generally involve obtaining a sample from a patient, analyzing DNA from the sample, optionally involving isolation or amplification of the DNA, and identifying the presence of the polymorphism in the DNA. For example, PCR may be used to amplify an appropriate fragment of genomic DNA which may then be sequenced. Alternatively, the DNA may be subjected to allele-specific oligonucleotide hybridization (in which appropriate oligonucleotides are hybridized to the DNA under conditions permitting detection of a single base mismatch) or to a single nucleotide extension assay (in which an oligonucleotide that hybridizes immediately adjacent to the position of the polymorphism is extended with one or more labeled nucleotides). In addition, traditional restriction fragment length polymorphism analysis (using restriction enzymes that provide differential digestion of the genomic DNA depending on the presence or absence of the polymorphism) may be performed. Arrays with nucleotide sequences of the present invention can be used to detect polymorphisms. The array can comprise modified nucleotide sequences of the present invention in order to detect the nucleotide sequences of the present invention. In the alternative, any one of the nucleotide sequences of the present invention can be placed on the array to detect changes from those sequences.  
       [0278] Alternatively a polymorphism resulting in a change in the amino acid sequence could also be detected by detecting a corresponding change in amino acid sequence of the protein, e.g., by an antibody specific to the variant sequence.  
       [0279] 4.10.20 Arthritis and Inflammation  
       [0280] The immunosuppressive effects of the compositions of the invention against rheumatoid arthritis is determined in an experimental animal model system. The experimental model system is adjuvant induced arthritis in rats, and the protocol is described by J. Holoshitz, et at., 1983, Science, 219:56, or by B. Waksman et al., 1963. Int. Arch. Allergy Appl. Immunol., 23:129. Induction of the disease can be caused by a single injection, generally intradermally, of a suspension of killed Mycobacterium tuberculosis in complete Freund&#39;s adjuvant (CFA). The route of injection can vary, but rats may be injected at the base of the tail with an adjuvant mixture. The polypeptide is administered in phosphate buffered solution (PBS) at a dose of about 1-5 mg/kg. The control consists of administering PBS only.  
       [0281] The procedure for testing the effects of the test compound would consist of intradermally injecting killed Mycobacterium tuberculosis in CFA followed by immediately administering the test compound and subsequent treatment every other day until day 24. At 14, 15, 18, 20, 22, and 24 days after injection of Mycobacterium CFA., an overall arthritis score may be obtained as described by J. Holoskitz above. An analysis of the data would reveal that the test compound would have a dramatic affect on the swelling of the joints as measured by a decrease of the arthritis score.  
       [0282] 4.11 Therapeutic Methods  
       [0283] The compositions (including polypeptide fragments, analogs, variants and antibodies or other binding partners or modulators including antisense polynucleotides) of the invention have numerous applications in a variety of therapeutic methods. Examples of therapeutic applications include, but are not limited to, those exemplified herein.  
       [0284] 4.11.1 EXAMPLE  
       [0285] One embodiment of the invention is the administration of an effective amount of the polypeptides or other composition of the invention to individuals affected by a disease or disorder that can be modulated by, regulating the peptides of the invention. While the mode of administration is not particularly important, parenteral administration is preferred. An exemplary mode of administration is to deliver an intravenous bolus. The dosage of the polypeptides or other composition of the invention will normally be determined by the prescribing physician. It is to be expected that the dosage will vary according to the age, weight, condition and response of the individual patient. Typically, the amount of polypeptide administered per dose will be in the range of about 0.01 μg/kg to 100 mg/kg of body weight, with the preferred dose being about 0.1 μg/kg to 10 mg/kg of patient body weight. For parenteral administration, polypeptides of the invention will be formulated in an injectable form combined with a pharmaceutically acceptable parenteral vehicle. Such vehicles are well known in the art and examples include water, saline, Ringer&#39;s solution, dextrose solution, and solutions consisting of small amounts of the human serum albumin. The vehicle may contain minor amounts of additives that maintain the isotonicity and stability of the polypeptide or other active ingredient. The preparation of such solutions is within the skill of the art.  
       [0286] 4.12 Pharmaceutical Formulations and Routes of Administration  
       [0287] A protein or other composition of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources and including antibodies and other binding partners of the polypeptides of the invention) may be administered to a patient in need, by itself, or in pharmaceutical compositions where it is mixed with suitable carriers or excipient(s) at doses to treat or ameliorate a variety of disorders. Such a composition may optionally contain (in addition to protein or other active ingredient and a carrier) diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the carrier will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF. GM-CSF, TNF, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNF0, TNF1, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the disease or disorder in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet-derived growth factor (PDGF), transforming growth factors (TGF-α and TGF-β), insulin-like growth factor (IGF), as well as cytokines described herein.  
       [0288] The pharmaceutical composition may further contain other agents which either enhance the activity of the protein or other active ingredient or complement its activity or use in treatment. Such additional factors and/or agents may be included in the pharmaceutical composition to produce a synergistic effect with protein or other active ingredient of the invention, or to minimize side effects. Conversely, protein or other active ingredient of the present invention may be included in formulations of the particular clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent to minimize side effects of the clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent (such as IL-1 Ra, IL-1 Hy1, IL-1 Hy2, anti-TNF, corticosteroids, immunosuppressive agents). A protein of the present invention may be active in multimers (e.g., heterodimers or homodimers) or complexes with itself or other proteins. As a result, pharmaceutical compositions of the invention may comprise a protein of the invention in such multimeric or complexed form.  
       [0289] As an alternative to being included in a pharmaceutical composition of the invention including a first protein, a second protein or a therapeutic agent may be concurrently administered with the first protein (e.g., at the same time, or at differing times provided that therapeutic concentrations of the combination of agents is achieved at the treatment site). Techniques for formulation and administration of the compounds of the instant application may be found in “Remington&#39;s Pharmaceutical Sciences.” Mack Publishing Co., Easton, Pa., latest edition. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, a therapeutically effective dose refers to that ingredient alone. When applied to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.  
       [0290] In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein or other active ingredient of the present invention is administered to a mammal having a condition to be treated. Protein or other active ingredient of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytokines, lymphokines or other hematopoletic factors. When co-administered with one or more cytokines, lymphokines or other hematopoietic factors, protein or other active ingredient of the present invention may be administered either simultaneously with the cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein or other active ingredient of the present invention in combination with cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.  
       [0291] 4.12.1 Routes of Administration  
       [0292] Suitable routes of administration may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections. Administration of protein or other active ingredient of the present invention used in the pharmaceutical composition or to practice the method of the present invention can be carried out in a variety of conventional ways, such as oral ingestion, inhalation, topical application or cutaneous, subcutaneous, intraperitoneal, parenteral or intravenous injection. Intravenous administration to the patient is preferred.  
       [0293] Alternately, one may administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into a arthritic joints or in fibrotic tissue, often in a depot or sustained release formulation. In order to prevent the scarring process frequently occurring as complication of glaucoma surgery, the compounds may be administered topically, for example, as eye drops. Furthermore, one may administer the drug in a targeted drug delivery system, for example, in a liposome coated with a specific antibody, targeting, for example, arthritic or fibrotic tissue. The liposomes will be targeted to and taken up selectively by the afflicted tissue.  
       [0294] The polypeptides of the invention are administered by any route that delivers an effective dosage to the desired site of action. The determination of a suitable route of administration and an effective dosage for a particular indication is within the level of skill in the art. Preferably for wound treatment, one administers the therapeutic compound directly to the site. Suitable dosage ranges for the polypeptides of the invention can be extrapolated from these dosages or from similar studies in appropriate animal models. Dosages can then be adjusted as necessary by the clinician to provide maximal therapeutic benefit.  
       [0295] 4.12.2 Compositions/Formulations  
       [0296] Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. These pharmaceutical compositions may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. When a therapeutically effective amount of protein or other active ingredient of the present invention is administered orally, protein or other active ingredient of the present invention will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95% protein or other active ingredient of the present invention, and preferably from about 25 to 90% protein or other active ingredient of the present invention. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90% by weight of protein or other active ingredient of the present invention, and preferably from about 1 to 50% protein or other active ingredient of the present invention.  
       [0297] When a therapeutically effective amount of protein or other active ingredient of the present invention is administered by intravenous, cutaneous or subcutaneous injection, protein or other active ingredient of the present invention will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. The preparation of such parenterally acceptable protein or other active ingredient solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to protein or other active ingredient of the present invention, an isotonic vehicle such as Sodium Chloride Injection, Ringer&#39;s Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection. Lactated Ringer&#39;s Injection, or other vehicle as known in the art. The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art. For injection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks&#39;s solution, Ringer&#39;s solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.  
       [0298] For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers ell known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained from a solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.  
       [0299] Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.  
       [0300] For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a real c to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.  
       [0301] Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.  
       [0302] The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.  
       [0303] A pharmaceutical carrier for the hydrophobic compounds of the invention is a co-solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent system. VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol. The VPD co-solvent system (VPD:5W) consists of VPD diluted 1:1 with a 5% dextrose in water solution. This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration. Naturally, the proportions of a co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics. Furthermore, the identity of the co-solvent components may be varied: for example, other low-toxicity nonpolar surfactants may be used instead of polysorbate 80: the fraction size of polyethylene glycol may be varied: other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are well known examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity. Additionally, the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent. Various types of sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein or other active ingredient stabilization may be employed.  
       [0304] The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols. Many of the active ingredients of the invention may be provided as salts with pharmaceutically compatible counter ions. Such pharmaceutically acceptable base addition salts are those salts which retain the biological effectiveness and properties of the free acids and which are obtained by reaction with inorganic or organic bases such as sodium hydroxide, magnesium hydroxide, ammonia, trialkylamine, dialkylamine, monoalkylamine, dibasic amino acids, sodium acetate, potassium benzoate, triethanol amine and the like.  
       [0305] The pharmaceutical composition of the invention may be in the form of a complex of the protein(s) or other active ingredient(s) of present invention along with protein or peptide antigens. The protein and/or peptide antigen will deliver a stimulatory signal to both B and T lymphocytes. B lymphocytes will respond to antigen through their surface immunoglobulin receptor. T lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigen(s) to T lymphocytes. The antigen components could also be supplied as purified MHC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells. Alternatively antibodies able to bind surface immunoglobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.  
       [0306] The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharmaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithins, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Pat. Nos. 4,235,871; 4,501,728; 4,837,028; and 4,737,323, all of which are incorporated herein by reference.  
       [0307] The amount of protein or other active ingredient of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone. Ultimately, the attending physician will decide the amount of protein or other active ingredient of the present invention with which to treat each individual patient. Initially, the attending physician will administer low doses of protein or other active ingredient of the present invention and observe the patient&#39;s response. Larger doses of protein or other active ingredient of the present invention may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should contain about 0.01 μg to about 100 mg (preferably about 0.1 μg to about 10 mg, more preferably about 0.1 μg to about 1 mg) of protein or other active ingredient of the present invention per kg body weight. For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition topically, systematically, or locally as an implant or device. When administered, the therapeutic composition for use in this invention is, of course, in a pyrogen-free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage or tissue damage. Topical administration may be suitable for wound healing and tissue repair. Therapeutically useful agents other than a protein or other active ingredient of the invention which may also optionally be included in the composition as described above, may alternatively or additionally, be administered simultaneously or sequentially with the composition in the methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing or other active ingredient-containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone and cartilage and optimally capable of being resorbed into the body. Such matrices may be formed of materials presently in use for other implanted medical applications.  
       [0308] The choice of matrix material is based on biocompatibility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the compositions will define the appropriate formulation. Potential matrices for the compositions may be biodegradable and chemically defined calcium sulfate, tricalcium phosphate, hydroxyapatite, polylactic acid, polyglycolic acid and polyanhydrides. Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability. Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns. In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.  
       [0309] A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, poly(ethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and poly(vinyl alcohol). The amount of sequestering agent useful herein is 0.5-20 wt %, preferably 1-10 wt % based on total formulation weight, which represents the amount necessary to prevent desorption of the protein from the polymer matrix and to provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells. In further compositions, proteins or other active ingredients of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-α and TGF-β), and insulin-like growth factor (IGF).  
       [0310] The therapeutic compositions are also presently valuable for veterinary applications. Particularly domestic animals and thoroughbred horses, in addition to humans, are desired patients for such treatment with proteins or other active ingredients of the present invention. The dosage regimen of a protein-containing, pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient&#39;s age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF 1 (insulin like growth factor 1), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.  
       [0311] Polynucleotides of the present invention can also be used for gene therapy. Such polynucleotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic purposes.  
       [0312] 4.12.3 Effective Dosage  
       [0313] Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. More specifically, a therapeutically effective amount means an amount effective to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from appropriate in vitro assays. For example, a dose can be formulated in animal models to achieve a circulating concentration range that can be used to more accurately determine useful doses in humans. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC 50  as determined in cell culture (i.e., the concentration of the test compound which achieves a half-maximal inhibition of the protein&#39;s biological activity). Such information can be used to more accurately determine useful doses in humans.  
       [0314] A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms or a prolongation of survival in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50  (the dose lethal to 50% of the population) and the ED 50  (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD 50  and ED 50 . Compounds which exhibit high therapeutic indices are preferred. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED 50  with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient&#39;s condition. See, e.g., Fingl et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p.1. Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the desired effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.  
       [0315] Dosage intervals can also be determined using MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.  
       [0316] An exemplary dosage regimen for polypeptides or other compositions of the invention will be in the range of about 0.01 μg/kg to 100 mg/kg of body weight daily, with the preferred dose being about 0.1 μg/kg to 25 mg/kg of patient body weight daily, varying in adults and children. Dosing may be once daily, or equivalent doses may be delivered at longer or shorter intervals.  
       [0317] The amount of composition administered will, of course, be dependent on the subject being treated, on the subject&#39;s age and weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.  
       [0318] 4.12.4 Packaging  
       [0319] The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.  
       [0320] 4.13 Antibodies  
       [0321] Also included in the invention are antibodies to proteins, or fragments of proteins of the invention. The term “antibody” as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, F ab , F ab  and F (ab′) 2 fragments, and an F ab  expression library. In general, an antibody molecule obtained from humans relates to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule. Certain classes have subclasses as well, such as IgG 1 , IgG 2 , and others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.  
       [0322] An isolated related protein of the invention may be intended to serve as an antigen, or a portion or fragment thereof, and additionally can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen for use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as the amino acid sequences shown in SEQ ID NO: 246-490, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope. Preferably, the antigenic peptide comprises at least 10 amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues. Preferred epitopes encompassed by the antigenic peptide are regions of the protein that are located on its surface; commonly these are hydrophilic regions.  
       [0323] In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a region of related protein that is located on the surface of the protein, e.g., a hydrophilic region. A hydrophobicity analysis of the human related protein sequence will indicate which regions of a related protein are particularly hydrophilic and, therefore, are likely to encode surface residues useful for targeting antibody production. As a means for targeting antibody production, hydropathy plots showing regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and Woods, 1981 . Proc. Nat. Acad Sci. USA  78: 3824-3828; Kyte and Doolittle 1982,  J. Mol. Biol.  157: 105-142, each of which is incorporated herein by reference in its entirety. Antibodies that are specific for one or more domains within an antigenic protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.  
       [0324] A protein of the invention, or a derivative, fragment, analog, homolog or ortholog thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifically bind these protein components.  
       [0325] Various procedures known within the art may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies: A Laboratory Manual, Harlow E. and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., incorporated herein by reference). Some of these antibodies are discussed below.  
       [0326] 4.13.1 Polyclonal Antibodies  
       [0327] For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing. An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the immunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but are not limited to, Freund&#39;s (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface active substances (e.g. lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory agents. Additional examples of adjuvants which can be employed include MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).  
       [0328] The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by immunoaffinity chromatography. Purification of immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia Pa., Vol. 14, No. 8 (Apr. 17, 2000), pp. 25-28).  
       [0329] 4.13.2 Monoclonal Antibodies  
       [0330] The term “monoclonal antibody” (MAb) or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody are identical in all the molecules of the population. MAbs thus contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.  
       [0331] Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein,  Nature,  256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes can be immunized in vitro. The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding,  Monoclonal Antibodies: Principles and Practice,  Academic Press, (1986) pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells can be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.  
       [0332] Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor,  J. Immunol.,  133:3001 (1984); Brodeur et al.,  Monoclonal Antibody Production Techniques and Applications,  Marcel Dekker, Inc., New York, (1987) pp. 51-63).  
       [0333] The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard,  Anal. Biochem.,  107:220 (1980). Preferably, antibodies having a high degree of specificity and a high binding affinity for the target antigen are isolated.  
       [0334] After the desired hybridoma cells are identified, the clones can be subcloned by limiting dilution procedures and grown by standard methods. Suitable culture media for this purpose include, for example. Dulbecco&#39;s Modified Eagle&#39;s Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.  
       [0335] The monoclonal antibodies secreted by the subclones can be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.  
       [0336] The monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567: Morrison,  Nature  368, 812-13 (1994)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.  
       [0337] 4.13.3 Humanized Antibodies  
       [0338] The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′) 2  or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. Humanization can be performed following the method of Winter and co-workers (Jones et al.,  Nature,  321:522-525 (1986); Riechmann et al.,  Nature,  332:323-327 (1988); Verhoeyen et al.,  Science,  239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. (See also U.S. Pat. No. 5,225,539.) In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies can also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986; Riechmann et al., 1988; and Presta.,  Curr. Op. Struct. Biol.,  2:593-596 (1992)).  
       [0339] 4.13.4 Human Antibodies  
       [0340] Fully human antibodies relate to antibody molecules in which essentially the entire sequences of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are termed “human antibodies”, or “fully human antibodies” herein. Human monoclonal antibodies can be prepared by the trioma technique: the human B-cell hybridoma technique (see Kozbor, et al. 1983 Immunol Today 4: 72) and the EBV hybridoma technique to produce human monoclonal antibodies (see Cole, et al. 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R. Liss, Inc. pp. 77-96). Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).  
       [0341] In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter,  J. Mol. Biol.,  227:381 (1991); Marks et al.,  J. Mol. Biol.,  222:581 (1991)). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks et al. ( Bio/Technology  10 779-783 (1992)); Lonberg et al. ( Nature  368 856-859 (1994)); Morrison ( Nature  368, 812-13 (1994)); Fishwild et al,( Nature Biotechnology  14, 845-51 (1996)); Neuberger ( Nature Biotechnology  14, 826 (1996)); and Lonberg and Huszar ( Intern. Rev. Immunol.  13 65-93 (1995)).  
       [0342] Human antibodies may additionally be produced using transgenic nonhuman animals which are modified so as to produce fully human antibodies rather than the animal&#39;s endogenous antibodies in response to challenge by an antigen. (See PCT publication WO94/02602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding human heavy and light chain immunoglobulins are inserted into the host&#39;s genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the Xenomouse™ as disclosed in PCT publications WO 96/33735 and WO 96/34096. This animal produces B cells which secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B cells derived from the animal, such as hybridomas producing monoclonal antibodies. Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules.  
       [0343] An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S. Pat. No. 5,939,598. It can be obtained by a method including deleting the J segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.  
       [0344] A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Pat. No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain.  
       [0345] In a further improvement on this procedure, a method for identifying a clinically relevant epitope on an immunogen, and a correlative method for selecting an antibody that binds immunospecifically to the relevant epitope with high affinity, are disclosed in PCT publication WO 99/53049.  
       [0346] 4.13.5 F ab  Fragments and Single Chain Antibodies  
       [0347] According to the invention, techniques can be adapted for the production of single-chain antibodies specific to an antigenic protein of the invention (see e.g., U.S. Pat. No. 4,946,778). In addition, methods can be adapted for the construction of Fab expression libraries (see e.g., Huse, et al., 1989 Science 246: 1275-1281) to allow rapid and effective identification of monoclonal F ab  fragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F (ab′)2  fragment produced by pepsin digestion of an antibody molecule; (ii) an F ab  fragment generated by reducing the disulfide bridges of an F (ab′)2  fragment; (iii) an F ab  fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F, fragments.  
       [0348] 4.13.6 Bispecific Antibodies  
       [0349] Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.  
       [0350] Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello,  Nature,  305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., 1991  EMBO J.,  10:3655-3659.  
       [0351] Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al.,  Methods in Enzymology,  121:210 (1986).  
       [0352] According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory “cavities” of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.  
       [0353] Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g. F(ab′) 2  bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al.  Science  229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab′) 2  fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab′ fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives is then reconverted to the Fab′-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab′-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.  
       [0354] Additionally, Fab′ fragments can be directly recovered from  E. coli  and chemically coupled to form bispecific antibodies. Shalaby et al.,  J. Exp. Med.  175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab′) 2  molecule. Each Fab′ fragment was separately secreted from  E. coli  and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.  
       [0355] Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al.,  J. Immunol.  148(5):1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab′ portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The “diabody” technology described by Hollinger et al.,  Proc. Natl. Acad. Sci. USA  90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (V H ) connected to a light-chain variable domain (V L ) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the V H  and V L  domains of one fragment are forced to pair with the complementary V L  and V H  domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al.,  J. Immunol.  152:5368 (1994).  
       [0356] Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al.,  J. Immunol.  147:60 (1991).  
       [0357] Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcγR), such as FcγRI (CD64), FcγRII (CD)32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen. Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).  
       [0358] 4.13.7 Heteroconjugate Antibodies  
       [0359] Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360; WO 92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.  
       [0360] 4.13.8 Effector Function Engineering  
       [0361] It can be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).  
       [0362] 4.13.9 Immunoconjugates  
       [0363] The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).  
       [0364] Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from  Pseudomonas aeruginosa ), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin,  Aleurites fordii  proteins, dianthin proteins,  Phytolaca americana  proteins (PAPI, PAPII, and PAP-S),  momordica charantia  inhibitor, curcin, crotin,  sapaonaria officinalis  inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include  212 Bi,  131 I,  131 In,    90 Y, and  189 Re.  
       [0365] Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026.  
       [0366] In another embodiment, the antibody can be conjugated to a “receptor” (such as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) that is in turn conjugated to a cytotoxic agent.  
       [0367] 4.14 Computer Readable Sequences  
       [0368] In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. As used herein, “recorded” refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.  
       [0369] A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.  
       [0370] By providing any of the nucleotide sequences SEQ ID NO: 1-245 or a representative fragment thereof, or a nucleotide sequence at least 95% identical to any of the nucleotide sequences of SEQ ID NO: 1-245 in computer readable form, a skilled artisan can routinely access the sequence information for a variety of purposes. Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system is used to identify open reading frames (ORFs) within a nucleic acid sequence. Such ORFs may be protein encoding fragments and may be useful in producing commercially important proteins such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.  
       [0371] As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable for use in the present invention. As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means. As used herein, “data storage means” refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.  
       [0372] As used herein, “search means” refers to one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of a known sequence which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, Smith-Waterman, MacPattern (EMBL), BLASTN and BLASTA (NPOLYPEPTIDEIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems. As used herein, a “target sequence” can be any nucleic acid or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 300 amino acids, more preferably from about 30 to 100 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.  
       [0373] As used herein. “a target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).  
       [0374] 4.15 Triple Helix Formation  
       [0375] In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA. Polynucleotides suitable for use in these methods are preferably 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al. Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 15241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Olmno, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide.  
       [0376] 4.16 Diagnostic Assays and Kits  
       [0377] The present invention further provides methods to identify the presence or expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using a nucleic acid probe or antibodies of the present invention, optionally conjugated or otherwise associated with a suitable label.  
       [0378] In general, methods for detecting a polynucleotide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polynucleotide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polynucleotide of the invention is detected in the sample. Such methods can also comprise contacting a sample under stringent hybridization conditions with nucleic acid primers that anneal to a polynucleotide of the invention under such conditions, and amplifying annealed polynucleotides, so that if a polynucleotide is amplified, a polynucleotide of the invention is detected in the sample.  
       [0379] In general, methods for detecting a polypeptide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polypeptide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polypeptide of the invention is detected in the sample.  
       [0380] In detail, such methods comprise incubating a test sample with one or more of the antibodies or one or more of the nucleic acid probes of the present invention and assaying for binding of the nucleic acid probes or antibodies to components within the test sample.  
       [0381] Conditions for incubating a nucleic acid probe or antibody with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the nucleic acid probe or antibody used in the assay. One skilled in the art still recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the nucleic acid probes or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques. Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985). The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.  
       [0382] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention. Specifically, the invention provides a compartment kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the probes or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound probe or antibody.  
       [0383] In detail, a compartment kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody or probe. Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed probes and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.  
       [0384] 4.17 Medical Imaging  
       [0385] The novel polypeptides and binding partners of the invention are useful in medical imaging of sites expressing the molecules of the invention (e.g. where the polypeptide of the invention is involved in the immune response, for imaging sites of inflammation or infection). See, e.g., Kunkel et al., U.S. Pat. No. 5,413,778. Such methods involve chemical attachment of a labeling or imaging agent, administration of the labeled polypeptide to a subject in a pharmaceutically acceptable carrier, and imaging the labeled polypeptide in vivo at the target site.  
       [0386] 4.18 Screening Assays  
       [0387] Using the isolated proteins and polynucleotides of the invention, the present invention further provides methods of obtaining and identifying agents which bind to a polypeptide encoded by an ORF corresponding to any of the nucleotide sequences set forth in SEQ ID NO: 1-245, or bind to a specific domain of the polypeptide encoded by the nucleic acid. In detail, said method comprises the steps of:  
       [0388] (a) contacting an agent with an isolated protein encoded by an ORF of the present invention, or nucleic acid of the invention; and  
       [0389] (b) determining whether the agent binds to said protein or said nucleic acid.  
       [0390] In general, therefore, such methods for identifying compounds that bind to a polynucleotide of the invention can comprise contacting a compound with a polynucleotide of the invention for a time sufficient to form a polynucleotide/compound complex, and detecting the complex, so that if a polynucleotide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.  
       [0391] Likewise, in general, therefore, such methods for identifying compounds that bind to a polypeptide of the invention can comprise contacting a compound with a polypeptide of the invention for a time sufficient to form a polypeptide/compound complex, and detecting the complex, so that if a polypeptide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.  
       [0392] Methods for identifying compounds that bind to a polypeptide of the invention can also comprise contacting a compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a receptor gene sequence in the cell, and detecting the complex by detecting reporter gene sequence expression, so that if a polypeptide/compound complex is detected, a compound that binds a polypeptide of the invention is identified.  
       [0393] Compounds identified via such methods can include compounds which modulate the activity of a polypeptide of the invention (that is, increase or decrease its activity, relative to activity observed in the absence of the compound). Alternatively, compounds identified via such methods can include compounds which modulate the expression of a polynucleotide of the invention (that is, increase or decrease expression relative to expression levels observed in the absence of the compound). Compounds, such as compounds identified via the methods of the invention, can be tested using standard assays well known to those of skill in the art for their ability to modulate activity/expression.  
       [0394] The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.  
       [0395] For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention. Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like, capable of binding to a specific peptide sequence, in order to generate rationally designed antipeptide peptides, for example see Hurby et al., Application of Synthetic Peptides: Antisense Peptides,” In Synthetic Peptides, A User&#39;s Guide, W. H. Freeman, N.Y. (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.  
       [0396] In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control. One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix formation by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.  
       [0397] Agents suitable for use in these methods preferably contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al. Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems.  
       [0398] Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide and other DNA binding agents.  
       [0399] Agents which bind to a protein encoded by one of the ORFs of the present invention can be used as a diagnostic agent. Agents which bind to a protein encoded by one of the ORFs of the present invention can be formulated using known techniques to generate a pharmaceutical composition.  
       [0400] 4.19 Use of Nucleic Acids as Probes  
       [0401] Another aspect of the subject invention is to provide for polypeptide-specific nucleic acid hybridization probes capable of hybridizing with naturally occurring nucleotide sequences. The hybridization probes of the subject invention may be derived from any of the nucleotide sequences SEQ ID NO: 1-245. Because the corresponding gene is only expressed in a limited number of tissues, a hybridization probe derived from any of the nucleotide sequences SEQ ID NO: 1-245 can be used as an indicator of the presence of RNA of cell type of such a tissue in a sample.  
       [0402] Any suitable hybridization technique can be employed, such as, for example, in situ hybridization. PCR as described in U.S. Pat. Nos. 4,683,195 and 4,965,188 provides additional uses for oligonucleotides based upon the nucleotide sequences. Such probes used in PCR may be of recombinant origin, may be chemically synthesized, or a mixture of both. The probe will comprise a discrete nucleotide sequence for the detection of identical sequences or a degenerate pool of possible sequences for identification of closely related genomic sequences.  
       [0403] Other means for producing specific hybridization probes for nucleic acids include the cloning of nucleic acid sequences into vectors for the production of MRNA probes. Such vectors are known in the art and are commercially available and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerase as T7 or SP6 RNA polymerase and the appropriate radioactively labeled nucleotides. The nucleotide sequences may be used to construct hybridization probes for mapping their respective genomic sequences. The nucleotide sequence provided herein may be mapped to a chromosome or specific regions of a chromosome using well known genetic and/or chromosomal mapping techniques. These techniques include in situ hybridization, linkage analysis against known chromosomal markers, hybridization screening with libraries or flow-sorted chromosomal preparations specific to known chromosomes, and the like. The technique of fluorescent in situ hybridization of chromosome spreads has been described, among other places, in Verma et al (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York N.Y.  
       [0404] Fluorescent in situ hybridization of chromosomal preparations and other physical chromosome mapping techniques may be correlated with additional genetic map data. Examples of genetic map data can be found in the 1994 Genome Issue of Science (265:1981 f). Correlation between the location of a nucleic acid on a physical chromosomal map and a specific disease (or predisposition to a specific disease) may help delimit the region of DNA associated with that genetic disease. The nucleotide sequences of the subject invention may be used to detect differences in gene sequences between normal, carrier or affected individuals.  
       [0405] 4.20 Preparation of Support Bound Oligonucleotides  
       [0406] Oligonucleotides, i.e. small nucleic acid segments, may be readily prepared by, for example, directly synthesizing the oligonucleotide by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer.  
       [0407] Support bound oligonucleotides may be prepared by any of the methods known to those of skill in the art using any suitable support such as glass, polystyrene or Teflon. One strategy is to precisely spot oligonucleotides synthesized by standard synthesizers. Immobilization can be achieved using passive adsorption (Inouye &amp; Hondo, (1990) J. Clin. Microbiol. 28(6) 1469-72); using UV light (Nagata et al., 1985; Dahlen et al., 1987; Morrissey &amp; Collins, (1989) Mol. Cell Probes 3(2) 189-207) or by covalent binding of base modified DNA (Keller et al, 1988; 1989); all references being specifically incorporated herein.  
       [0408] Another strategy that may be employed is the use of the strong biotin-streptavidin interaction as a linker. For example, Broude et al. (1994) Proc. Natl. Acad. Sci. USA 91(8) 3072-6, describe the use of biotinylated probes, although these are duplex probes, that are immobilized on streptavidin-coated magnetic beads. Streptavidin-coated beads may be purchased from Dynal. Oslo. Of course, this same linking chemistry is applicable to coating any surface with streptavidin. Biotinylated probes may be purchased from various sources, such as, e.g., Operon Technologies (Alameda, Calif.).  
       [0409] Nunc Laboratories (Naperville, Ill.) is also selling suitable material that could be used. Nunc Laboratories have developed a method by which DNA can be covalently bound to the microwell surface termed Covalink NH. CovaLink NH is a polystyrene surface grafted with secondary amino groups (&gt;NH) that serve as bridge-heads for further covalent coupling. CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be bound to CovaLink exclusively at the 5′-end by a phosphoramidate bond, allowing immobilization of more than 1 μmol of DNA (Rasmussen et al., (1991) Anal. Biochem. 198(1) 138-42).  
       [0410] The use of CovaLink NH strips for covalent binding of DNA molecules at the 5′-end has been described (Rasmussen et al. (1991). In this technology, a phosphoramidate bond is employed (Chu et al. (1983) Nucleic Acids Res. 11 (8) 6513-29). This is beneficial as immobilization using only a single covalent bond is preferred. The phosphoramidate bond joins the DNA to the CovaLink NH secondary amino groups that are positioned at the end of spacer arms covalently grafted onto the polystyrene surface through a 2 nm long spacer arm. To link an oligonucleotide to CovaLink NH via an phosphoramidate bond, the oligonucleotide terminus must have a 5′-end phosphate group. It is, perhaps, even possible for biotin to be covalently bound to CovaLink and then streptavidin used to bind the probes.  
       [0411] More specifically, the linkage method includes dissolving DNA in water (7.5 ng/μl) and denaturing for 10 min. at 95° C. and cooling on ice for 10 min. Ice-cold 0.1 M 1-methylimidazole pH 7.0 (1-MeIm 7 ), is then added to a final concentration of 10 mM I-MeIm 7 . The single-stranded DNA solution is then dispensed into CovaLink NH strips (75 μl/well) standing on ice.  
       [0412] Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), dissolved in 10 mM 1-MeIm 7 , is made fresh and 25 μl added per well. The strips are incubated for 5 hours at 50° C. After incubation the strips are washed using, e.g., Nunc-Immuno Wash; first the wells are washed 3 times, then they are soaked with washing solution for 5 min., and finally they are washed 3 times (where in the washing solution is 0.4 N NaOH, 0.25% SDS heated to 50° C.).  
       [0413] It is contemplated that a further suitable method for use with the present invention is that described in PCT Patent Application WO 90/03382 (Southern &amp; Maskos), incorporated herein by reference. This method of preparing an oligonucleotide bound to a support involves attaching a nucleoside 3′-reagent through the phosphate group by a covalent phosphodiester link to aliphatic hydroxyl groups carried by the support. The oligonucleotide is then synthesized on the supported nucleoside and protecting groups removed from the synthetic oligonucleotide chain under standard conditions that do not cleave the oligonucleotide from the support. Suitable reagents include nucleoside phosphoramidite and nucleoside hydrogen phosphorate.  
       [0414] An on-chip strategy for the preparation of DNA probe for the preparation of DNA probe arrays may be employed. For example, addressable laser-activated photodeprotection may be employed in the chemical synthesis of oligonucleotides directly on a glass surface, as described by Fodor et al. (1991) Science 251(4995) 767-73, incorporated herein by reference. Probes may also be immobilized on nylon supports as described by Van Ness et al (1991) Nucleic Acids Res. 19(12) 3345-50; or linked to Teflon using the method of Duncan &amp; Cavalier (1988) Anal. Biochem. 169(1) 104-8; all references being specifically incorporated herein.  
       [0415] To link an oligonucleotide to a nylon support, as described by Van Ness et al. (1991), requires activation of the nylon surface via alkylation and selective activation of the 5′-amine of oligonucleotides with cyanuric chloride.  
       [0416] One particular way to prepare support bound oligonucleotides is to utilize the light-generated synthesis described by Pease et al., (1994) PNAS USA 91(11) 5022-6, incorporated herein by reference). These authors used current photolithographic techniques to generate arrays of immobilized oligonucleotide probes (DNA chips). These methods, in which light is used to direct the synthesis of oligonucleotide probes in high-density, miniaturized arrays, utilize photolabile 5′-protected N-acyl-deoxynucleoside phosphoramidites, surface linker chemistry and versatile combinatorial synthesis strategies. A matrix of 256 spatially defined oligonucleotide probes may be generated in this manner.  
       [0417] 4.21 Preparation of Nucleic Acid Fragments  
       [0418] The nucleic acids may be obtained from any appropriate source, such as cDNAs, genomic DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC inserts, and RNA, including mRNA without any amplification steps. For example, Sambrook et al. (1989) describes three protocols for the isolation of high molecular weight DNA from mammalian cells (p. 9.14-9.23).  
       [0419] DNA fragments may be prepared as clones in M13, plasmid or lambda vectors and/or prepared directly from genomic DNA or cDNA by PCR or other amplification methods. Samples may be prepared or dispensed in multiwell plates. About 100-1000 ng of DNA samples may be prepared in 2-500 ml of final volume.  
       [0420] The nucleic acids would then be fragmented by any of the methods known to those of skill in the art including, for example, using restriction enzymes as described at 9.24-9.28 of Sambrook et al. (1989), shearing by ultrasound and NaOH treatment.  
       [0421] Low pressure shearing is also appropriate, as described by Schriefer et al. (1990) Nucleic Acids Res. 18(24) 7455-6, incorporated herein by reference). In this method, DNA samples are passed through a small French pressure cell at a variety of low to intermediate pressures. A lever device allows controlled application of low to intermediate pressures to the cell. The results of these studies indicate that low-pressure shearing is a useful alternative to sonic and enzymatic DNA fragmentation methods.  
       [0422] One particularly suitable way for fragmenting DNA is contemplated to be that using the two base recognition endonuclease. CviJI, described by Fitzgerald et al. (1992) Nucleic Acids Res. 20(14) 3753-62. These authors described an approach for the rapid fragmentation and fractionation of DNA into particular sizes that they contemplated to be suitable for shotgun cloning and sequencing.  
       [0423] The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions, which alter the specificity of this enzyme (CviJI**), yield a quasi-random distribution of DNA fragments form the small molecule pUC19 (2688 base pairs). Fitzgerald et al. (1992) quantitatively evaluated the randomness of this fragmentation strategy, using a CviJI** digest of pUC19 that was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lac Z minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI** restricts pyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation.  
       [0424] As reported in the literature, advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 μg instead of 2-5 μg); and fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed.  
       [0425] Irrespective of the manner in which the nucleic acid fragments are obtained or prepared, it is important to denature the DNA to give single stranded pieces available for hybridization. This is achieved by incubating the DNA solution for 2-5 minutes at 80-90° C. The solution is then cooled quickly to 2° C. to prevent renaturation of the DNA fragments before they are contacted with the chip. Phosphate groups must also be removed from genomic DNA by methods known in the art.  
       [0426] 4.22 Preparation of DNA Arrays  
       [0427] Arrays may be prepared by spotting DNA samples on a support such as a nylon membrane. Spotting may be performed by using arrays of metal pins (the positions of which correspond to an array of wells in a microtiter plate) to repeated by transfer of about 20 nl of a DNA solution to a nylon membrane. By offset printing, a density of dots higher than the density of the wells is achieved. One to 25 dots may be accommodated in 1 mm 2 , depending on the type of label used. By avoiding spotting in some preselected number of rows and columns, separate subsets (subarrays) may be formed. Samples in one subarray may be the same genomic segment of DNA (or the same gene) from different individuals, or may be different, overlapped genomic clones. Each of the subarrays may represent replica spotting of the same samples. In one example, a selected gene segment may be amplified from 64 patients. For each patient, the amplified gene segment may be in one 96-well plate (all 96 wells containing the same sample). A plate for each of the 64 patients is prepared. By using a 96-pin device, all samples may be spotted on one 8×12 cm membrane. Subarrays may contain 64 samples, one from each patient. Where the 96 subarrays are identical, the dot span may be 1 mm 2  and there may be a 1 mm space between subarrays.  
       [0428] Another approach is to use membranes or plates (available from NUNC, Naperville. Ill.) which may be partitioned by physical spacers e.g. a plastic grid molded over the membrane, the grid being similar to the sort of membrane applied to the bottom of multiwell plates, or hydrophobic strips. A fixed physical spacer is not preferred for imaging by exposure to flat phosphor-storage screens or x-ray films.  
       [0429] The present invention is illustrated in the following examples. Upon consideration of the present disclosure, one of skill in the art will appreciate that many other embodiments and variations may be made in the scope of the present invention. Accordingly, it is intended that the broader aspects of the present invention not be limited to the disclosure of the following examples. The present invention is not to be limited in scope by the exemplified embodiments which are intended as illustrations of single aspects of the invention, and compositions and methods which are functionally equivalent are within the scope of the invention. Indeed, numerous modifications and variations in the practice of the invention are expected to occur to those skilled in the art upon consideration of the present preferred embodiments. Consequently, the only limitations which should be placed upon the scope of the invention are those which appear in the appended claims.  
       [0430] All references cited within the body of the instant specification are hereby incorporated by reference in their entirety. 
     
    
    
     5. EXAMPLES  
     5.1 Example 1  
     [0431] Novel Nucleic Acid Sequences Obtained from Various Libraries  
     [0432] A plurality of novel nucleic acids were obtained from cDNA libraries prepared from various human tissues and in some cases isolated from a genomic library derived from human chromosome using standard PCR, SBH sequence signature analysis and Sanger sequencing techniques. The inserts of the library were amplified with PCR using primers specific for the vector sequences which flank the inserts. Clones from cDNA libraries were spotted on nylon membrane filters and screened with oligonucleotide probes (e.g., 7-mers) to obtain signature sequences. The clones were clustered into groups of similar or identical sequences. Representative clones were selected for sequencing.  
     [0433] In some cases, the 5′ sequence of the amplified inserts was then deduced using a typical Sanger sequencing protocol. PCR products were purified and subjected to fluorescent dye terminator cycle sequencing. Single pass gel sequencing was done using a 377 Applied Biosystems (ABI) sequencer to obtain the novel nucleic acid sequences.  
     5.2 Example 2  
     [0434] Assemblage of Novel Nucleic Acids  
     [0435] The nucleic acids of the present invention, were assembled using an EST sequence as a seed. Then a recursive algorithm was used to extend the seed EST into an extended assemblage, by pulling additional sequences from different databases (i.e., Hyseq&#39;s database containing EST sequences, dbEST, gb pri, UniGene, and exons from public domain genomic sequences predicated by GenScan) that belong to this assemblage. The algorithm terminated when there was no additional sequences from the above databases that would extend the assemblage. Further, inclusion of component sequences into the assemblage was based on a BLASTN hit to the extending assemblage with BLAST score greater than 300 and percent identity greater than 95%.  
     [0436] Using PHRAP (Univ. of Washington) or CAP4 (Paracel), full-length gene sequences and their corresponding protein sequences were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTXY algorithm against Genbank (i.e., dbEST, gb pri, UniGene, and Genpept). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). In some cases RACE (Rapid Amplification of cDNA Ends) was performed to further extend the sequence in the 5′ direction. The full-length nucleotide sequences are shown in the Sequence Listing as SEQ ID NO: 1-245. The corresponding polypeptide sequences are SEQ ID NO: 246-490.  
     [0437] Table 1 shows the various tissue sources of SEQ ID NO: 1-245.  
     [0438] The nearest neighbor results for polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were obtained by a BLASTP (version 2.0al 19MP-WashU) search against Genpept release 124 using BLAST algorithm. The nearest neighbor result showed the closest homologue with functional annotation for SEQ ID NO: 1-245 from Genpept. The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 1-245 are shown in Table 2 below.  
     [0439] Using eMatrix software package (Stanford University, Stanford, Calif.) (Wu et al., J. Comp. Biol., Vol. 6 pp. 219-235 (1999) herein incorporated by reference), polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were examined to determine whether they had identifiable signature regions. Table 3 shows the signature region found in the indicated polypeptide sequences, the description of the signature, the eMatrix p-value(s) and the position(s) of the signature within the polypeptide sequence.  
     [0440] Using the pFam software program (Sonnhammer et al., Nucleic Acids Res., Vol. 26(1) pp. 320-322 (1998) herein incorporated by reference) polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were examined for domains with homology to certain peptide domains. Table 4 shows the name of the domain found, the description, the p-value and the pFam score for the identified domain within the sequence.  
     [0441] The GeneAtlasr™ software package (Molecular Simulations Inc. (MSI). San Diego, Calif.) was used to predict the three-dimensional structure models for the polypeptides encoded by SEQ ID NO 1-216 (i.e. SEQ ID NO: 246-490). Models were generated by (I) PSI-BLAST which is a multiple alignment sequence profile-based searching developed by Altschul et al, (Nucl. Acids. Res. 25, 3389-3408 (1997)), (2) High Throughput Modeling (HTM) (Molecular Simulations Inc. (MSI) San Diego, Calif.,) which is an automated sequence and structure searching procedure (http://www.msi.coni/), and (3) SeqFold™ which is a fold recognition method described by Fischer and Eisenberg (J. Mol. Biol. 209, 779-791 (1998)). This analysis was carried out, in part, by comparing the polypeptides of the invention with the known NMR (nuclear magnetic resonance) and x-ray crystal three-dimensional structures as templates. Table 5 shows, “PDB ID”, the Protein DataBase (PDB) identifier given to template structure; “Chain ID”, identifier of the subcomponent of the PDB template structure; “Compound Information”, information of the PDB template structure and/or its subcomponents; “PDB Function Annotation” gives function of the PDB template as annotated by the PDB files (http:/www.rcsb.org/PDB/); start and end amino acid position of the protein sequence aligned; PSI-BLAST score, the verify score, the SeqFold score, and the Potential(s) of Mean Force (PMF). The verify score is produced by GeneAtlas™ software (MSI), is based on Dr. Eisenberg&#39;s Profile-3D threading program developed in Dr. David Eisenberg&#39;s laboratory (U.S. Pat. No. 5,436,850 and Luthy, Bowie, and Eisenberg, Nature, 356:83-85 (1992)) and a publication by R. Sanchez and A. Sali, Proc. Natl. Acad. Sci. USA, 95:13597-12502. The verify score produced by GeneAtlas normalizes the verify score for proteins with different lengths so that a unified cutoff can be used to select good models as follows:  
     Verify score (normalized)=(raw score−1/2 high score)/(1/2 high score)  
     [0442] The PFM score, produced by GeneAtlas™ software (MSI), is a composite scoring function that depends in part on the compactness of the model, sequence identity in the alignment used to build the model, pairwise and surface mean force potentials (MFP). As given in Table 5, a verify score between 0 to 1.0, with 1 being the best, represents a good model. Similarly, a PMF score between 0 to 1.0, with 1 being the best, represents a good model. A SeqFold™ score of more than 50 is considered significant. A good model may also be determined by one of skill in the art based all the information in Table 5 taken in totality.  
     [0443] The nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determined from using Neural Network SignalP V1.1 program (from Center for Biological Sequence Analysis. The Technical University of Denmark). The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson. Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication “Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites” Protein Engineering, Vol. 10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et al, as reference, were obtained for the polypeptide sequences. Table 6 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.  
     [0444] Table 7 correlates each of SEQ ID NO: 1-245 to a specific chromosomal location.  
     [0445] Table 8 is a correlation table of the novel polynucleotide sequences SEQ ID NO: 1-245, and their corresponding priority full length nucleotide sequences in the priority application U.S. Ser. No. 09/654,935, the contents of which is incorporated herein by reference in its entirety.  
                           TABLE 1                           Tissue/RNA   Library           Tissue Origin   Source   Name   SEQ ID NO:                  adult brain   GIBCO   AB3001   8 24 38 42 56 63-64 93-94 113 130 183 195-196 206 210                   227 233 236 240       adult brain   GIBCO   ABD003   2-4 15 19-21 29 31-32 34-39 41-43 45 54 56 67 80 82 84 88                   94 103-104 107 113 117 130-131 154 159 178 195 199 206                   210 220-221 223       adult brain   Clontech   ABR001   2-3 17 33 35 43 56 62 67 84 113 191 220       adult brain   Clontech   ABR006   2-4 34 82 89 101-102 113 127 146 152 158 162 181 191                   197-198 200-201 214 221-223 234 241       adult brain   Clontech   ABR008   2-4 9-12 15 17 19 21 24 29 36-41 54 64 70 74-75 77 79-80                   82 84 93-94 97-98 101-102 104 107 109 117 121-124 127                   131 140 143-144 146 148-149 151-152 155 158 162 164                   167 169 178 193 196 200-202 204 206 221 223-225 227                   229 233       adult brain   BioChain   ABR012   2-3 54       adult brain   BioChain   ABR013   17 43 209 240       adult brain   Invitrogen   ABR014   23 43 227 232       adult brain   Invitrogen   ABR015   43 54 65 67 89 142 159 232       adult brain   Invitrogen   ABR016   2-3 28 54 56 64 104 159 229       adult brain   Invitrogen   ABT004   2-3 23 30 33 36-38 40 100 145 152 154 177 191 206 220                   242       cultured   Stratagene   ADP001   2-3 15 29 36 38 40 43 56 100 104-105 130 142-144 158-159       preadipocytes           177 182 206 236 240       adrenal gland   Clontech   ADR002   11-12 19-20 28 37-38 42 50 56 70 76 82 84 102 104-105                   127 130 145 148-150 181 183 189 191 209-210 224-225       adult heart   GIBCO   AHR001   2-5 8-9 11-12 19-22 24 29 36 38 40 43 45 47 54 56 62-63                   70 72 74 76 79 82 84 86 92 94 101-104 107 113 127 130-131                   137-138 140 143-144 148-149 159 166 169 177-178                   183 196 206-207 210 214 229-233 236-237       adult kidney   GIBCO   AKD001   2-3 7-9 11-12 15 18 20-21 24 26-27 29 31-33 36-43 52 54                   56 61-62 64 80 82 91 95 98 101-104 107 113 117 130-131                   143-144 146 154 159 169 178 181 183 191 195-199 204                   206 210 214 220 223-225 227 229 233 240 244       adult kidney   Invitrogen   AKT002   6 8-9 11-12 18 33 36-37 40 43 46 56 64 82 84 86-87 91 107                   113 130 142 144 148-149 152 159 167 169 183 191 193                   206 223 226 228 232 240-241 244       adult lung   GIBCO   ALG001   5 15 20 29 43 47 54 56 88 103 130 173 177 183 191 214                   232 240 244       lymph node   Clontech   ALN001   8 29 36 46 104 130 159 183 206 214 240       young liver   GIBCO   ALV001   2-3 11-12 15 19 37-38 40 43 47 56 62 70 94 103 107 112                   143-144 162 181 183 191 195 206 214 220 224-225 236-237                   243       adult liver   Invitrogen   ALV002   2-3 10-12 15 20 22 26-27 37 50 89 143 148-149 173 181                   183 191 193 206 217 220 240 244       adult liver   Clontech   ALV003   21 181 232       adult ovary   Invitrogen   AOV001   2-3 8 10-12 14-15 19-23 26-29 31-32 34 36-43 47 50 56 62-64                   67 70 75 78 82 84 86 89 94 101-102 104 107 109 113                   118 125 130-131 140 142 144 146 148-150 152 155 158-159                   162 166-167 169 173 177-178 182-183 189 193 195                   204 206 210 214 223-225 227 232 240-244       adult placenta   Clontech   APL001   43 159 169 206 240       placenta   Invitrogen   APL002   20 26-27 36 38 64 71 100 178 196 220 228 233       adult spleen   GIBCO   ASP001   2-3 8 26-27 29 35 37 42-43 46-47 54 56 62 64 87 94 104                   130 143-144 152 159 183 199 206 214 220 227 232 236                   244       adult testis   GIBCO   ATS001   5 8 11-12 20 23-24 29 31-32 37-38 41 43 54 56 62 64 86 89                   104 107 130-131 137-138 159 178 183 195 210 229 232                   236-237       adult bladder   Invitrogen   BLD001   8 54 159 195 206       bone marrow   Clontech   BMD001   2-5 8-12 19 22 26-27 29 31-32 34 36-38 42-43 46-47 56 63-64                   70 80 86-87 89 91 93-94 98 103-104 107 109 113 118                   130-131 144 146 152 159 162 167 178 182 193 199 206-207                   210 214 220 223 228 232 240 244       bone marrow   Clontech   BMD002   2-3 5 8 11-12 15 21 26-27 29 36 40 42 45-46 50 54 56 91                   94 97-98 104-105 107 109 120 124 137-138 140 142 144                   159 165 167 169 173 183 189 191 193 196 204-206 226                   232-234 236-237 244       bone marrow   Clontech   BMD004   232       bone marrow   Clonetech   BMD007   43 232       adult colon   Invitrogen   CLN001   38 43 45-46 50 84 87 143 193 195 222 244       mixture of   various   CTL016   20       16 tissues-   vendors       mRNAs*       mixture of   various   CTL021   46 54 159 232       16 tissues-   vendors       mRNAs*       mixture of   various   CTL028   159 237       16 tissues-   vendors       mRNAs*       adult cervix   BioChain   CVX001   2-3 8 11-12 15 21 24 31-32 35-36 39-43 46 56 62-65 70 82                   87 89 93-94 98 105 107 120 125-126 131 144 148-150 152                   159 165 178 182-183 189 191 193 195 223 236 240       endothelial   Strategene   EDT001   2-4 8 10-12 15 21-24 28-30 33-34 36-37 40 42-43 45 47 50       cells           56 62 64 67 70 72 80 82 86 94 103-104 107 109 126 130-131                   142-144 146 148-149 152 154 158-159 162 169 177-178                   182-183 191 193 195-199 206 210 214 223-226 229                   233 236 240-242       fetal brain   Clontech   FBR001   43 130 199       fetal brain   Clontech   FBR004   31-32       fetal brain   Clontech   FBR006   2-4 8 10 29 39 41 43 49 70 77 80 82 84 89 94 104-105 118                   121-123 142 150-152 154-155 165 178 186 200-201 204                   206-207 210       fetal brain   Invitrogen   FBT002   2-3 8 11-12 29 37 43 67 82 89 134 142-143 152 159 177                   189 191 193 199 206 210 220 227       fetal heart   Invitrogen   FHR001   41       fetal kidney   Clontech   FKD001   2-3 10-12 17 29 38 40 43 54 69 75 80 127 159 229 231 236                   240       fetal kidney   Clontech   FKD002   56       fetal kidney   Invitrogen   FKD007   19 36 43 56 159       fetal lung   Clontech   FLG001   2-3 54 69 109 113       fetal lung   Invitrogen   FLG003   10 21 35 43 50 54 69 80 92 125-126 143 148-149 158-159                   199 221 231-232       fetal liver-   Columbia   FLS001   1-5 7-12 14-15 18-24 26-28 30 36-38 40-43 50 54 56 62 64       spleen   University       70 72 75 82 84 86 89 91 94-95 98 100 102-105 107 109                   112-113 121 130-131 137-138 140 142-144 146 151-152                   158-159 162 165-166 169 177-178 181 183 189 191 193                   195-198 204-206 210 214 216 220 223-228 230-233 236-237                   240-241 244       fetal liver-   Columbia   FLS002   1-4 6 10-12 14-15 17-18 20-22 29-30 33 36 38-40 42 45 56       spleen   University       62-64 70 75 80 82 91-92 94-95 98 103-105 109 112-113                   121 126 131 142 144 146 148-149 152 162 165-167 169                   181 183 186 189 191 193 195-199 205-207 214 223 227-228                   233       fetal liver-   Columbia   FLS003   94 112 167 181 183 185 223 232       spleen   University       fetal liver   Invitrogen   FLV001   1-3 6-8 15 18 23 36-39 43 62 80 82 143 145 152 177 181                   191 195 206 232       fetal liver   Clontech   FLV004   2-3 22 24 36 82 109 122-123 152 162 181 232       fetal muscle   Invitrogen   FMS001   5 28 43 47 56 72 78-79 100 137-138 144 152 154 159 169                   193 207 210 237 241       fetal muscle   Invitrogen   FMS002   5 137-138 241       fetal skin   Invitrogen   FSK001   2-3 8 10 21 35-36 40 43 54 56 62-63 65 69 71 80 84 91                   104-105 124 130 132 137-138 142-143 148-151 158-159                   166 177-178 182 185 197-198 200-201 206 210 217 230                   232 241       fetal skin   Invitrogen   FSK002   2-3 8 11-12 21 24 26-27 29 40 43 50 62 82 88 94 98 104                   107 142 148-149 169 185 193 195 216 237       fetal spleen   BioChain   FSP001   183       umbilical cord   BioChain   FUC001   2-3 5 7-8 15 20 26-27 31-32 34 36 38-40 43 45 50 54 56 62                   76 82 84 94 103-105 107 121-123 130 143-144 146 148-149                   152 154 158-159 178 193 197-198 210 227 232 237                   240       fetal brain   GIBCO   HFB001   2-3 8 10-12 15 20-22 24 28-29 31-33 36-38 41 43 54 62 64                   67 70 82 88-89 93 98 101-104 107 109 113 117 130-131                   140 142 144-145 162 167 178 182-183 189 193 195 197-199                   207 210 223 227 229 232       macrophage   Invitrogen   HMP001   8 169       infant brain   Columbia   IB2002   2-3 9-12 15 20-21 23-24 33-34 38 41-43 49 56 63-64 84 89           University       100 104-105 107 113 118 146 148-150 152 154-155 158                   162 165-166 173 177-178 182 191 193 195 197-201 206                   223 227 230-231 237 241       infant brain   Columbia   IB2003   2-3 11-12 17 100 113 150 158 166 178 191 220-221 223           University       227       infant brain   Columbia   IBM002   43 117 173           University       infant brain   Columbia   IBS001   23 29 54 94 109 166 220           University       fibroblast   Strategene   LFB001   2-3 8 11-12 19 29 36-37 43 45 54 56 104-105 113 130 148-149                   154 159 169 178 182-183 214 236 240       lung tumor   Invitrogen   LGT002   2-3 5-6 8 11-12 20-22 24 38 40-41 43 46 52 54 56 62 64-65                   70 72 80 82 87 89 93 100 104 107 130-131 140 142-145                   152 154 159 162 167 177 182-183 195 197-199 206 210                   214 223 236 244       lymphocytes   ATCC   LPC001   2-3 11-12 20 22 38 42 50 54 73 80 86 89 94 97 105 127                   145 159 162 177 206 213-214 232 234       leukocyte   GIBCO   LUC001   2-4 8 10-12 15 17 19-22 24 26-27 29 35-38 40-43 47 54 56                   62 64 70 72 80 82 84 86 89 91 93-94 101-102 104-105 107                   109 130-131 143-144 146 154 158-159 162 165 167 169                   177-178 182-183 189 191 193 195 200-202 204 206 210                   214 217 223 228-229 231-232 236 240-242       leukocyte   Clontech   LUC003   20 42 80 94 105 140 165 191 205 207 214 231       melanoma   Clontech   MEL004   42-43 56 64 82 103 107 130 202 206 214 224-225 229 240       from cell line       ATCC #CRL       1424       mammary   Invitrogen   MMG001   2-4 8-9 11-12 15 17 21 26-27 35-36 38-40 43 46 56 61 64-65       gland           71 80 84 87 89 92 94-95 100-102 107 125 131-132 137-138                   140 143 145 150 152 154 159 162 166 169 173 177                   182-183 191 193 195 197-199 206 210 224-225 227 237                   243-244       induced   Strategene   NTD001   2-3 29 34 43 45 54 70 89 159 224-225       neuron cells       retinoic acid-   Strategene   NTR001   20 124 130 150 152 178 202 217       induced       neuronal cells       neuronal cells   Strategene   NTU001   40 43 47 72 131 217 237       pituitary gland   Clontech   PIT004   15 37-38 43 56 130-131 240       placenta   Clontech   PLA003   2-3       prostate   Clontech   PRT001   5 11-12 43 62 65 83 103 134 152 232 237       rectum   Invitrogen   REC001   2-3 15 18 26-27 43 54 56 73 80 130 145 152 183 199 244       salivary gland   Clontech   SAL001   14 17 29 43 47 70 98 104 132 159 178 196 204 232-233                   236-237       salivary gland   Clontech   SALs03   37 137-138 244       skin fibroblast   ATCC   SFB001   43 47       skin fibroblast   ATCC   SFB002   54       skin fibroblast   ATCC   SFB003   100       small intestine   Clontech   SIN001   21 34 46 73-74 86 103 107 130 137-138 144 169 183 193                   227-228 237 242-244       skeletal   Clontech   SKM001   5 20 45 79 86 137-138 152 206       muscle       skeletal   Clontech   SKM002   137-138       muscle       skeletal   Clonetech   SKMS03   137-138       muscle       skeletal   NULL   SKMS04   137-138       muscle       spinal cord   Clontech   SPC001   29 40 43 54 69 75 88-89 91 152 159 162 178 191 195 206                   210 223 229 232       adult spleen   Clontech   SPLc01   6 46 50 70 130 140 152 216 240       stomach   Clontech   STO001   18 21 63 67 71 107 159 210 220 229 241 244       thalamus   Clontech   THA002   9 21 42 45 89 100 117 162 183 220 226-227 242       thymus   Clonetech   THM001   2-3 8 11-12 15 21 23-24 29 38-40 43 46 67 80 82 105 131                   151 159 162 191 214 244       thymus   Clontech   THMc02   2-4 10-12 22 26-27 31-32 38 43 47 50 54 80 92 94 101-102                   127 134 144 146 152 154-155 158-159 162 167 178 182-183                   191 193 195-196 200-201 205 210 214 216 218 233                   237 240       thyroid gland   Clontech   THR001   2-3 5 8 10-12 17-18 20-21 23-24 29 38 42-43 45 49 54 56                   61-62 64 67 70 75-76 78 84 91-92 94 103-105 107 109 122-123                   130 134 143 148-149 155 162 167 169 178 182-183                   186 191 193 195-198 200-201 214 229 232-233 237 240                   244       trachea   Clontech   TRC001   2-3 15 19 36-37 40 47 54 65 72 89 95 107 204-205 210 232                   237 244       uterus   Clontech   UTR001   8 31-32 54 56 178 183 206 232 236 243                       #lymphablastic mRNA (Clontech), 11) human thymus mRNA (Clontech). 12) human lymph node mRNA (Clontech), 13) human spinal cord mRNA (Clontech), 14) human thyroid mRNA (Clontech), 15) human esophagus mRNA (BioChain), 16) human conceptional umbilical cord mRNA (BioChain).           
 
     [0446]                                   TABLE 2                       SEQ                           ID   Accession               %       NO:   Number   Species   Description   Score   Identity                                                        246   AF145657     Drosophila     BcDNA.GH10120   728   38                 melanogaster         247   X58141     Homo     mRNA for erythrocyte adducin alpha subunit.   3826   99                 sapiens         248   L29296     Homo     (clone: SS20B/E6.0) alpha-adducin gene, exons   3387   99                 sapiens     14, 15, 16.       249   AAB63963     Homo     26-MAR-2001 26-MAY-2000 Human prostate   1095   97                 sapiens     cancer associated antigen protein sequence SEQ                   ID NO: 1325.       250   M29458     Homo     carbonic anhydrase III gene, exon 7.   1441   100                 sapiens         251   AJ006529     Gallus gallus     putative phosphatase   867   60       252   Y08302     Homo     mRNA for MAP kinase phosphatase 4.   1996   100                 sapiens         253   X53280     Homo     BTF3a mRNA.   1048   100                 sapiens         254   AB013790     Ateles     immunoglobulin alpha heavy chain   74   43                 belzebuth         255   AK027387     Homo     FLJ14481 fis, clone MAMMA1002351, highly   964   100                 sapiens     similar to  Mus musculus  dynactin subunit p25                   (p25) mRNA.       256   AK001686     Homo     FLJ10824 fis, clone NT2RP4001086.   3013   93                 sapiens         257   AK001686     Homo     FLJ10824 fis, clone NT2RP4001086.   4089   98                 sapiens         258   AK026076     Homo     FLJ22423 fis, clone HRC08678.   689   100                 sapiens         259   AY037207     Arabidopsis     AT3g22240/MMP21_1   66   31                 thaliana         260   AAW58394     Homo     14-SEP-1998 09-OCT-1997 Human   797   92                 sapiens     spermidine/spermine NI-acetyltransferase.       261   AF220051     Homo     hematopoietic stem/progenitor cells protein   844   98                 sapiens     MDS031 mRNA, complete cds.       262   AB017563     Homo     gene, exon 10 and complete cds.   2283   100                 sapiens         263   J03910     Homo     (clone 14VS) metallothionein-IG (MTIG) gene,   367   98                 sapiens     complete cds.       264   X56351     Homo     ALASI (ALASH) mRNA for delta-   3333   100                 sapiens     aminolevulinate synthase (housekeeping) (EC                   2.3.1.37).       266   U79241     Homo     clone 23759 mRNA. partial cds.   2304   100                 sapiens         267   AF068291     Homo     mRNA, partial cds.   699   99                 sapiens         268   BC007235     Homo     clone MGC: 15430, mRNA, complete cds.   398   100                 sapiens         269   X69151     Homo     mRNA for subunit C of vacuolar proton-   1958   100                 sapiens     ATPase V1 domain.       270   AF271784     Homo     mRNA, complete cds.   1017   92                 sapiens         271   AB025220     Homo     mRNA for p40phox. complete cds.   1737   100                 sapiens         272   AB025220     Homo     mRNA for p40phox. complete cds.   1644   96                 sapiens         273   BC001426     Homo     Similar to ubiquinol-cytochrome c reductase   346   100                 sapiens     hinge protein, clone MGC: 1361, mRNA,                   complete cds.       274   AL050051     Homo     cDNA DKFZp566D193 (from clone   481   98                 sapiens     DKFZp566D193); partial cds.       275   BC002517     Homo     Pirin, clone MGC: 2083, mRNA, complete cds.   1543   100                 sapiens         276   X69962     Homo     FMR-1 mRNA.   2384   100                 sapiens         277   L29074     Homo     X mental retardation syndrome protein (FMRI)   2144   92                 sapiens     gene, alternative splice products, complete cds;                   and pseudogene, complete sequence.       278   AK001711     Homo     FLJ10849 fis, clone NT2RP4001414, highly   2179   99                 sapiens     similar to SEPTIN 2 HOMOLOG.       279   AK027641     Homo     FLJ14735 fis, clone NT2RP3002054.   651   99                 sapiens         280   BC009256     Homo     clone MGC: 14860, mRNA, complete cds.   1065   94                 sapiens         281   AL110239     Homo     cDNA DKFZp566E144 (from clone   1234   99                 sapiens     DKFZp566E144); complete cds.       282   BC008714     Homo     prostatic binding protein, clone MGC: 8531,   1017   100                 sapiens     mRNA, complete cds.       283   BC004374     Homo     ARPI (actin-related protein 1, yeast) homolog B   1949   100                 sapiens     (centractin beta), clone MGC: 10568, mRNA,                   complete cds.       284   AF201334     Homo     mRNA, complete cds.   2395   100                 sapiens         285   BC008743     Homo     zyxin, clone MGC: 3071, mRNA, complete cds.   3145   100                 sapiens         286   BC005957     Homo     solute carrier family 25 (mitochondrial carrier;   1557   100                 sapiens     peroxisomal membrane protein, 34 kD), member                   17, clone MGC: 14604, mRNA, complete cds.       287   AF273053     Homo     tumor antigen se89-1 mRNA, complete cds.   3570   82                 sapiens         288   AB028893     Homo     U32, U33, U34, U35, RPS11, U35 genes for   595   100                 sapiens     ribosomal protein L13a and S11, U32, U33,                   U34, U35, and U35 snoRNA, complete cds and                   sequence.       289   AC003973     Homo     from chromosome 19, BAC 33152, complete   5273   81                 sapiens     sequence.       290   AF253978     Homo     mRNA, partial cds.   487   85                 sapiens         291   AF018265   synthetic   immunoglobulin lambda light chain   278   79               construct       292   BC005134     Homo     Similar to ribosomal protein L14, clone   1102   99                 sapiens     MGC: 11208, mRNA, complete cds.       293   AK000869     Homo     FLJ10007 fis, clone HEMBA 1000193.   2635   100                 sapiens         294   AAB73229     Homo     11-MAY-2001 11-AUG-2000 Human   2127   98                 sapiens     phosphatase MTMR7_h.       295   BC003618     Homo     Similar to putative nuclear protein, clone   3042   100                 sapiens     MGC: 1819, mRNA, complete cds.       296   AAB54346     Homo     09-MAR-2001 08-MAR-2000 Human   4092   99                 sapiens     pancreatic cancer antigen protein sequence SEQ                   ID NO: 798.       297   AK000330     Homo     FLJ20323 fis. clone HEP09648.   2229   100                 sapiens         298   AF176701     Homo     protein FBL9 mRNA. partial cds.   1072   100                 sapiens         299   X54977     Bos taurus     17,000 dalton myosin light chain   789   100       300   AL096746     Homo     cDNA DKFZp586E1322 (from clone   1186   100                 sapiens     DKFZp586E1322): partial cds.       301   BC000502     Homo     ribosomal protein L17, clone MGC: 8457,   970   100                 sapiens     mRNA, complete cds.       302   AC004079     Homo     clone RP1-167F23 from 7p15, complete   1965   100                 sapiens     sequence.       303   X92485     Plasmodium     pval   149   55                 vivax         304   AK006347     Mus     putative   429   86                 musculus         305   AL137544     Homo     cDNA DKFZp434A 1520 (from clone   974   98                 sapiens     DKFZp434A 1520); partial cds.       306   AC006276     Homo     19, cosmid R28379, complete sequence.   900   99                 sapiens         307   AK024297     Homo     FLJ14235 fis, clone NT2RP4000167.   2325   100                 sapiens         308   AK005941     Mus     putative   460   88                 musculus         309   AF265440     Homo     mRNA, complete cds.   1413   100                 sapiens         311   AB027251     Homo     for zinc finger protein (ZFD25), complete cds.   4369   100                 sapiens         312   AK008240     Mus     putative   455   100                 musculus         313   AAB75337     Homo     03-APR-2001 01-JUN-2000 Human secreted   138   60                 sapiens     protein sequence encoded by gene 47 SEQ ID                   NO: 156.       314   AF321191     Homo     (PRX) mRNA, complete cds, alternatively   7312   99                 sapiens     spliced.       315   AF225417     Homo     kDa protein mRNA, complete cds.   3701   99                 sapiens         316   AK000265     Homo     FLJ20258 fis, clone COLF7250.   2797   97                 sapiens         317   D90070     Homo     ATL-derived PMA-responsive (APR) peptide   278   100                 sapiens     mRNA.       318   U79725     Homo     A33 antigen precursor mRNA, complete cds.   1678   100                 sapiens         319   M83679     Rattus     RAB15   1077   97                 norvegicus         320   AK024715     Homo     FLJ21062 fis, clone CAS01044.   927   98                 sapiens         321   AK000075     Homo     FLJ20068 fis, clone COL01755.   1729   99                 sapiens         322   AC007954     Homo     14 clone RP11-493G17 and CTD-2516D11 map   4243   100                 sapiens     14q24.3, complete sequence.       323   Z33905     Homo     gene for 43 kD acetylcholine receptor-associated   2150   99                 sapiens     protein (Rapsyn).       324   AF030027   Equine   71   118   22               herpesvirus 4       325   AJ291606     Xenopus     gamma tubulin ring protein   2024   55                 laevis         326   AAB64610     Homo     22-MAR-2001 01-JUN-2000 Human secreted   197   72                 sapiens     protein BLAST search protein SEQ ID NO:                   120.       327   AAB53677     Homo     09-MAR-2001 08-MAR-2000 Human colon   694   99                 sapiens     cancer antigen protein sequence SEQ ID                   NO: 1217.       328   AF159055     Homo     zipper-like protein (LZLP) mRNA, complete   116   79                 sapiens     cds.       329   AL160111     Homo     1 of a novel human mRNA from chromosome   2126   100                 sapiens     22.       330   AF159055     Homo     zipper-like protein (LZLP) mRNA, complete   130   80                 sapiens     cds.       331   AK026264     Homo     FLJ22611 fis, clone HS104961.   685   96                 sapiens         332   X57809     Homo     rearranged immunoglobulin lambda light chain   1223   100                 sapiens     mRNA.       333   AAB87440     Homo     22-MAY-2001 31-AUG-2000 Human gene 32   513   75                 sapiens     encoded secreted protein fragment, SEQ ID                   NO: 181.       334   AK012475     Mus     putative   2259   84                 musculus         335   AF090930     Homo     HQ0478 PRO0478 mRNA, complete cds.   146   72                 sapiens         336   AL080196     Homo     cDNA DKFZp434C212 (from clone   2292   94                 sapiens     DKFZp434C212).       337   AK019766     Mus     putative   1288   71                 musculus         338   X69398     Homo     mRNA for OA3 antigenic surface determinant.   1632   100                 sapiens         339   AK019305     Mus     putative   506   96                 musculus         340   AL078630     Mus     573K1.15 (mm17M1-6 (novel 7 transmembrane   1023   81                 musculus     receptor (rhodopsin family) (olfactory receptor                   LIKE) protein))       341   AF118078     Homo     PRO1848   574   100                 sapiens         342   AK005566     Mus     putative   1218   94                 musculus         343   U71363     Homo     zinc finger protein zfp6 (ZF6) mRNA, partial   1367   70                 sapiens     cds.       344   AK015315     Mus     putative   556   76                 musculus         345   AF218451     Homo     substrate p130Cas mRNA, complete cds.   4579   99                 sapiens         346   AF151046     Homo     HSPC212   1345   87                 sapiens         347   AF151046     Homo     HSPC212   817   74                 sapiens         348   Z14244     Homo     coxVIIb mRNA for cytochrome c oxidase   426   100                 sapiens     subunit VIIb.       349   BC001037     Homo     ribosomal protein L35a, clone MGC: 1639,   581   100                 sapiens     mRNA, complete cds.       351   AAB45018     Homo     12-FEB-2001 09-MAR-2000 Human secreted   142   57                 sapiens     protein encoded by gene 41 homologue.       352   AAY94885     Homo     12-JUN-2000 22-JUL-1999 Human protein   540   99                 sapiens     clone HP10550.       353   AF161557     Homo     HSPC072   472   100                 sapiens         354   AAG01438     Homo     06-OCT-2000 21-FEB-2000 Human secreted   353   92                 sapiens     protein, SEQ ID NO: 5519.       355   AF161507     Homo     HSPC158   1197   99                 sapiens         356   AL122111     Homo     cDNA DKFZp434A1721 (from clone   2868   99                 sapiens     DKFZp434A1721).       357   AF349540     Homo     XIII secreted phospholipase A2 mRNA.   1073   100                 sapiens     complete cds.       358   AF274714     Homo     protein-related protein (ORPI) mRNA.   2363   100                 sapiens     complete cds.       359   AAG03793     Homo     06-OCT-2000 21-FEB-2000 Human secreted   222   67                 sapiens     protein, SEQ ID NO: 7874.       360   BC000705     Homo     clone MGC: 861, mRNA, complete cds.   908   100                 sapiens         361   AAG03789     Homo     06-OCT-2000 21-FEB-2000 Human secreted   188   60                 sapiens     protein, SEQ ID NO: 7870.       362   AAB62810     Homo     02-MAY-2001 06-JUL-2000 Human nervous   501   96                 sapiens     system associated protein NSPRT3 amino acid                   sequence.       363   AF161370     Homo     mRNA, partial cds.   654   91                 sapiens         364   AK011592     Mus     putative   1245   66                 musculus         365   AK002154     Homo     FLJ11292 fis, clone PLACE1009665.   230   64                 sapiens         366   AF159297     Zea mays     extensin-like protein   349   28       367   AF125096     Homo     HSPC042 protein   137   96                 sapiens         368   AF125096     Homo     HSPC042 protein   243   98                 sapiens         369   AK001745     Homo     FLJ10883 fis, clone NT2RP4001946, weakly   1880   99                 sapiens     similar to PROTEIN-L-ISOASPARTATE O-                   METHYLTRANSFERASE (EC 2.1.1.77).       370   AF151783     Homo     (MEG3) mRNA, complete cds.   3651   99                 sapiens         371   X16707     Homo     fra-1 mRNA.   1443   100                 sapiens         372   AF176555     Homo     anchoring protein 220 mRNA, complete cds.   9783   99                 sapiens         373   X78121     Homo     mRNA.   3404   100                 sapiens         374   U82670     Homo     Xq28 psHMG17 pseudogene, complete   2513   99                 sapiens     sequence; and melanoma antigen family A1                   (MAGEA1) and zinc finger protein 275                   (ZNF275) genes, complete cds.       375   AK018726     Mus     putative   670   100                 musculus         376   BC000187     Homo     cytochrome c oxidase subunit VIc, clone   379   100                 sapiens     MGC: 1520, mRNA, complete cds.       377   AAY87548     Homo     18-JUL-2000 03-NOV-1997 Human disease-   729   100                 sapiens     associated calmodulin protein (DACP-1).       378   AK003198     Mus     putative   562   100                 musculus         379   AK000496     Homo     FLJ20489 fis, clone KAT08285.   333   69                 sapiens         380   AF130079     Homo     PRO2852   308   74                 sapiens         381   AAY91961     Homo     19-JUL-2000 17-SEP-1999 Human   1293   96                 sapiens     cytoskeleton associated protein 16 (CYSKP-16).       382   M15202     Rattus     troponin T class IIIa beta   1155   94                 norvegicus         383   AF026276     Homo     skeletal troponin T (TNNT3) gene, complete   1205   94                 sapiens     cds.       384   AF090694     Homo     RNA binding protein (NAPOR-2) mRNA,   2519   98                 sapiens     complete cds.       385   BC007655     Homo     protein phosphatase 1, regulatory (inhibitor)   1051   100                 sapiens     subunit 2, clone MGC: 1327, mRNA, complete                   cds.       386   AF161533     Homo     HSPC048   573   100                 sapiens         387   BC002801     Homo     p47, clone MGC: 3347, mRNA, complete cds.   1812   96                 sapiens         388   AK027878     Homo     FLJ14972 fis, cloneTHYRO1000715.   2669   98                 sapiens         389   AF161418     Homo     HSPC300   378   100                 sapiens         390   AK010720     Mus     putative   105   28                 musculus         391   X66358     Homo     mRNA KKIALRE for serine/threonine protein   1929   99                 sapiens     kinase.       392   AF290612     Homo     Q0310 liver nuclear protein mRNA, complete   2246   98                 sapiens     cds.       393   U69263     Homo     precursor, mRNA, complete cds.   4516   99                 sapiens         394   U69263     Homo     precursor, mRNA, complete cds.   4021   99                 sapiens         395   AK000838     Homo     FLJ20831 fis, clone ADKA03080.   761   100                 sapiens         396   AK006393     Mus     putative   819   90                 musculus         397   AF312033     Mus     ASR2A   4584   97                 musculus         398   BC001904     Homo     Similar to phosphoglycerate mutase 2 (muscle),   270   100                 sapiens     clone MGC: 2269, mRNA, complete cds.       399   Y14391     Homo     for putative GTP-binding protein.   2042   99                 sapiens         400   AF242528     Homo     finger protein 291 (ZNF291) mRNA, complete   294   100                 sapiens     cds.       401   AF116695     Homo     PRO2221   173   46                 sapiens         402   AAR32020     Homo     11-JUL-1993 14-AUG-1992 Sequence of a   734   66                 sapiens     eukaryotic transcription factor (TF).       403   AB049127     Homo     mRNA for MAP/microtubule affinity-regulating   2227   73                 sapiens     kinase like 1. complete cds.       404   K03250     Rattus     ribosomal protein S11   824   100                 norvegicus         405   AF144233     Homo     binding peptide mRNA, partial cds.   328   96                 sapiens         406   AC007055     Homo     14 clone BAC 201F1 map 14q24.3, complete   519   100                 sapiens     sequence.       407   AK001752     Homo     FLJ10890 fis, clone NT2RP4002071.   5019   99                 sapiens         408   AF090931     Homo     HQ0483$ PRO0483 mRNA, complete cds.   133   58                 sapiens         409   A28080     Mycobacterium     34 kDa protein   75   36                 avium                 subsp.                 paratuberculosis         410   AL136704     Homo     cDNA DKFZp566A1524 (from clone   1662   99                 sapiens     DKFZp566A1524); complete cds.       411   AL137347     Homo     cDNA DKFZp761M1511 (from clone   473   100                 sapiens     DKFZp761M1511); partial cds.       412   AK027527     Homo     FLJ14621 fis, clone NT2RP2000079.   1012   100                 sapiens         413   AAG01083     Homo     06-OCT-2000 21-FEB-2000 Human secreted   274   96                 sapiens     protein. SEQ ID NO: 5164.       414   BC009405     Homo     adenylate kinase 2, clone MGC: 15301, mRNA,   1094   100                 sapiens     complete cds.       415   U34994     Homo     dependent protein kinase catalytic subunit   21178   100                 sapiens     (PRKDC) mRNA, complete cds; alternatively                   spliced.       416   U47077     Homo     protein kinase catalytic subunit (DNA-PKcs)   21319   99                 sapiens     mRNA, complete cds.       417   U22229     Felis catus     ribosomal protein L41   128   100       418   AF361481     Homo     GTP-binding protein 1 (GTPBP3) gene,   1402   94                 sapiens     complete cds; nuclear gene for mitochondrial                   product.       419   BC000606     Homo     Similar to ribosomal protein L14, clone   1094   100                 sapiens     MGC: 1644, mRNA, complete cds.       421   AAY73345     Homo     24-FEB-2000 04-MAY-1999 HTRM clone   2171   73                 sapiens     438283 protein sequence.       422   AK000632     Homo     FLJ20625 fis, clone KAT04008.   816   100                 sapiens         423   AC004668     Homo     clone CTA-276O3 from 7q22-q31.1, complete   1976   99                 sapiens     sequence.       424   AK000496     Homo     FLJ20489 fis, clone KAT08285.   238   73                 sapiens         425   AAY02785     Homo     11-JUN-1999 07-JUL-1998 Human secreted   82   43                 sapiens     protein encoded by gene 51 clone HUKEX85.       426   AF118092     Homo     PRO2061   1440   96                 sapiens         427   AK000382     Homo     FLJ20375 fis, clone HUV00942.   1330   99                 sapiens         428   Y15286     Homo     for vacuolar proton-ATPase subunit M9.2.   459   100                 sapiens         429   AK014098     Mus     putative   524   68                 musculus         430   AF286095     Homo     receptor (IL22R) mRNA, complete cds.   629   86                 sapiens         431   AK023266     Homo     FLJ13204 fis, clone NT2RP3004507, weakly   758   90                 sapiens     similar to MOB1 PROTEIN.       432   AF047354     Homo     and spleen DNase precursor (LSD) mRNA,   1046   99                 sapiens     complete cds.       433   X53682     Homo     LAG-1 gene.   484   100                 sapiens         434   AC000064     Homo     BAC clone RG083M05 from 7q21-7q22,   298   100                 sapiens     complete sequence.       435   AL390921     Arabidopsis     putative protein   72   44                 thaliana         436   AAB87440     Homo     22-MAY-2001 31-AUG-2000 Human gene 32   1572   100                 sapiens     encoded secreted protein fragment, SEQ ID                   NO: 181.       437   AP003001     Mesorhizobium     O-linked GlcNAc transferase   153   30                 loti         438   AK000642     Homo     FLJ20635 fis, clone KAT03466.   1854   99                 sapiens         439   Z48810     Homo     mRNA for TX protease precursor.   306   92                 sapiens         441   AC003002     Homo     DNA from overlapping chromosome 19-   436   98                 sapiens     specific cosmids R29515 and R28253, genomic                   sequence, complete sequence.       442   AF109377     Mus     ldlBp   3979   82                 musculus         443   AF109377     Mus     ldlBp   2711   81                 musculus         444   AAG02042     Homo     06-OCT-2000 21-FEB-2000 Human secreted   797   100                 sapiens     protein, SEQ ID NO: 6123.       445   M17877     Plasmodium     interspersed repeat antigen   291   27                 falciparum         446   M17877     Plasmodium     interspersed repeat antigen   291   27                 falciparum         447   AB025784     Rattus     PPAR gamma coactivator   331   46                 norvegicus         448   AK000755     Homo     FLJ20748 fis, clone HEP05772.   831   96                 sapiens         449   AK001714     Homo     FLJ10852 fis, clone NT2RP4001498, weakly   2586   100                 sapiens     similar to ANKYRIN REPEAT-CONTAINING                   PROTEIN AKR1.       450   AB042646     Homo     mRNA, complete cds.   1224   100                 sapiens         451   AF125533     Homo     b5 reductase isoform mRNA, complete cds.   1606   100                 sapiens         452   AAY02591     Homo     19-JUL-1999 09-OCT-1998 A human   849   100                 sapiens     progesterone receptor complex p23-like protein.       453   BC000600     Homo     Similar to from HeLa cyclin-dependent kinase 2   1106   100                 sapiens     interacting protein, clone MGC: 849, mRNA,                   complete cds.       454   Z46937     Caenorhabdit     similarity with ribosomal protein L21   140   38                 is elegans         455   AF161556     Homo     HSPC071   941   100                 sapiens         456   AF225971     Homo     (TUBG2) mRNA, complete cds.   2346   99                 sapiens         458   AF343664     Homo     receptor translocation associated protein 2c   736   55                 sapiens     (IRTA2) mRNA, complete cds, alternatively                   spliced.       459   AF191545     Homo     mRNA, complete cds.   4141   99                 sapiens         460   AF118082     Homo     PRO1902   202   58                 sapiens         461   D00531     Oncorhynchus     apopolysialoglycoprotein   512   30                 masou         462   Z11898     Homo     OTF3 mRNA encoding octamer binding protein   1948   100                 sapiens     3A.       464   AL162044     Homo     cDNA DKFZp761L0812 (from clone   220   41                 sapiens     DKFZp761L0812); partial cds.       465   AL137301     Homo     cDNA DKFZp434N1429 (from clone   543   100                 sapiens     DKFZp434N1429); partial cds.       466   AB032593     Homo     for PXR2b, complete cds.   3201   100                 sapiens         467   AL050075     Homo     cDNA DKFZp566F0546 (from clone   407   100                 sapiens     DKFZp566F0546); partial cds.       468   AK000732     Homo     FLJ20725 fis, clone HEP13903.   1653   99                 sapiens         469   AB049638     Homo     mRNA for mitochondrial ribosomal protein L11   941   100                 sapiens     (L11mt), complete cds.       470   AB049638     Homo     mRNA for mitochondrial ribosomal protein L11   737   99                 sapiens     (L11mt), complete cds.       471   AB014772     Homo     for MOP-3, complete cds.   1722   99                 sapiens         472   AAY59808     Homo     18-JAN-2000 03-APR-1998 Human normal   778   100                 sapiens     ovarian tissue derived protein 85.       473   AF331500   multiple   recombinant envelope protein   1177   92               sclerosis               associated               retrovirus               element       474   AF257330     Homo     protein mRNA, complete cds.   962   96                 sapiens         475   AK000632     Homo     FLJ20625 fis, clone KAT04008.   809   99                 sapiens         476   M58511     Homo     iron-responsive element-binding protein/iron   4968   99                 sapiens     regulatory protein 2 (IRE-BP2/IRP2) mRNA,                   partial cds.       477   AF181989     Homo     beta subunit variant (HBB) mRNA, complete   588   90                 sapiens     cds.       478   AC003002     Homo     DNA from overlapping chromosome 19-   752   100                 sapiens     specific cosmids R29515 and R28253, genomic                   sequence, complete sequence.       479   BC002924     Homo     clone IMAGE: 3956179, mRNA, partial cds.   1221   99                 sapiens         480   AF109146     Homo     lectin superfamily 6 (CLECSF6) mRNA,   958   99                 sapiens     complete cds.       481   BC005374     Homo     Similar to RIKEN cDNA 1110001E24 gene,   995   100                 sapiens     clone MGC: 12490, mRNA, complete cds.       482   X75285     Mus     fibulin-2   5621   81                 musculus         483   AC007954     Homo     14 clone RP11-493G17 and CTD-2516D11 map   1342   100                 sapiens     14q24.3, complete sequence.       484   AK016295     Mus     putative   116   27                 musculus         485   AB028893     Homo     U32, U33, U34, U35, RPS11, U35 genes for   434   100                 sapiens     ribosomal protein L13a and S11, U32, U33,                   U34, U35, and U35 snoRNA, complete cds and                   sequence.       486   BC003681     Homo     clone IMAGE: 3453235, mRNA, partial cds.   2829   96                 sapiens         487   AK009235     Mus     putative   1648   92                 musculus         488   AF294900     Homo     beta-carotene 15,15′- dioxygenase (BCDO)   2912   100                 sapiens     mRNA, complete cds.       489   AAB43979     Homo     08-FEB-2001 08-MAR-2000 Human cancer   1051   86                 sapiens     associated protein sequence SEQ ID NO: 1424.       490   AF220025     Homo     motif protein TRIM5 isoform alpha (TRIM5)   1299   95                 sapiens     mRNA, complete cds; alternatively spliced.                    
     [0447]                           TABLE 3                       SEQ ID   Accession               NO:   Number   Description   Results*                                                247   PF00596   Class II Aldolases and Adducin N-   PF00596C 17.24 9.710e−20 217-243               terminal domain proteins.   PF00596B 15.07 4.938e−14                   180-202 PF00596D 13.89                   4.079e−12 297-315       248   PF00596   Class II Aldolases and Adducin N-   PF00596C 17.24 9.710e−20 217-243               terminal domain proteins.   PF00596B 15.07 4.938e−14                   180-202 PF00596D 13.89                   4.079e−12 297-315       250   BL00162   Eukaryotic-type carbonic anhydrases   BL00162C 17.78 1.000e−40 88-125               proteins.   BL00162E 14.93 6.478e−34                   189-222 BL00162F 22.68                   6.727e−30 226-260 BL00162A                   22.92 5.179e−26 16-47                   BL00162D 15.06 4.960e−22 126-151                   BL00162B 21.43 5.345e−17                   51-74       252   BL00383   Tyrosine specific protein phosphatases   BL00383E 10.35 1.196e−11 288-299               proteins.       253   PD02749   TRANSCRIPTION PROTEIN   PD02749B 12.75 1.000e−40 84-120               FACTOR BTF3 REGULATION   PD02749C 13.96 3.739e−34               NUCL.   136-170 PD02749A 9.56 6.000e−15                   51-64       256   BL00824   Elongation factor 1 beta/beta&#39;/delta   BL00824B 9.21 8.419e−09 281-301               chain proteins.       257   BL00824   Elongation factor 1 beta/beta&#39;/delta   BL00824B 9.21 8.419e−09 281-301               chain proteins.       260   PF00583   Acetyltransferase (GNAT) family.   PF00583A 12.53 3.571e−12 175-186       262   PD01364   MUCIN GLYCOPROTEIN   PD01364B 13.94 1.000e−10 336-352               PRECURSOR MEM.       263   PR00860   VERTEBRATE   PR00860B 7.04 2.929e−20 28-42               METALLOTHIONEIN SIGNATURE   PR00860C 9.61 1.474e−14 42-52                   PR00860A 5.46 9.229e−12 6-19       264   BL00599   Aminotransferases class-II pyridoxal-   BL00599B 18.93 8.800e−27 278-307               phosphate attachment sit.   BL00599D 13.25 8.773e−13                   411-424 BL00599C 9.13 5.235e−11                   334-344       266   PD01769   REDUCTASE PAPS   PD01769C 21.60 8.393e−18 416-452               BIOSYNTHESIS PHOSPHOADENO.       271   PR00497   NEUTROPHIL CYTOSOL FACTOR   PR00497D 11.91 1.176e−28 192-214               P40 SIGNATURE   PR00497E 10.43 1.123e−26                   241-261 PR00497A 6.92 1.136e−24                   56-74 PR00497B 4.99 1.125e−23                   74-93 PR00497C 8.89 1.100e−21                   131-147 PR00497F 8.66                   1.138e−15 297-309       272   BL50002   Src homology 3 (SH3) domain   BL50002A 14.19 6.538e−11 177-196               proteins profile.       276   PF00013   KH domain proteins family of RNA   PF00013 5.78 2.059e−10 268-280               binding proteins.       277   PF00013   KH domain proteins family of RNA   PF00013 5.78 2.059e−10 268-280               binding proteins.       280   PF00930   Dipeptidyl peptidase IV (DPP IV) N-   PF00930J 8.78 4.231e−09 394-415               terminal region.       282   BL01220   Phosphatidylethanolamine-binding   BL01220B 16.65 1.000e−40 105-146               protein family proteins.   BL01220C 14.75 5.846e−34                   146-174 BL01220A 22.62                   3.400e−31 67-98 BL01220D                   18.75 5.364e−31 189-221       283   BL00406   Actins proteins.   BL00406B 5.47 1.000e−40 88-143                   BL00406C 6.75 1.000e−40 147-202                   BL00406D 12.58 7.000e−40                   270-325 BL00406E 8.44 6.087e−39                   327-377 BL00406A 9.95                   6.087e−29 11-46       284   BL00227   Tubulin subunits alpha, beta, and   BL00227C 25.48 7.792e−26 119-171               gamma proteins.   BL00227D 18.46 2.286e−20                   253-307 BL00227B 19.29                   4.720e−13 58-113 BL00227A                   24.55 4.649e−12 1-35       285   BL00478   LIM domain proteins.   BL00478B 14.79 3.739e−14 463-478                   BL00478B 14.79 3.500e−12                   405-420 BL00478B 14.79                   6.000e−12 530-545       286   PR00927   ADENINE NUCLEOTIDE   PR00927B 14.66 6.236e−14 146-168               TRANSLOCATOR 1 SIGNATURE       288   BL00783   Ribosomal protein L13 proteins.   BL00783C 22.43 8.071e−20 87-117                   BL00783A 14.55 1.600e−19                   8-33 BL00783B 12.76 3.500e−12                   74-86       289   PD01066   PROTEIN ZINC FINGER ZINC-   PD01066 19.43 2.500e−38 422-461               FINGER METAL-BINDING NU.       291   DM00031   IMMUNOGLOBULIN V REGION.   DM00031A 16.80 8.364e−11 20-68       292   PD02808   PROTEIN RIBOSOMAL L14   PD02808A 12.03 3.739e−38 5-42               PROBABLE 60.   PD02808B 19.19 8.500e−36 85-120       294   BL00383   Tyrosine specific protein phosphatases   BL00383E 10.35 2.756e−12 263-274               proteins.       295   BL01160   Kinesin light chain repeat proteins.   BL01160B 19.54 8.093e−09 510-564       297   PR00706   PYROGLUTAMYL PEPTIDASE I   PR00706B 10.56 6.870e−09 74-87               (C15) FAMILY SIGNATURE       300   PR00453   VON WILLEBRAND FACTOR   PR00453A 12.79 4.750e−15 40-58               TYPE A DOMAIN SIGNATURE       301   BL00464   Ribosomal protein L22 proteins.   BL00464B 28.48 4.960e−35 106-151                   BL00464A 29.41 9.700e−23                   17-54       302   BL00027   ‘Homeobox’ domain proteins.   BL00027 26.43 6.727e−36 158-201       307   BL01113   C1q domain proteins.   BL01113A 17.99 2.558e−09 712-739       310   BL00226   Intermediate filaments proteins.   BL00226D 19.10 9.571e−40 371-418                   BL00226B 23.86 4.600e−38                   205-253 BL00226C 13.23                   9.500e−26 270-301 BL00226A                   12.77 4.000e−16 104-119       311   PD01066   PROTEIN ZINC FINGER ZINC-   PD01066 19.43 5.135e−34 6-45               FINGER METAL-BINDING NU.       312   PD01861   PROTEIN NUCLEAR   PD01861A 14.06 4.393e−11 26-50               RIBONUCLEOPROTEIN SMALL               MRNA RNA.       315   BL00192   Cytochrome b/b6 heme-ligand   BL00192A 11.90 3.700e−09 96-136               proteins.       316   PR00049   WILM&#39;S TUMOR PROTEIN   PR00049D 0.00 6.445e−11 661-676               SIGNATURE       318   DM00031   IMMUNOGLOBULIN V REGION.   DM00031B 15.41 4.423e−11 103-137       319   BL01115   GTP-binding nuclear protein ran   BL01115A 10.22 7.455e−13 9-53               proteins.       321   BL00378   Hexokinases proteins.   BL00378A 19.01 8.375e−09 279-307       323   BL00405   43 Kd postsynaptic protein.   BL00405C 10.15 1.000e−40 65-115                   BL00405D 6.60 1.000e−40                   123-166 BL00405G 7.78 1.000e−40                   226-263 BL00405H 16.83                   1.000e−40 263-302 BL004051                   13.75 1.000e−40 302-339                   BL00405J 13.28 1.000e−40 339-373                   BL00405K 7.57 1.000e−40                   373-413 BL00405B 15.33                   6.538e−39 26-58 BL00405F 8.07                   1.900e−38 195-226 BL00405E                   8.84 1.529e−34 166-192                   BL00405A 9.73 1.643e−31 2-26       327   BL00048   Protamine P1 proteins.   BL00048 6.39 8.475e−15 24-51                   BL00048 6.39 2.918e−14 26-53                   BL00048 6.39 5.279e−14 34-61                   BL00048 6.39 5.721e−14 32-59                   BL00048 6.39 7.197e−14 11-38                   BL00048 6.39 8.082e−14 22-49                   BL00048 6.39 2.246e−13 10-37                   BL00048 6.39 6.677e−13 33-60                   BL00048 6.39 7.092e−13 7-34                   BL00048 6.39 7.785e−13 8-35                   BL00048 6.39 7.923e−13 23-50                   BL00048 6.39 1.926e−12 9-36                   BL00048 6.39 1.926e−12 31-58                   BL00048 6.39 2.456e−12 20-47                   BL00048 6.39 6.294e−12 14-41                   BL00048 6.39 7.221e−12 25-52                   BL00048 6.39 7.750e−12 12-39                   BL00048 6.39 9.868e−12 21-48                   BL00048 6.39 1.125e−11 19-46                   BL00048 6.39 2.375e−11 13-40                   BL00048 6.39 6.875e−11 6-33                   BL00048 6.39 8.125e−11 36-63                   BL00048 6.39 8.250e−11 18-45                   BL00048 6.39 8.250e−11 30-57                   BL00048 6.39 1.947e−10 5-32                   BL00048 6.39 3.605e−10 4-31                   BL00048 6.39 4.908e−10 27-54                   BL00048 6.39 5.974e−10 42-69                   BL00048 6.39 7.039e−10 15-42                   BL00048 6.39 7.750e−10 17-44                   BL00048 6.39 7.987e−10 39-66                   BL00048 6.39 9.526e−10 1-28                   BL00048 6.39 1.225e−09 38-65                   BL00048 6.39 3.363e−09 16-43                   BL00048 6.39 4.038e−09 3-30                   BL00048 6.39 5.950e−09 28-55                   BL00048 6.39 6.288e−09 29-56                   BL00048 6.39 6.400e−09 40-67                   BL00048 6.39 6.738e−09 2-29                   BL00048 6.39 7.863e−09 35-62       331   PR00221   CAULIMOVIRUS COAT PROTEIN   PR00221H 12.82 1.217e−09 27-41               SIGNATURE       332   BL00290   Immunoglobulins and major   BL00290A 20.89 1.529e−14 187-210               histocompatibility complex proteins.   BL00290B 13.17 9.000e−12                   247-265       334   BL00415   Synapsins proteins.   BL00415N 4.29 8.420e−10 334-378       336   PR00779   INOSITOL 1,4,5-TRISPHOSPHATE-   PR00779F 14.51 5.147e−09 512-535               BINDING PROTEIN RECEPTOR               SIGNATURE       338   DM00179   w KINASE ALPHA ADHESION T-   DM00179 13.97 7.158e−10 107-117               CELL.       339   BL00224   Clathrin light chain proteins.   BL00224B 16.94 8.200e−09 167-220       340   PR00237   RHODOPSIN-LIKE GPCR   PR00237B 13.50 1.000e−11 1-23               SUPERFAMILY SIGNATURE       343   PD00066   PROTEIN ZINC-FINGER METAL-   PD00066 13.92 5.154e−15 321-334               BINDI.   PD00066 13.92 2.800e−14                   237-250 PD00066 13.92 8.800e−14                   265-278 PD00066 13.92                   3.000e−13 293-306 PD00066                   13.92 9.217e−11 209-222       345   PR00452   SH3 DOMAIN SIGNATURE   PR00452B 11.65 4.600e−15 20-36       347   BL00563   Stathmin family proteins.   BL00563D 11.38 4.835e−09 279-315       349   BL01105   Ribosomal protein L35Ae proteins.   BL01105A 17.37 1.000e−40 16-61                   BL01105B 12.95 1.000e−40 80-120       350   PD02411   PROTEIN TRANSCRIPTION   PD02411 21.89 2.929e−15 2227-2261               REGULATION NUCLEAR.       355   BL00464   Ribosomal protein L22 proteins.   BL00464B 28.48 4.908e−10 128-173                   BL00464A 29.41 7.045e−09                   69-106       358   BL01013   Oxysterol-binding protein family   BL01013D 26.81 8.000e−26 358-402               proteins.   BL01013A 25.14 7.231e−21                   45-81 BL01013C 9.97 1.000e−13                   132-142 BL01013B 11.33                   1.000e−11 110-121       366   PD02557   UREASE ACCESSORY PROTEIN   PD02557C 10.85 6.262e−09 29-44               UREF NICKEL.       369   BL01279   Protein-L-isoaspartate(D-aspartate) O-   BL01279A 24.27 7.614e−12 67-115               methyltransferase signa.       371   PR00042   FOS TRANSFORMING PROTEIN   PR00042E 9.69 8.200e−25 154-178               SIGNATURE   PR00042D 8.97 9.735e−24                   133-155 PR00042C 8.29 4.549e−21                   115-132 PR00042B 10.70                   2.983e−20 98-115 PR00042A                   10.04 6.400e−20 39-57       373   PR00893   RAB ESCORT   PR00893H 7.37 2.588e−34 411-439               (CHOROIDERAEMIA) PROTEIN   PR00893J 1.42 1.500e−28               SIGNATURE   565-586 PR00893D 13.14                   1.563e−28 114-138 PR00893C                   15.10 2.500e−27 94-115                   PR00893K 7.01 1.000e−26 600-620                   PR00893I 14.97 2.667e−26                   543-563 PR00893A 10.55                   1.134e−25 45-64 PR00893F                   10.78 3.314e−25 294-313                   PR00893E 13.94 1.231e−22 213-230                   PR00893G 12.88 5.500e−22                   351-368 PR00893B 8.07 6.192e−22                   75-93       374   BL00028   Zinc finger. C2H2 type. domain   BL00028 16.07 9.471e−14 508-525               proteins.   BL00028 16.07 9.100e−13                   424-441 BL00028 16.07 2.957e−12                   536-553 BL00028 16.07                   4.115e−11 340-357 BL00028                   16.07 8.269e−11 452-469                   BL00028 16.07 4.300e−10 312-329                   BL00028 16.07 7.600e−10                   480-497       375   PF01020   Ribosomal L40e family.   PF01020 15.00 1.000e−40 80-129       377   PR00450   RECOVERIN FAMILY SIGNATURE   PR00450C 12.22 7.840e−10 86-108                   PR00450C 12.22 7.380e−09                   52-74 PR00450C 12.22 7.835e−09                   16-38       381   PF00992   Troponin.   PF00992B 26.31 4.000e−30 178-213                   PF00992A 16.67 2.636e−29                   100-135 PF00992C 16.35                   2.800e−15 244-262       382   PF00992   Troponin.   PF00992B 26.31 4.000e−30 157-192                   PF00992A 16.67 2.636e−29                   79-114 PF00992C 16.35 2.800e−15                   223-241       383   PF00992   Troponin.   PF00992B 26.31 4.000e−30 162-197                   PF00992A 16.67 2.636e−29                   84-119 PF00992C 16.35 2.800e−15                   228-246       384   PD02784   PROTEIN NUCLEAR   PD02784B 26.46 8.307e−10 455-498               RIBONUCLEOPROTEIN.       385   PF01140   Matrix protein (MA), p15.   PF01140D 15.54 9.686e−09 112-147       388   DM00892   3 RETROVIRAL PROTEINASE.   DM00892C 23.55 3.323e−14 340-374       391   PR00109   TYROSINE KINASE CATALYTIC   PR00109B 12.27 6.553e−13 117-136               DOMAIN SIGNATURE       393   PR00453   VON WILLEBRAND FACTOR   PR00453A 12.79 9.571e−16 528-546               TYPE A DOMAIN SIGNATURE   PR00453B 14.65 5.000e−13                   567-582       394   PR00453   VON WILLEBRAND FACTOR   PR00453A 12.79 9.571e−16 528-546               TYPE A DOMAIN SIGNATURE   PR00453B 14.65 5.000e−13                   567-582       399   PR00326   GTPI/OBG GTP-BINDING   PR00326A 8.75 1.514e−09 184-205               PROTEIN FAMILY SIGNATURE       402   PD00066   PROTEIN ZINC-FINGER METAL-   PD00066 13.92 1.692e−10 235-248               BINDI.       403   BL00239   Receptor tyrosine kinase class II   BL00239B 25.15 1.529e−16 106-154               proteins.       404   BL00056   Ribosomal protein S17 proteins.   BL00056A 28.90 3.769e−32 75-115                   BL00056B 20.86 6.727e−23                   123-147       406   BL00150   Acylphosphatase proteins.   BL00150 25.33 1.000e−40 9-56       410   PR00245   OLFACTORY RECEPTOR   PR00245D 10.47 5.224e−09 186-198               SIGNATURE       413   BL00019   Actinin-type actin-binding domain   BL00019A 12.56 1.000e−13 38-49               proteins.       414   BL00113   Adenylate kinase proteins.   BL00113B 20.49 5.667e−32 784-828                   BL00113D 24.41 2.565e−27                   889-920 BL00113C 12.82                   2.286e−16 832-847       415   BL00915   Phosphatidylinositol 3-and 4-kinases   BL00915B 22.78 9.022e−19 3750-3788               proteins.   BL00915C 22.43 6.250e−18                   3873-3912       416   BL00915   Phosphatidylinositol 3-and 4-kinases   BL00915B 22.78 9.022e−19 3750-3788               proteins.   BL00915C 22.43 6.250e−18                   3904-3943       418   PR00326   GIPI/OBG GTP-BINDING   PR00326A 8.75 2.364e−10 186-207               PROTEIN FAMILY SIGNATURE       419   PD02808   PROTEIN RIBOSOMAL L14   PD02808A 12.03 3.739e−38 5-42               PROBABLE 60.   PD02808B 19.19 8.500e−36 85-120       421   PD01066   PROTEIN ZINC FINGER ZINC-   PD01066 19.43 4.767e−31 26-65               FINGER METAL-BINDING NU.       423   BL00143   Insulinase family, zinc-binding region   BL00143B 14.41 4.115e−13 102-117               proteins.       426   BL00514   Fibrinogen beta and gamma chains C-   BL00514C 17.41 1.000e−40 206-243               terminal domain proteins.   BL00514D 15.35 7.000e−16                   251-264 BL00514B 16.42                   4.000e−15 150-166 BL00514A                   11.68 6.885e−12 40-50       427   PR00536   MELANOCYTE STIMULATING   PR00536G 6.26 2.688e−09 333-342               HORMONE RECEPTOR               SIGNATURE       432   PR00130   DNASE I SIGNATURE   PR00130E 14.66 5.871e−16 146-176                   PR00130D 8.65 2.862e−15                   116-146 PR00130H 14.38                   1.106e−11 229-250 PR00130F                   11.23 1.086e−10 176-206                   PR00130G 7.22 2.340e−10 206-229                   PR00130A 11.39 7.000e−10                   31-61       433   PR00437   SMALL CXC CYTOKINE FAMILY   PR00437C 14.85 4.696e−09 68-87               SIGNATURE       445   PF00624   Flocculin repeat proteins.   PF00624J 6.21 9.782e−10 429-484       446   PF00624   Flocculin repeat proteins.   PF00624J 6.21 9.782e−10 429-484       447   PF01140   Matrix protein (MA), p15.   PF01140D 15.54 2.256e−09 222-257       449   PF00791   Domain present in ZO-1 and Unc5-like   PF00791B 28.49 8.515e−10 120-175               netrin receptors.       450   BL00027   ‘Homeobox’ domain proteins.   BL00027 26.43 1.818e−21 36-79       451   BL00191   Cytochrome b5 family, heme-binding   BL00191K 17.38 4.951e−27 184-228               domain proteins.   BL00191J 11.37 6.447e−17                   128-150       454   BL00028   Zinc finger, C2H2 type, domain   BL00028 16.07 8.457e−09 22-39               proteins.       456   BL00227   Tubulin subunits alpha, beta, and   BL00227B 19.29 1.000e−40 51-106               gamma proteins.   106 BL00227C 25.48 1.000e−40                   113-165 BL00227D 18.46                   1.000e−40 223-277 BL00227A                   24.55 2.607e−31 2-36 BL00227F                   21.16 4.316e−30 382-436                   BL00227E 24.15 2.667e−23 331-366       457   PR00301   70 KD HEAT SHOCK PROTEIN   PR00301C 8.62 8.875e−11 235-244               SIGNATURE       458   DM00179   w KINASE ALPHA ADHESION T-   DM00179 13.97 6.870e−09 47-57               CELL.   DM00179 13.97 8.435e−09 238-248       459   PR00756   MEMBRANE ALANYL   PR00756D 10.58 1.529e−21 367-383               DIPEPTIDASE (MI) FAMILY   PR00756B 14.06 5.737e−16               SIGNATURE   253-269 PR00756A 12.90                   1.237e−13 205-221 PR00756E                   11.91 4.094e−13 386-399                   PR00756C 11.60 6.108e−11 331-342       461   PR00648   GPR3 ORPHAN RECEPTOR   PR00648B 7.41 8.340e−09 1029-1048               SIGNATURE       462   BL00027   ‘Homeobox’ domain proteins.   BL00027 26.43 5.500e−27 245-288       466   PD00126   PROTEIN REPEAT DOMAIN TPR   PD00126A 22.53 2.862e−09 515-536               NUCLEA.       469   BL00359   Ribosomal protein L11 proteins.   BL00359A 20.66 5.395e−23 20-56                   BL00359B 23.07 4.176e−19 66-107                   BL00359C 22.18 2.000e−12                   123-157       470   BL00359   Ribosomal protein L11 proteins.   BL00359B 23.07 4.176e−19 40-81                   BL00359C 22.18 2.000e−12 97-131       473   PF00429   ENV polyprotein (coat polyprotein).   PF00429 31.08 3.195e−12 299-349       476   BL00450   Aconitase family proteins.   BL00450B 42.34 8.393e−30 281-336                   BL00450D 21.14 2.800e−18                   560-584 BL00450B 42.34                   6.400e−12 341-396 BL00450A                   13.76 2.406e−11 246-260                   BL00450C 11.95 6.657e−10 507-517       477   BL01033   Globins profile.   BL01033A 16.94 7.923e−18 25-47                   BL01033B 13.81 1.000e−15 93-105       480   BL00615   C-type lectin domain proteins.   BL00615A 16.68 5.500e−10 78-96                   BL00615B 12.25 7.577e−09 178-192       482   BL01177   Anaphylatoxin domain proteins.   BL01177E 20.64 5.800e−24 1043-1070                   BL01177C 17.39 5.333e−19                   997-1016 BL01177B 13.61                   7.840e−16 703-719 BL01177D                   17.50 1.900e−15 1022-1040       487   BL01032   Protein phosphatase 2C proteins.   BL01032H 11.25 8.200e−09 253-266       489   BL00290   Immunoglobulins and major   BL00290A 20.89 1.563e−15 154-177               histocompatibility complex proteins.   BL00290B 13.17 9.000e−12                   214-232       490   PR00245   OLFACTORY RECEPTOR   PR00245A 18.03 5.886e−10 461-483               SIGNATURE                            
     [0448]                               TABLE 4                       SEQ ID               Pfam       NO:   Pfam Model   Description   E-value   Score                                                    247   Aldolase_II   Class II Aldolase and Adducin N-terminal   7.3e−105   361.8       248   Aldolase_II   Class II Aldolase and Adducin N-terminal   7.3e−105   361.8       249   rrm   RNA recognition motif.   8.8e−06   32.6       250   carb_anhydrase   Eukaryotic-type carbonic anhydrase   7.8e−178   604.2       252   DSPc   Dual specificity phosphatase, catalytic doma   3.6e−69   243.2       253   NAC   NAC domain   4.7e−30   113.3       255   hexapep   Bacterial transferase hexapeptide   6.2e−06   33.1       260   Acetyltransf   Acetyltransferase (GNAT) family   2.8e−19   77.5       262   ig   Immunoglobulin domain   5.2e−20   69.5       263   metalthio   Metallothionein   1.3e−22   88.6       264   aminotran_2   Aminotransferases class-II   2.4e−109   376.7       265   IPP_isomerase   Isopentenyl-diphosphate delta-isomerase   1.6e−128   440.4       266   PAPS_reduct   Phosphoadenosine phosphosulfate reductase   6.2e−14   59.7       271   PX   PX domain   7.4e−31   115.9       272   PX   PX domain   7.4e−31   115.9       276   KH-domain   KH domain   7.2e−13   56.2       277   KH-domain   KH domain   7.2e−13   56.2       278   GTP_CDC   Cell division protein   7.6e−119   408.2       280   abhydrolase_2   Phospholipase/Carboxylesterase   0.013   −41.9       282   PBP   Phosphatidylethanolamine-binding protein   7.8e−88   305.2       283   actin   Actin     1e−174   574.6       284   tubulin   Tubulin/FtsZ family     5e−99   342.4       285   LIM   LIM domain containing proteins   4.6e−36   132.3       286   mito_carr   Mitochondrial carrier proteins   1.4e−41   145.5       288   Ribosomal_L13   Ribosomal protein L13   4.1e−56   199.8       289   zf-C2H2   Zinc finger, C2H2 type   5.4e−268   903.7       291   ig   Immunoglobulin domain   0.053   11.5       292   Ribosomal_L14e   Ribosomal protein L14   3.4e−34   127.0       295   PH   PH domain   3.1e−20   77.3       296   Lysyl_hydro   Lysyl hydrolase   0   2058.2       299   efhand   EF hand   0.075   19.5       300   vwa   von Willebrand factor type A domain   2.8e−35   130.6       301   Ribosomal_L22   Ribosomal protein L22p/L17e     4e−67   236.4       302   homeobox   Homeobox domain     4e−34   126.8       309   IF3   Translation initiation factor IF-3   0.00048   15.1       310   filament   Intermediate filament proteins   9.2e−178   604.0       311   zf-C2H2   Zinc finger, C2H2 type   5.6e−143   488.4       312   Sm   Sm protein   5.6e−26   99.7       314   PDZ   PDZ domain (Also known as DHR or GLGF)   0.037   15.2       316   SH3   SH3 domain   3.6e−12   53.9       318   ig   Immunoglobulin domain   1.5e−12   45.5       319   ras   Ras family   5.1e−94   325.8       321   SAM   SAM domain (Sterile alpha motif)   9.9e−10   45.8       323   TPR   TPR Domain   1.1e−12   55.5       329   rrm   RNA recognition motif.   4.7e−09   43.5       332   ig   Immunoglobulin domain     1e−20   71.8       336   VPS9   Vacuolar sorting protein 9 (VPS9) domain   1.1e−30   115.4       338   ig   Immunoglobulin domain   0.0079   14.2       340   7tm_1   7 transmembrane receptor (rhodopsin family)   2.7e−20   66.6       342   Hydrolase   haloacid dehalogenase-like hydrolase   7.9e−28   105.9       343   zf-C2H2   Zinc finger. C2H2 type   5.1e−35   129.8       345   SH3   SH3 domain   2.2e−14   61.2       349   Ribosomal_L35Ae   Ribosomal protein L35Ae     6e−77   269.0       350   SET   SET domain   1.1e−56   201.7       358   Oxysterol_BP   Oxysterol-binding protein   3.4e−95   329.7       369   PCMT   Protein-L-isoaspartate(D-aspartate) O-methyl     5e−10   1.8       370   PH   PH domain   9.6e−05   22.0       371   bZIP   bZIP transcription factor   3.2e−07   30.8       373   GDI   GDP dissociation inhibitor   7.4e−25   64.8       374   zf-C2H2   Zinc finger, C2H2 type   7.1e−78   272.1       375   ubiquitin   Ubiquitin family   3.7e−61   193.6       377   efhand   EF hand   1.5e−37   138.2       381   Troponin   Troponin   4.7e−42   153.1       382   Troponin   Troponin   4.7e−42   153.1       383   Troponin   Troponin   4.7e−42   153.1       384   rrm   RNA recognition motif.   7.5e−51   182.4       387   UBX   UBX domain   1.5e−25   98.3       388   G-patch   G-patch domain   4.4e−10   46.9       391   pkinase   Eukaryotic protein kinase domain   1.2e−110   381.1       393   EGF   EGF-like domain   3.6e−82   286.4       394   EGF   EGF-like domain   3.6e−82   286.4       398   PGAM   Phosphoglycerate mutase family   6.1e−07   29.2       402   zf-C2H2   Zinc finger, C2H2 type     4e−24   93.6       403   pkinase   Eukaryotic protein kinase domain   1.1e−101   351.3       404   Ribosomal_S17   Ribosomal protein S17     6e−43   148.6       406   Acylphosphatase   Acylphosphatase   8.5e−64   225.4       407   TPR   TPR Domain   1.2e−14   62.1       414   adenylatekinase   Adenylate kinase   1.9e−119   410.3       415   FAT   FAT domain   9.3e−192   650.4       416   FAT   FAT domain   9.3e−192   650.4       418   MMR_HSR1   GTPase of unknown function   0.00015   −32.8       419   Ribosomal_L14e   Ribosomal protein L14   3.4e−34   127.0       421   zf-C2H2   Zinc finger, C2H2 type   5.2e−99   342.3       423   Peptidase_M16   Insulinase (Peptidase family M16)   4.3e−42   153.3       426   fibrinogen_C   Fibrinogen beta and gamma chains, C-term   2.4e−68   238.3       432   DNase_I   Deoxyribonuclease I (DNase I)   1.2e−171   583.6       433   IL8   Small cytokines (intecrine/chemokine), inter   2.3e−33   115.6       437   TPR   TPR Domain   4.4e−08   40.3       440   PDZ   PDZ domain (Also known as DHR or GLGF)   0.038   15.1       445   zf-C2H2   Zinc finger, C2H2 type   2.7e−22   87.5       446   zf-C2H2   Zinc finger, C2H2 type   4.1e−23   90.2       447   rrm   RNA recognition motif.   0.0029   24.3       449   ank   Ank repeat   4.1e−31   116.8       451   Cyt_reductase   FAD/NAD-binding Cytochrome reductase   7.7e−61   215.5       455   Ribosomal_L18p   Ribosomal L18p/L5e family   0.084   −34.1       456   tubulin   Tubulin/FtsZ family   3.4e−283   954.2       457   laminin_G   Laminin G domain   1.1e−51   185.1       458   ig   Immunoglobulin domain   2.7e−23   80.1       459   Peptidase_M1   Peptidase family M1   6.4e−184   533.4       462   pou   Pou domain - N-terminal to homeobox   1.3e−48   175.0               domain       466   TPR   TPR Domain   2.4e−30   114.2       469   Ribosomal_L11   Ribosomal protein L11   7.3e−53   189.0       470   Ribosomal_L11   Ribosomal protein L11     7e−40   145.9       473   ENV_polyprotein   ENV polyprotein (coat polyprotein)   1.5e−37   129.4       476   aconitase   Aconitase family (aconitate hydratase)     2e−189   621.7       477   globin   Globin   5.5e−44   157.8       480   lectin_c   Lectin C-type domain   1.5e−21   85.0       482   EGF   EGF-like domain     1e−22   88.9       487   PP2C   Protein phosphatase 2C   1.1e−13   51.7       489   ig   Immunoglobulin domain   1.8e−20   71.0       490   7tm_1   7 transmembrane receptor (rhodopsin family)   3.1e−13   44.2                    
     [0449]                                                       TABLE 5                       SEQ ID   PDB   Chain                                       NO:   ID   ID   Start AA   End AA   PSI BLAST   Verify Score   PMF Score   SeqFold Score   Compound   PDB Annotation                                                                            252   1mkp       201   344   3e−40           205.21   PYST1; CHAIN: NULL;   HYDROLASE DUAL SPECIFICITY                                               PHOSPHATASE, MAP KINASE                                               HYDROLASE       262   1b2w   L   43   241   8.5e−66           67.25   ANTIBODY (LIGHT CHAIN);   IMMUNE SYSTEM                                           CHAIN: L; ANTIBODY (HEAVY   IMMUNOGLOBULIN;                                           CHAIN); CHAIN: H;   IMMUNOGLOBULIN ANTIBODY                                               ENGINEERING, HUMANIZED AND                                               CHIMERIC ANTIBODY, FAB, 2 X-RAY                                               STRUCTURE, THREE-DIMENSIONAL                                               STRYCTURE, GAMMA-3                                               INTERFERON, IMMUNE SYSTEM       262   1b6d   A   43   238   3.4e−65           68.72   IMMUNOGLOBULIN; CHAIN: A, B;   IMMUNOGLOBULIN                                               IMMUNOGLOBULIN, KAPPA LIGHT-                                               CHAIN DIMER HEADER       262   1bjl   L   43   240   6.8e−67           71.40   FAB FRAGMENT; CHAIN: L, H, J,   COMPLEX (ANTIBODY/ANTIGEN)                                           K; VASCULAR ENDOTHELIAL   FAB-12; VEGF; COMPLEX                                           GROWTH FACTOR; CHAIN: V, W;   (ANTIBODY/ANTIGEN), ANGIOGENIC                                               FACTOR       262   1bog   A   43   241   6.8e−61           67.70   ANTIBODY (CB 4-1); CHAIN: A, B;   COMPLEX (ANTIBODY/PEPTIDE)                                           PEPTIDE; CHAIN: C;   POLYSPECIFICITY, CROSS                                               REACTIVITY, FAB-FRAGMENT,                                               PEPTIDE, 2 HIV-1, COMPLEX                                               (ANTIBODY/PEPTIDE)       262   1bz7   A   43   232   8.5e−60           69.74   ANTIBODY R24 (LIGHT CHAIN);   IMMUNE SYSTEM ANTIBODY (FAB                                           CHAIN: A; ANTIBODY R24   FRAGMENT), IMMUNE SYSTEM                                           (HEAVY CHAIN); CHAIN: B;       262   1cel   L   43   238   5.1e−65           68.83   CAMPATH-1H: LIGHT CHAIN;   ANTIBODY THERAPEUTIC,                                           CHAIN: L; CAMPATH-1H: HEAVY   ANTIBODY, CD52                                           CHAIN; CHAIN: H; PEPTIDE                                           ANTIGEN; CHAIN: P;       262   1dfb   L   43   241   8.5e−66           69.59   IMMUNOGLOBULIN 3D6 FAB                                           1DFB 3       262   1fvd   A   43   241   6.8e−66           72.66   IMMUNOGLOBULIN FAB                                           FRAGMENT OF HUMANIZED                                           ANTIBODY 4D5, VERSION 4 1FVD 3       262   1gcl   L   43   238   1.2e−62           71.86   ENVELOPE PROTEIN GP120;   COMPLEX (HIV ENVELOPE                                           CHAIN: G; CD4; CHAIN: C;   PROTEIN/CD4/FAB) COMPLEX (HIV                                           ANTIBODY 17B; CHAIN: L, H;   ENVELOPE PROTEIN/CD4/FAB), HIV-1                                               EXTERIOR 2 ENVELOPE GPI20. T-                                               CELL SURFACE GLYCOPROTEIN                                               CD4. 3 ANTIGEN-BINDING                                               FRAGMENT OF HUMAN                                               IMMUNOGLOBULIN 17B, 4                                               GLYCOSYLATED PROTEIN       262   1itb   B   149   429   12e−22           67.34   INTERLEUKIN-I BETA; CHAIN: A;   COMPLEX                                           TYPE I INTERLEUKIN-I   (IMMUNOGLOBULIN/RECEPTOR)                                           RECEPTOR; CHAIN: B;   IMMUNOGLOBULIN FOLD,                                               TRANSMEMBRANE, GLYCOPROTEIN,                                               RECEPTOR, 2 SIGNAL, COMPLEX                                               (IMMUNOGLOBULIN/RECEPTOR)       262   1mco   H   29   427   3.4e−68           93.46   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN G1 (IGGI)                                           (MCG) WITH A HINGE DELETION                                           IMCO 3       262   1osp   L   43   241   1.7e−59           69.80   FAB 184.1; CHAIN: L, H; OUTER   COMPLEX                                           SURFACE PROTEIN A; CHAIN: O;   (IMMUNOGLOBULIN/LIPOPROTEIN)                                               OSPA; COMPLEX                                               (IMMUNOGLOBULIN/LIPOPROTEIN),                                               OUTER SURFACE 2 PROTEIN A                                               COMPLEXED WITH FAB184.1,                                               BORRELIA BURGDORFERI 3 STRAIN                                               B31       262   1wio   A   49   408   9e−17           75.16   T-CELL SURFACE   GLYCOPROTEIN CD4;                                           GLYCOPROTEIN CD4; CHAIN: A,   IMMUNOGLOBULIN FOLD,                                           B;   TRANSMEMBRANE, GLYCOPROTEIN,                                               T-CELL, 2 MHC LIPOPROTEIN,                                               POLYMORPHISM       262   2fgw   L   43   241   1.2e−67           67.57   IMMUNOGLOBULIN FAB                                           FRAGMENT OF A HUMANIZED                                           VERSION OF THE ANTI-CD18                                           2FGW 3 ANTIBODY ‘H52’ (HUH52-                                           OZ FAB) 2FGW 4       262   6fab   L   43   241   5.1e−63           68.83   IMMUNOGLOBULIN ANTIGEN-                                           BINDING FRAGMENT OF THE                                           MURINE ANTI-                                           PHENYLARSONATE 6FAB 3                                           ANTIBODY 36-71, FAB 36-71 6FAB4               263   1mhu       32   62   1.4e−17           67.02   METALLOTHIONEIN CD-7                                           METALLOTHIONEIN-2 (ALPHA                                           DOMAIN) (/NMR$) 1MHUA 2       263   4mt2       1   62   1.7e−08           126.36   METALLOTHIONEIN                                           METALLOTHIONEIN ISOFORM II                                           4MT2 3               264   1ax4   A   190   616   5.1e−l0           76.11   TRYPTOPHANASE; CHAIN: A, B,   TRYPTOPHAN BIOSYNTHESIS                                           C, D;   TRYPTOPHAN INDOLE-LYASE;                                               TRYPTOPHAN BIOSYNTHESIS,                                               TRYPTOPHAN INDOLE-LYASE,                                               PYRIDOXAL 2 5′-PHOSPHATE,                                               MONOVALENT CATION BINDING                                               SITE       264   1bjw   A   212   590   5.1e−58           85.17   ASPARTATE   AMINOTRANSFERASE                                           AMINOTRANSFERASE; CHAIN: A,   AMINOTRANSFERASE, PYRIDOXAL                                           B;   ENZYME       264   1bs0   A   203   593   3.4e−72           224.70   8-AMINO-7-OXONANOATE   TRANSFERASE AONS, 8-AMINO-7-                                           SYNTHASE; CHAIN: A;   KETOPELARGONATE SYNTHASE;                                               PLP-DEPENDENT ACYL-COA                                               SYNTHASE, BIOTIN BIOSYNTHESIS,                                               8-2 AMINO-7-OXONANOATE                                               SYNTHASE, 8-AMINO-7-                                               KETOPELARGONATE 3 SYNTHASE,                                               TRANSFERASE       264   1csl   A   242   640   3.4e−45           79.69   CYSTATHIONINE GAMMA-   LYASE CGS; LYASE, LLP-                                           SYNTHASE; CHAIN: A, B, C, D;   DEPENDENT ENZYMES,                                               METHIONINE BIOSYNTHESIS       264   1d7u   A   213   597   1.7e−46           78.45   2,2-DIALKYLGLYCINE   LYASE DGD; ENZYME COMPLEXES,                                           DECARBOXYLASE (PYRUVATE);   CATALYTIC MECHANISM,                                           CHAIN: A;   DECARBOXYLATION 2 INHIBITOR,                                               LYASE       264   1qgn   A   215   635   6e−67           88.98   CYSTATHIONINE GAMMA-   LYASE METHIONINE BIOSYNTHESIS,                                           SYNTHASE; CHAIN: A, B, C, D, E,   PYRIDOXAL 5′-PHOSPHATE,                                           F, G, H;   GAMMA-2 FAMILY, LYASE       264   1tpl   A   209   612   5.1e−06           86.06   LYASE(CARBON-CARBON)                                           TYROSINE PHENOL-LYASE                                           (E.C.4.1.99.2) ITPL 3       264   2gsa   A   170   593   1.4e−72           95.88   GLUTAMATE SEMIALDEHYDE   CHLOROPHYLL BIOSYNTHESIS                                           AMINOTRANSFERASE; CHAIN: A,   GLUTAMATE SEMIALDEHYDE                                           B;   AMINOMUTASE; CHLOROPHYLL                                               BIOSYNTHESIS, PYRIDOXAL-5′-                                               PHOSPHATE, 2 PYRIDOXAMINE-5′-                                               PHOSPHATE, ASYMMETRIC DIMER               266   1sur       226   454   3e−31           66.05   PAPS REDUCTASE; CHAIN: NULL;   OXIDOREDUCTASE                                               PHOSPHOADENOSINE                                               PHOSPHOSULFATE REDUCTASE;                                               ASSIMILATORY SULFATE                                               REDUCTION, 3-PHOSPHO-                                               ADENYLYL-SULFATE 2 REDUCTASE,                                               OXIDOREDUCTASE               271   1gri   A   7   231   5.1e−22           57.45   GROWTH FACTOR BOUND   SIGNAL TRANSDUCTION ADAPTOR                                           PROTEIN 2; 1GRI 5 CHAIN: A, B;   SH2, SH3 1GRI 14                                           IGRI 6       272   1gri   A   7   231   5.1e−22           57.45   GROWTH FACTOR BOUND   SIGNAL TRANSDUCTION ADAPTOR                                           PROTEIN 2; 1GRI 5 CHAIN: A, B;   SH2, SH3 1GRI 14                                           IGRI 6               273   1be3   H   22   85   7.5e−26           95.55   CYTOCHROME BCI COMPLEX;   ELECTRON TRANSPORT UBIQUINOL                                           CHAIN: A, B, C, D, E, F, G, H, I, J, K;   CYTOCHROMEC                                               OXIDOREDUCTASE, COMPLEX                                               ELECTRON TRANSPORT,                                               CYTOCHROME, MEMBRANE                                               PROTEIN               276   1dt4   A   258   304   1.5e−09   −0.52   0.07       NEURO-ONCOLOGICAL   IMMUNE SYSTEM KH DOMAIN,                                           VENTRAL ANTIGEN I; CHAIN: A;   ALPHA-BETA FOLD, RNA-BINDING                                               MOTIF       276   1dtj   C   258   298   3e−06   −0.27   0.75       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       276   1dtj   D   258   298   3e−06   −0.30   0.93       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL,   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       276   1vig       258   296   1.3e−06   −0.20   0.82       VIGILIN; 1VIG 5 CHAIN: NULL;   RIBONUCLEOPROTEIN RNA-                                           1VIG 6   BINDING PROTEIN 1VIG 19       276   2fmr       188   252   3.4e−31   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       276   2fmr       188   252   6e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDlNG PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       276   2fmr       188   252   6e−32           96.30   FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       276   1dt4   A   258   304   1.5e−09   −0.52   0.07       NEURO-ONCOLOGICAL   IMMUNE SYSTEM KH DOMAIN,                                           VENTRAL ANTIGEN I; CHAIN: A;   ALPHA-BETA FOLD, RNA-BINDING                                               MOTIF       276   1dtj   C   258   298   3e−06   −0.27   0.75       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       276   1dtj   D   258   298   3e−06   −0.30   0.93       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       276   1vig       258   296   1.3e−06   −0.20   0.82       VIGILIN; IVIG 5 CHAIN: NULL;   RIBONUCLEOPROTEIN RNA-                                           IVIG 6   BINDING PROTEIN IVIG 19       276   2fmr       188   252   6e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       276   2fmr       188   252   6e−32           96.99   FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       276   2fmr       188   252   8.5e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR               277   1dt4   A   258   304   1.5e−09   −0.52   0.07       NEURO-ONCOLOGICAL   IMMUNE SYSTEM KH DOMAIN,                                           VENTRAL ANTIGEN 1; CHAIN: A;   ALPHA-BETA FOLD, RNA-BINDING                                               MOTIF       277   1dtj   C   258   298   3e−06   −0.27   0.75       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       277   1dtj   D   258   298   3e−06   −0.30   0.93       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       277   1vig       258   296   1.3e−06   −0.20   0.82       VIGILIN; IVIG 5 CHAIN: NULL;   RIBONUCLEOPROTEIN RNA-                                           IVIG 6   BINDING PROTEIN IVIG 19       277   2fmr       188   252   3.4e−31   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       277   2fmr       188   252   6e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       277   2fmr       188   252   6e−32           96.30   FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       277   1dt4   A   258   304   1.5e−09   −0.52   0.07       NEURO-ONCOLOGICAL   IMMUNE SYSTEM KH DOMAIN,                                           VENTRAL ANTIGEN I; CHAIN: A;   ALPHA-BETA FOLD, RNA-BINDING                                               MOTIF       277   1dtj   C   258   298   3e−06   −0.27   0.75       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       277   1dtj   D   258   298   3e−06   −0.30   0.93       RNA-BINDING   IMMUNE SYSTEM KH DOMAIN,                                           NEUROONCOLOGICAL VENTRAL   ALPHA-BETA FOLD RNA-BINDING                                           ANTIGEN 2; CHAIN: A, B, C, D;   MOTIF       277   1vig       258   296   1.3e−06   −0.20   0.82       VIGILIN; IVIG 5 CHAIN: NULL;   RIBONUCLEOPROTEIN RNA-                                           IVIG 6   BINDING PROTEIN IVIG 19       277   2fmr       188   252   6e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       277   2fmr       188   252   6e−32           96.99   FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; EMRI,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR       277   2fmr       188   252   8.5e−32   0.53   1.00       FMR1 PROTEIN; CHAIN: NULL;   RNA-BINDING PROTEIN KH1; FMR1,                                               FRAGILE X, MODULAR PROTEINS,                                               RNA-BINDING PROTEIN, NMR               278   1zbd   A   35   239   6.8e−56   −0.01   0.01       RAB-3A; CHAIN: A; RABPHILIN-   COMPLEX (GTP-BINDING/EFFECTOR)                                           3A; CHAIN: B;   RAS-RELATED PROTEIN RAB3A;                                               COMPLEX (GTP-                                               BINDING/EFFECTOR), G PROTEIN,                                               EFFECTOR, RABCDR, 2 SYNAPTIC                                               EXOCYTOSIS, RAB PROTEIN, RAB3A,                                               RARPHILIN       278   3rab   A   37   236   3.4e−56   0.14   −0.07       RAB3A; CHAIN: A;   HYDROLASE G PROTEIN,                                               VESICULAR TRAFFICKING, GTP                                               HYDROLYSIS, RAB 2 PROTEIN,                                               NEUROTRANSMITTER RELEASE,                                               HYDROLASE               280   1a88   A   225   450   5.1e−20   −0.05   0.03       CHLOROPEROXIDASEL; CHAIN:   HALOPEROXIDASE                                           A, B, C;   BROMOPEROXIDASE L,                                               HALOPEROXIDASE L;                                               HALOPEROXIDASE,                                               OXIDOREDUCTASE       280   1azw   A   225   449   1e−21   0.15   −0.13       PROLINE IMINOPEPTIDASE;   AMINOPEPTIDASE                                           CHAIN: A, B;   AMINOPEPTIDASE, PROLINE                                               IMINOPEPTIDASE, SERINE                                               PROTEASE, 2 XANTHOMONAS                                               CAMPESTRIS       280   1brt       239   451   1.7e−20   0.07   0.22       BROMOPEROXIDASE, A2: CHAIN:   HALOPEROXIDASE                                           NULL;   HALOPEROXIDASE A2,                                               CHLOROPEROXIDASE A2;                                               HALOPEROXIDASE,                                               OXIDOREDUCTASE, PEROXIDASE,                                               ALPHA/BETA 2 HYDROLASE FOLD,                                               MUTANT M99T       280   1cqw   A   233   378   5.1e−21   0.22   −0.18       HALOALKANE DEHALOGENASE;   HYDROLASE A/B HYDROLASE FOLD,                                           I-CHLOROHEXANE CHAIN: A;   DEHALOGENASE I-S BOND       280   1chy   A   235   447   1.7e−21   0.07   −0.17       SOLUBLE EPOXIDE HYDROLASE;   HYDROLASE HYDROLASE,                                           CHAIN: A, B, C, D;   ALPHA/BETA HYDROLASE FOLD,                                               EPOXIDE DEGRADATION, 2                                               EPICHLOROHYDRIN       280   1ekl   B   220   394   1.7e−22   0.07   −0.08       EPOXIDE HYDROLASE; CHAIN: A,   HYDROLASE HOMODIMER,                                           B;   ALPHA/BETA HYDROLASE FOLD,                                               DISUBSTITUTED UREA 2 INHIBITOR       280   1evq   A   232   438   1.7e−20   0.34   0.24       SERINE HYDROLASE; CHAIN: A;   HYDROLASE ALPHA/BETA                                               HYDROLASE FOLD       280   1qfm   A   157   453   8.5e−33   −0.05   0.01       PROLYL OLIGOPEPTIDASE;   HYDROLASE PROLYL                                           CHAIN: A;   ENDOPEPTIDASE, POST-PROLINE                                               CLEAVING PROLYL                                               OLIGOPEPTIDASE, AMNESIA,                                               ALPHA/BETA-HYDROLASE, BETA-2                                               PROPELLER               281   1fxx   A   134   302   6.8e−27   −0.08   0.23       EXONUCLEASE I; CHAIN: A;   HYDROLASE                                               EXODEOXYRIBONUCLEASE I;                                               ALPHA-BETA DOMAIN, SH3-LIKE                                               DOMAIN, DNAQ SUPERFAMILY               282   1a44       48   232   3e−83   1.02   1.00       PHOSPHATIDYLETHANOLAMINE-   LIPID-BINDING PROTEIN PEBP.PBP                                           BINDING PROTEIN; CHAIN:   LIPID-BINDING                                           NULL;       282   1a44       48   232   3e−83           317.69   PHOSPHATIDYLETHANOLAMINE-   LIPID-BINDING PROTEIN PEBP, PBP                                           BINDING PROTEIN; CHAIN:   LIPID-BINDING                                           NULL;       282   1a44       48   232   6.8e−80   1.02   1.00       PHOSPHATIDYLETHANOLAMINE-   LIPID-BINDING PROTEIN PEBP, PBP                                           BINDING PROTEIN; CHAIN:   LIPID-BINDING                                           NULL;       282   1beh   A   49   232   6e−82   1.05   1.00       PHOSPHATIDYLETHANOLAMINE   LIPID-BINDING LIPID-BINDING,                                           BINDING PROTEIN; CHAIN: A, B;   SIGNALLING       282   1beh   A   49   232   6e−82           324.00   PHOSPHATIDYLETHANOLAMINE   LIPID-BINDING LIPID-BINDING,                                           BINDING PROTEIN; CHAIN: A, B;   SIGNALLING       282   1beh   A   49   232   8.5e−80   1.05   1.00       PHOSPHATIDYLETHANOLAMINE   LIPID-BINDING LIPID-BINDING,                                           BINDING PROTEIN; CHAIN: A, B;   SIGNALLING               283   1dga   A   8   376   0   0.95   1.00       ACTIN; CHAIN: A; GELSOLIN;   CONTRACTILE PROTEIN ACTIN,                                           CHAIN: G;   GELSOLIN, CYTOSKELETON                                               ORGANIZATION, ACTIN-2                                               ASSOCIATED PROTEIN       283   1esv   A   10   376   0   0.87   1.00       GELSOLIN; CHAIN: S; ALPHA   CONTRACTILE PROTEIN                                           ACTIN; CHAIN: A   LATRUNCULIN A, GELSOLIN, ACTIN,                                               DEPOLYMERISATION, 2                                               SEQUESTRATION       283   1yag   A   8   376   0   0.99   1.00       ACTIN; CHAIN: A; GELSOLIN;   CONTRACTILE PROTEIN ACTIN-                                           CHAIN: G;   DEPOLYMERIZING FACTOR (ADF);                                               COMPLEX, ACTIN, GELSOLIN,                                               CONTRACTILE PROTEIN       283   1yag   A   8   376   0           413.68   ACTIN; CHAIN: A; GELSOLIN;   CONTRACTILE PROTEIN ACTIN-                                           CHAIN: G;   DEPOLYMERIZING FACTOR (ADF);                                               COMPLEX, ACTIN, GELSOLIN,                                               CONTRACTILE PROTEIN       283   2btf   A   7   376   0   0.91   1.00       ACETYLATION AND ACTIN-                                           BINDING BETA-ACTIN-PROFILIN                                           COMPLEX 2BTF 3       283   2btf   A   9   376   0           414.62   ACETYLATION AND ACTIN-                                           BINDING BETA-ACTIN-PROFILIN                                           COMPLEX 2BTF 3               284   1tub   A   1   461   0           285.64   TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX       284   1tub   A   1   462   0   0.09   1.00       TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX       284   1tub   B   1   459   0   0.11   1.00       TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX       284   1tub   B   1   459   0           307.13   TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX               285   1a7i       384   437   3e−14   0.43   0.58       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1a7i       384   441   6.8e−10   0.31   0.80       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1a7i       443   500   1.5e−16   0.08   0.58       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1a7i       443   501   1.4e−12   −0.13   0.82       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1a7i       504   566   4.5e−11   −0.40   0.24       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1a7i       504   571   1.2e−09   0.38   0.76       QCRP2 (LIM1); CHAIN: NULL;   LIM DOMAIN CONTAINING                                               PROTEINS LIM DOMAIN                                               CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN, ZINC 2 FINGER       285   1b8t   A   375   572   1.4e−23           71.26   CRP1; CHAIN: A;   CONTRACTILE LIM DOMAIN, CRP,                                               NMR, MUSCLE DIFFERENTIATION,                                               CONTRACTILE       285   1b8t   A   379   510   1.4e−23   0.01   −0.17       CRP1; CHAIN: A;   CONTRACTILE LIM DOMAIN, CRP,                                               NMR, MUSCLE DIFFERENTIATION,                                               CONTRACTILE       285   1ctl       376   437   1.7e−12   −0.22   0.10       AVIAN CYSTEINE RICH PROTEIN;   METAL-BINDING PROTEIN LIM                                           1CTL 3   DOMAIN CONTAINING PROTEINS                                               1CTL 15       285   1ctl       444   510   3.4e−15   −0.26   0.05       AVIAN CYSTEINE RICH PROTEIN;   METAL-BINDING PROTEIN LIM                                           1CTL 3   DOMAIN CONTAINING PROTEINS                                               1CTL 15       285   1ctl       504   571   5.1e−13   0.03   0.22       AVIAN CYSTEINE RICH PROTEIN;   METAL-BINDING PROTEIN LIM                                           1CTL 3   DOMAIN CONTAINING PROTEINS                                               1CTL 15       285   1cxx   A   381   437   1.7e−11   −0.17   0.41       CYSTEINE AND GLYCINE-RICH   SIGNALING PROTEIN LIM DOMAIN                                           PROTEIN CRP2; CHAIN: A;   CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN       285   1cxx   A   443   496   5.1e−13   0.38   0.53       CYSTEINE AND GLYCINE-RICH   SIGNALING PROTEIN LIM DOMAIN                                           PROTEIN CRP2; CHAIN: A;   CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN       285   1cxx   A   501   568   3.4e−12   0.41   0.87       CYSTEINE AND GLYCINE-RICH   SIGNALING PROTEIN LIM DOMAIN                                           PROTEIN CRP2; CHAIN: A;   CONTAINING PROTEINS, METAL-                                               BINDING PROTEIN       285   1iml       382   440   1.4e−10   −0.25   0.41       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1iml       384   451   4.5e−17   0.21   0.22       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1iml       443   510   1.4e−15   −0.13   0.09       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1iml       443   513   3e−20   0.13   0.12       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1iml       502   569   1.5e−12   0.32   0.93       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1iml       502   571   3.4e−11   0.28   0.99       CYSTEINE RICH INTESTINAL   METAL-BINDING PROTEIN CRIP;                                           PROTEIN; CHAIN: NULL;   METAL-BINDING PROTEIN, LIM                                               DOMAIN PROTEIN       285   1zfo       381   410   1.4e−06   −0.13   0.29       LASP-1; CHAIN: NULL;   METAL-BINDING PROTEIN LIM                                               DOMAIN, ZINC-FINGER, METAL-                                               BINDING PROTEIN       285   1zfo       502   535   0.0012   −0.34   0.15       LASP-1; CHAIN: NULL;   METAL-BINDING PROTEIN LIM                                               DOMAIN, ZINC-FINGER, METAL-                                               BINDING PROTEIN               288   1ffk   G   5   114   9e−49   −0.14   1.00       23S RRNA; CHAIN: 0; 5S RRNA;   RIBOSOME 50S RIBOSOMAL                                           CHAIN: 9; RIBOSOMAL PROTEIN   PROTEIN L2P, HMAL2, HL4; 50S                                           L2; CHAIN: A; RIBOSOMAL   RIBOSOMAL PROTEIN L3P, HMAL3,                                           PROTEIN L3; CHAIN: B;   HL1; 50S RIBOSOMAL PROTEIN L4E,                                           RIBOSOMAL PROTEIN L4; CHAIN:   HMAL4, HL6; 50S RIBOSOMAL                                           C; RIBOSOMAL PROTEIN L5;   PROTEIN L5P, HMAL5, HL13; 30S                                           CHAIN: D; RIBOSOMAL PROTEIN   RIBOSOMAL PROTEIN HS6; 50S                                           L7AE; CHAIN: E; RIBOSOMAL   RIBOSOMAL PROTEIN L13P, HMAL13;                                           PROTEIN L10E; CHAIN: F;   50S RIBOSOMAL PROTEIN L14P,                                           RIBOSOMAL PROTEIN L13;   HMAL14, HL27; 50S RIBOSOMAL                                           CHAIN: G; RIBOSOMAL PROTEIN   PROTEIN L15P, HMAL15, HL9; 50S                                           L14; CHAIN: H; RIBOSOMAL   RIBOSOMAL PROTEIN L18P, HMAL18,                                           PROTEIN L15E; CHAIN: I;   HL12; 50S RIBOSOMAL PROTEIN                                           RIBOSOMAL PROTEIN L15;   L18E, HL29, L19; 50S RIBOSOMAL                                           CHAIN: J; RIBOSOMAL PROTEIN   PROTEIN L19E, HMAL19, HL24; 50S                                           L18; CHAIN: K; RIBOSOMAL   RIBOSOMAL PROTEIN L21E, HL31;                                           PROTEIN L18E; CHAIN: L;   50S RIBOSOMAL PROTEIN L22P,                                           RIBOSOMAL PROTEIN L19;   HMAL22, HL23; 50S RIBOSOMAL                                           CHAIN: M; RIBOSOMAL PROTEIN   PROTEIN L23P, HMAL23, HL25, L21;                                           L21E; CHAIN: N; RIBOSOMAL   50S RIBOSOMAL PROTEIN L24P,                                           PROTEIN L22; CHAIN: O;   HMAL24, HL16, HL15; 50S                                           RIBOSOMAL PROTEIN L23;   RIBOSOMAL PROTEIN L24E,                                           CHAIN: P; RIBOSOMAL PROTEIN   HL21/HL22; 50S RIBOSOMAL                                           L24; CHAIN: Q; RIBOSOMAL   PROTEIN L29P, HMAL29, HL33; 50S                                           PROTEIN L24E; CHAIN: R;   RIBOSOMAL PROTEIN L30P, HMAL30,                                           RIBOSOMAL PROTEIN L29;   HL20, HL16; 50S RIBOSOMAL                                           CHAIN: S; RIBOSOMAL PROTEIN   PROTEIN L31E, L34, HL30; 50S                                           L30; CHAIN: T; RIBOSOMAL   RIBOSOMAL PROTEIN L32E, HL5; 50S                                           PROTEIN L31E; CHAIN: U;   RIBOSOMAL PROTEIN L37E, L35E;                                           RIBOSOMAL PROTEIN L32E;   50S RIBOSOMAL PROTEINS L39E,                                           CHAIN: V; RIBOSOMAL PROTEIN   HL39E, HL46E; 50S RIBOSOMAL                                           L37AE; CHAIN: W; RIBOSOMAL   PROTEIN L44E, LA, HLA; 50S                                           PROTEIN L37E; CHAIN: X;   RIBOSOMAL PROTEIN L6P, HMAL6,                                           RIBOSOMAL PROTEIN L39E;   HL10 RIBOSOME ASSEMBLY, RNA-                                           CHAIN: Y; RIBOSOMAL PROTEIN   RNA, PROTEIN-RNA, PROTEIN-                                           L44E; CHAIN: Z; RIBOSOMAL   PROTEIN                                           PROTEIN L6; CHAIN: 1;       288   1ffk   G   7   135   5.1e−32   0.18   1.00       23S RRNA; CHAIN: 0; 5S RRNA;   RIBOSOME 50S RIBOSOMAL                                           CHAIN: 9; RIBOSOMAL PROTEIN   PROTEIN L2P, HMAL2, HL4; 50S                                           L2; CHAIN: A; RIBOSOMAL   RIBOSOMAL PROTEIN L3P, HMAL3,                                           PROTEIN L3; CHAIN: B;   HL1; 50S RIBOSOMAL PROTEIN L4E,                                           RIBOSOMAL PROTEIN L4; CHAIN:   HMAL4, HL6; 50S RIBOSOMAL                                           C; RIBOSOMAL PROTEIN L5;   PROTEIN L5P, HMAL5, HL13; 30S                                           CHAIN: D; RIBOSOMAL PROTEIN   RIBOSOMAL PROTEIN HS6; 50S                                           L7AE; CHAIN: E; RIBOSOMAL   RIBOSOMAL PROTEIN L13P, HMAL13;                                           PROTEIN L10E; CHAIN: F;   50S RIBOSOMAL PROTEIN L14P,                                           RIBOSOMAL PROTEIN L13;   HMAL14, HL27; 50S RIBOSOMAL                                           CHAIN: G; RIBOSOMAL PROTEIN   PROTEIN L15P, HMAL15, HL9; 50S                                           L14; CHAIN: H; RIBOSOMAL   RIBOSOMAL PROTEIN L18P, HMAL18,                                           PROTEIN L15E; CHAIN: I;   HL12; 50S RIBOSOMAL PROTEIN                                           RIBOSOMAL PROTEIN L15;   L18E, HL29, L19; 50S RIBOSOMAL                                           CHAIN: J; RIBOSOMAL PROTEIN   PROTEIN L19E, HMAL19, HL24; 50S                                           L18; CHAIN: K; RIBOSOMAL   RIBOSOMAL PROTEIN L21E, HL31;                                           PROTEIN L18E; CHAIN: L;   50S RIBOSOMAL PROTEIN L22P,                                           RIBOSOMAL PROTEIN L19;   HMAL22, HL23; 50S RIBOSOMAL                                           CHAIN: M; RIBOSOMAL PROTEIN   PROTEIN L23P, HMAL23, HL25, L21;                                           L21E; CHAIN: N; RIBOSOMAL   50S RIBOSOMAL PROTEIN L24P,                                           PROTEIN L22; CHAIN: O;   HMAL24, HL16, HL15; 50S                                           RIBOSOMAL PROTEIN L23;   RIBOSOMAL PROTEIN L24E,                                           CHAIN: P; RIBOSOMAL PROTEIN   HL21/HL22; 50S RIBOSOMAL                                           L24; CHAIN: Q; RIBOSOMAL   PROTEIN L29P, HMAL29, HL33; 50S                                           PROTEIN L24E; CHAIN: R;   RIBOSOMAL PROTEIN L30P, HMAL30,                                           RIBOSOMAL PROTEIN L29;   HL20, HL16; 50S RIBOSOMAL                                           CHAIN: S; RIBOSOMAL PROTEIN   PROTEIN L31E, L34, HL30; 50S                                           L30; CHAIN: T; RIBOSOMAL   RIBOSOMAL PROTEIN L32E, HL5; 50S                                           PROTEIN L31E; CHAIN: U;   RIBOSOMAL PROTEIN L37E, L35E;                                           RIBOSOMAL PROTEIN L32E;   50S RIBOSOMAL PROTEINS L39E,                                           CHAIN: V; RIBOSOMAL PROTEIN   HL39E, HL46E; 50S RIBOSOMAL                                           L37AE; CHAIN: W; RIBOSOMAL   PROTEIN L44E, LA, HLA; 50S                                           PROTEIN L37E; CHAIN: X;   RIBOSOMAL PROTEIN L6P, HMAL6,                                           RIBOSOMAL PROTEIN L39E;   HL10 RIBOSOME ASSEMBLY, RNA-                                           CHAIN: Y; RIBOSOMAL PROTEIN   RNA, PROTEIN-RNA, PROTEIN-                                           L44E; CHAIN: Z; RIBOSOMAL   PROTEIN                                           PROTEIN L6; CHAIN: I;               289   1alh   A   1023   1104   1.4e−40   0.06   0.98       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   1051   1132   9e−44   0.09   0.84       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   1611   1715   1.2e−39   0.04   0.46       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   1826   1906   1.7e−30   −0.47   0.45       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   1854   1934   6.8e−31   −0.10   0.05       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   559   639   5.1e−27   0.05   0.17       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   592   668   1.5e−29   0.15   0.11       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   911   992   6e−45   0.22   0.93       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   939   1020   3e−42   0.04   0.72       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   967   1047   4.5e−42   −0.00   0.78       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1alh   A   995   1075   9e−42   0.21   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       289   1mey   C   1022   1103   1.4e−39   0.28   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1050   1131   1.7e−41   0.34   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1078   1159   1.7e−43   0.35   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1106   1187   3.4e−45   0.16   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1134   1215   6.8e−47   −0.08   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1162   1243   5.1e−48   0.45   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1190   1271   1.7e−48   0.44   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1218   1299   1.4e−49   0.22   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1246   1327   1.4e−49   0.05   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1274   1355   3.4e−50   0.29   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1302   1383   3.4e−49   0.04   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1330   1411   1e−47   0.24   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1358   1439   8.5e−47   0.50   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1386   1467   1.7e−47   0.31   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1414   1495   1.2e−48   0.50   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1414   1496   1.4e−49           103.44   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1442   1523   1.4e−49   0.38   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1470   1551   1e−49   0.31   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1498   1579   1.7e−49   0.13   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1526   1607   3.4e−49   0.34   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1554   1635   1.7e−49   0.26   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1582   1663   1.7e−48   0.09   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1610   1686   1.7e−44   0.28   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1666   1742   8.5e−44   0.52   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1689   1770   5.1e−49   0.41   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1717   1798   1.4e−49   0.03   0.98       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1745   1822   3.4e−45   −0.22   0.12       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1825   1906   1e−49   −0.28   0.48       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1853   1934   1e−49   −0.20   0.78       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   1881   1938   1.7e−33   0.35   0.58       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   558   639   3.4e−44   −0.04   0.55       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   586   667   3.4e−46   −0.05   0.82       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   614   695   1.4e−47   0.23   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   642   723   8.5e−49   0.03   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   698   779   1e−49   0.11   0.98       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   726   807   6.8e−50   0.19   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   754   835   6.8e−50   0.05   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   782   863   1e−49   0.34   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   810   891   3.4e−49   0.32   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   838   935   3.4e−44   0.04   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   866   963   8.5e−41   0.03   0.98       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   910   991   3.4e−42   0.16   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   C   994   1075   1.4e−39   0.59   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1mey   G   908   935   1.5e−10   0.46   0.94       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       289   1tf6   A   1051   1196   1.2e−33   0.18   0.86       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1106   1272   1.7e−36           113.59   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1163   1308   1.7e−36   −0.10   0.86       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1275   1420   6.8e−37   0.07   0.99       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1387   1532   1.4e−36   0.39   0.90       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1443   1588   3.4e−37   0.20   0.76       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1555   1695   1.2e−33   −0.13   0.64       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   1667   1808   1e−33   −0.29   0.25       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   532   676   1.7e−30   0.04   0.17       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   643   788   3.4e−36   0.06   0.95       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   699   849   6.8e−38   −0.10   0.94       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   811   951   3.4e−30   0.05   0.87       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1tf6   A   867   1033   6.8e−31   −0.12   0.42       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       289   1ubd   C   1020   1131   1.5e−54   0.04   0.94       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1077   1187   1e−55   0.05   0.94       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1104   1244   3e−53   −0.46   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1160   1271   1.5e−52   0.00   0.72       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1198   1299   3.4e−34   0.18   0.58       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1216   1327   6e−52   0.06   0.89       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1226   1327   1.4e−34   0.30   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENI, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1245   1356   1.2e−52   0.33   0.99       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1272   1383   7.5e−50   0.01   0.78       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1328   1439   3e−50   0.26   0.86       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1384   1496   4.5e−52   0.11   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1469   1579   4.5e−55   0.03   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1506   1607   3.4e−34   0.09   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1524   1635   4.5e−49   −0.29   0.99       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1562   1663   1e−32   0.04   0.94       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1608   1714   6e−52   0.12   0.31       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1618   1714   3.4e−30   −0.01   0.49       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1636   1742   7.5e−51   −0.22   0.83       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1674   1770   6.8e−32   −0.19   0.90       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   1725   1822   1.7e−30   −0.13   0.12       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   540   639   6.8e−29   −0.21   0.06       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   561   667   1.5e−31   0.20   0.41       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   584   695   3e−42   −0.19   0.86       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   589   695   3.4e−32   −0.17   0.86       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   619   724   1.5e−47   0.04   0.51       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   640   752   1.2e−52   −0.15   0.77       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   650   751   1.2e−33   −0.06   0.92       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   668   779   7.5e−51   0.01   0.57       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   725   835   7.5e−53   −0.06   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   734   835   1e−33   0.22   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   790   891   8.5e−33   0.26   0.87       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   808   935   9e−53   0.00   0.95       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   818   935   1.2e−31   −0.14   0.92       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   864   991   9e−53   0.04   0.83       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   874   991   1.5e−27   −0.28   0.66       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   1ubd   C   964   1076   3e−53   0.10   0.99       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       289   2gli   A   1022   1188   3e−72   −0.09   0.96       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1106   1273   7.5e−71   0.05   0.89       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1190   1329   1.3e−67   0.30   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1254   1382   5.1e−34   0.12   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1302   1469   4.5e−67   0.04   0.86       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAlN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1386   1525   4.5e−67   0.19   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1414   1580   6e−71   −0.20   0.92       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FlNGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1498   1716   1.5e−66   −0.17   0.16       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1534   1662   1.7e−32   0.03   0.63       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1554   1744   4.5e−67   −0.17   0.59       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1590   1713   1.7e−30   −0.13   0.78       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1638   1768   4.5e−65   0.18   0.86       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   1646   1797   8.5e−33   0.00   0.62       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   558   694   3.4e−33   −0.28   0.62       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   587   725   1.5e−53   −0.31   0.19       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   614   781   1.5e−63   −0.20   0.49       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   622   753   1e−33   0.11   0.46       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   642   809   1.5e−68   0.01   0.96       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   670   837   3e−66   −0.19   0.84       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   726   893   6e−68   0.00   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   734   862   1.5e−33   0.06   0.82       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   790   934   1.7e−30   −0.04   0.40       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BlNDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   838   992   1.5e−69   −0.00   0.69       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   874   993   1.7e−26   −0.10   0.81       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   910   1077   4.5e−70   −0.01   0.96       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       289   2gli   A   938   1105   1.5e−69   0.03   0.87       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER (GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               291   1cic   B   20   66   1.5e−23   −0.58   0.06       IG HEAVY CHAIN V REGIONS;   IMMUNOGLOBULIN                                           CHAIN: A; IG HEAVY CHAIN V   IMMUNOGLOBULIN, FAB COMPLEX,                                           REGIONS; CHAIN: B; IG HEAVY   IDIOTOPE, ANTI-IDIOTOPE                                           CHAIN V REGIONS; CHAIN: C; IG                                           HEAVY CHAIN V REGIONS;                                           CHAIN: D;       291   1fsk   C   20   66   8.5e−22   −0.56   0.00       MAJOR POLLEN ALLERGEN BET   IMMUNE SYSTEM BET V I-A, BETVI                                           V I-A; CHAIN: A, D, G, J;   ALLERGEN; BV16 FAB-FRAGMENT,                                           IMMUNOGLOBULIN KAPPA   KAPPA MOPC21 CODING SEQUENCE;                                           LIGHT CHAIN; CHAIN: B, E, H, K;   HEAVY CHAIN OF THE                                           ANTIBODY HEAVY CHAIN FAB;   MONOCLONAL ANTIBODY MST2;                                           CHAIN: C, F, I, L;   BET V I, BV16 FAB FRAGMENT,                                               ANTIBODY ALLERGEN COMPLEX       291   1jhl   11   20   66   6.8e−22   −0.72   0.09       COMPLEX(ANTIBODY-ANTIGEN)                                           FV FRAGMENT (IGG1, KAPPA)                                           (LIGHT AND HEAVY VARIABLE                                           DOMAINS 1JHL 3 NON-                                           COVALENTLY ASSOCIATED) OF                                           MONOCLONAL ANTI-HEN EGG                                           1JHL 4 LYSOZYME ANTIBODY                                           DI1.15 COMPLEX WITH                                           PHEASANT EGG 1JHL 5                                           LYSOZYME 1JHL 6               292   1vsg   A   123   181   0.00075   0.36   0.09       GLYCOPROTEIN VARIANT                                           SURFACE GLYCOPROTEIN (N-                                           TERMINAL DOMAIN) 1VSG 3               295   1btk   A   30   118   6e−09   0.21   0.07       BRUTON&#39;S TYROSINE KINASE;   TRANSFERASE BRUTON&#39;S                                           CHAIN: A, B;   AGAMMAGLOBULINEMIA                                               TYROSINE KINASE, BTK;                                               TRANSFERASE, PH DOMAIN, BTK                                               MOTIF, ZINC BINDING, X-LINKED 2                                               AGAMMAGLOBULINEMIA,                                               TYROSINE-PROTEIN KINASE       295   1btn       30   110   1.3e−08   0.20   0.25       BETA-SPECTRIN; 1BTN 4 CHAIN:   SIGNAL TRANSDUCTION PROTEIN                                           NULL; 1BTN 5       295   1tb8   A   22   114   1.5e−18   0.62   0.92       DUAL ADAPTOR OF   SIGNALING PROTEIN DAPPI, PHISH,                                           PHOSPHOTYROSINE AND 3-   BAM32; PLECKSTRIN, 3-                                           CHAIN: A;   PHOSPHOINOSITIDES, INOSITOL                                               TETRAKISPHOSPHATE 2 SIGNAL                                               TRANSDUCTION PROTEIN, ADAPTOR                                               PROTEIN       295   1fgy   A   9   115   1.5e−14   0.48   0.77       GRP1; CHAIN: A;   SIGNALING PROTEIN ARFI GUANINE                                               NUCLEOTIDE EXCHANGE FACTOR                                               AND PH DOMAIN       295   1pls       1   115   1.5e−14   0.69   0.95       PHOSPHORYLATION                                           PLECKSTRIN (N-TERMINAL                                           PLECKSTRIN HOMOLOGY                                           DOMAIN) MUTANT 1PLS 3 WITH                                           LEU GLU (HIS)6 ADDED TO THE C                                           TERMINUS 1PLS 4 (INS(G105-                                           LEHHHHHH)) (NMR, 25                                           STRUCTURES) 1PLS 5       295   1pms       33   114   1.5e−11   0.13   0.01       SOS 1; CHAIN: NULL;   SIGNAL TRANSDUCTION SON OF                                               SEVENLESS; PLECKSTRIN, SON OF                                               SEVENLESS, SIGNAL                                               TRANSDUCTION       295   1qqg   A   33   204   3e−18   0.20   −0.14       INSULIN RECEPTOR SUBSTRATE   SIGNAL TRANSDUCTION IRS-1;                                           1; CHAIN: A, B;   BETA-SANDWHICH, SIGNAL                                               TRANSDUCTION               296   1qgq   A   296   467   4.5e−05   −0.21   0.13       SPORE COAT POLYSACCHARIDE   TRANSFERASE                                           BIOSYNTHESIS PROTEIN CHAIN:   GLYCOSYLTRANSFERASE                                           A;               297   1erj   A   106   437   1.7e−59   0.03   0.34       TRANSCRIPTIONAL REPRESSOR   TRANSCRIPTION INHIBITOR BETA-                                           TUP1; CHAIN: A, B, C;   PROPELLER       297   1erj   A   183   481   5.1e−58   0.24   −0.09       TRANSCRIPTIONAL REPRESSOR   TRANSCRIPTION INHIBITOR BETA-                                           TUP1; CHAIN: A, B, C;   PROPELLER       297   1erj   A   5   251   1.7e−47   −0.04   0.34       TRANSCRIPTIONAL REPRESSOR   TRANSCRIPTION INHIBITOR BETA-                                           TUP1; CHAIN: A, B, C;   PROPELLER       297   1erj   A   54   352   6.8e−50   0.21   0.95       TRANSCRIPTIONAL REPRESSOR   TRANSCRIPTION INHIBITOR BETA-                                           TUP1; CHAIN: A, B, C;   PROPELLER       297   1got   B   170   479   3.4e−56   0.24   −0.14       GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1, TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION       297   1got   B   2   252   3.4e−39   −0.24   0.16       GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1, TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION       297   1got   B   31   297   3.4e−44   0.33   0.98       GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1, TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION       297   1got   B   35   369   3.4e−66           59.96   GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1, TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION       297   1got   B   52   349   8.5e−51   0.12   0.96       GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1,TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION       297   1got   B   98   389   3.4e−66   0.28   0.77       GT-ALPHA/GI-ALPHA CHIMERA;   COMPLEX (GTP-                                           CHAIN: A; GT-BETA; CHAIN: B;   BINDING/TRANSDUCER) BETA1,                                           GT-GAMMA; CHAIN: G;   TRANSDUCIN BETA SUBUNIT;                                               GAMMA1, TRANSDUCIN GAMMA                                               SUBUNIT; COMPLEX (GTP-                                               BINDING/TRANSDUCER), G PROTEIN,                                               HETEROTRIMER 2 SIGNAL                                               TRANSDUCTION               298   1a4y   A   32   208   7.5e−12   0.44   0.58       RIBONUCLEASE INHIBITOR;   COMPLEX (INHIBITOR/NUCLEASE)                                           CHAIN: A, D; ANGIOGENIN;   COMPLEX (INHIBITOR/NUCLEASE),                                           CHAIN: B, E;   COMPLEX (RI-ANG), HYDROLASE 2                                               MOLECULAR RECOGNITION,                                               EPITOPE MAPPING, LEUCINE-RICH 3                                               REPEATS       298   1a4y   A   49   223   1.4e−10   0.05   0.98       RIBONUCLEASE INHIBITOR;   COMPLEX (INHIBITOR/NUCLEASE)                                           CHAIN: A, D; ANGIOGENIN;   COMPLEX (INHIBITOR/NUCLEASE),                                           CHAIN: B, E;   COMPLEX (RI-ANG), HYDROLASE 2                                               MOLECULAR RECOGNITION,                                               EPITOPE MAPPING, LEUCINE-RICH 3                                               REPEATS       298   1a9n   A   112   218   0.00051   0.18   0.40       U2 RNA HAIRPIN IV; CHAIN: Q, R;   COMPLEX (NUCLEAR PROTEIN/RNA)                                           U2 A′; CHAIN: A, C; U2 B″; CHAIN:   COMPLEX (NUCLEAR                                           B, D;,   PROTEIN/RNA), RNA,                                               SNRNP, RIBONUCLEOPROTEIN       298   1d0b   A   49   219   5.1e−13   0.22   0.64       INTERNALIN B; CHAIN: A;   CELL ADHESION LEUCINE RICH                                               REPEAT, CALCIUM BINDING, CELL                                               ADHESION       298   1dce   A   53   174   1.7e−07   0.02   0.05       RAB   TRANSFERASE CRYSTAL                                           GERANYLGERANYLTRANSFERA   STRUCTURE, RAB                                           SE ALPHA SUBUNIT; CHAIN: A, C;   GERANYLGERANYLTRANSFERASE,                                           RAB   2.0 A 2 RESOLUTION, N-                                           GERANYLGERANYLTRANSFERA   FORMYLMETHIONINE, ALPHA                                           SE BETA SUBUNIT; CHAIN: B, D;   SUBUNIT, BETA SUBUNIT       298   1ds9   A   113   216   1.2e−09   −0.06   0.04       OUTER ARM DYNEIN; CHAIN: A;   CONTRACTILE PROTEIN LEUCINE-                                               RICH REPEAT, BETA-BETA-ALPHA                                               CYLINDER, DYNEIN, 2                                               CHLAMYDOMONAS, FLAGELLA       298   1fol   A   124   210   1.7e−09   0.13   0.37       NUCLEAR RNA EXPORT FACTOR   RNA BINDING PROTEIN TAP (NFX1);                                           1; CHAIN: A, B;   RIBONUCLEOPROTEIN (RNP, RBD OR                                               RRM) AND LEUCINE-RICH-REPEAT 2                                               (LRR)       298   1fol   B   124   210   1.7e−09   0.06   0.13       NUCLEAR RNA EXPORT FACTOR   RNA BINDING PROTEIN TAP (NFX1);                                           1; CHAIN: A, B;   RIBONUCLEOPROTEIN (RNP, RBD OR                                               RRM) AND LEUCINE-RICH-REPEAT 2                                               (LRR)       298   1fqv   A   129   214   5.1e−11   0.28   0.46       SKP2; CHAIN: A, C, E, G, I, K, M, O;   LIGASE CYCLIN A/CDK2-                                           SKP1; CHAIN: B, D, F, H, J, I, N, P;   ASSOCIATED PROTEIN P45; CYCLIN                                               A/CDK2-ASSOCIATED PROTEIN P19;                                               SKP1, SKP2, F-BOX, LRR, LEUCINE-                                               RICH REPEAT, SCF, UBIQUITIN, 2 E3,                                               UBIQUITIN PROTEIN LIGASE       298   1fqv   A   33   140   1.5e−08   0.04   −0.02       SKP2; CHAIN: A, C, E, G, I, K, M, O;   LIGASE CYCLIN A/CDK2-                                           SKP1; CHAIN: B, D, F, H, J, L, N, P;   ASSOCIATED PROTEIN P45; CYCLIN                                               A/CDK2-ASSOCIATED PROTEIN P19;                                               SKP1, SKP2, F-BOX, LRR, LEUCINE-                                               RICH REPEAT, SCF, UBIQUITIN, 2 E3,                                               UBIQUITIN PROTEIN LIGASE       298   1fqv   A   39   191   3e−21   0.95   1.00       SKP2; CHAIN: A, C, E, G, I, K, M, O;   LIGASE CYCLIN A/CDK2-                                           SKP1; CHAIN: B, D, F, H, J, L, N, P;   ASSOCIATED PROTEIN P45; CYCLIN                                               A/CDK2-ASSOCIATED PROTEIN P19;                                               SKP1, SKP2, F-BOX, LRR, LEUCINE-                                               RICH REPEAT, SCF, UBIQUITIN, 2 E3,                                               UBIQUITIN PROTEIN LIGASE       298   1fqv   A   49   207   6.8e−19   0.54   0.96       SKP2; CHAIN: A, C, E, G, I, K, M, O;   LIGASE CYCLIN A/CDK2-                                           SKP1; CHAIN: B, D, F, H, J, L, N, P;   ASSOCIATED PROTEIN P45; CYCLIN                                               A/CDK2-ASSOCIATED PROTEIN P19;                                               SKP1, SKP2, F-BOX, LRR, LEUCINE-                                               RICH REPEAT, SCF, UBIQUITIN, 2 E3,                                               UBIQUITIN PROTEIN LIGASE       298   1fqv   A   70   199   4.5e−19   0.85   0.92       SKP2; CHAIN: A, C, E, G, I, K, M, O;   LIGASE CYCLIN A/CDK2-                                           SKP1; CHAIN: B, D, F, H, J, L, N, P;   ASSOCIATED PROTEIN P45; CYCLIN                                               A/CDK2-ASSOCIATED PROTEIN P19;                                               SKP1, SKP2, F-BOX, LRR, LEUCINE-                                               RICH REPEAT, SCF, UBIQUITIN, 2 E3,                                               UBIQUITIN PROTEIN LIGASE       298   1fs2   A   129   214   5.1e−11   −0.35   0.27       SKP2; CHAIN: A, C; SKP1; CHAIN:   LIGASE CYCLIN A/CDK2-                                           B, D;   ASSOCIATED P45; CYCLIN A/CDK2-                                               ASSOCIATED P19; SKP1, SKP2, F-BOX,                                               LRRS, LEUCINE-RICH REPEATS, SCF,                                               2 UBIQUITIN, E3, UBIQUITIN                                               PROTEIN LIGASE       298   1fs2   A   49   207   6.8e−19   0.64   0.77       SKP2; CHAIN: A, C; SKP1; CHAIN:   LIGASE CYCLIN A/CDK2-                                           B, D;   ASSOCIATED P45; CYCLIN A/CDK2-                                               ASSOCIATED P19; SKP1, SKP2, F-BOX,                                               LRRS, LEUCINE-RICH REPEATS, SCF,                                               2 UBIQUITIN, E3, UBIQUITIN                                               PROTEIN LIGASE       298   1yrg   A   111   220   1e−08   −0.38   0.23       GTPASE-ACTIVATING PROTEIN   TRANSCRIPTION RNA1P; RANGAP;                                           RNA1_SCHPO; CHAIN: A, B;   GTPASE-ACTIVATING PROTEIN FOR                                               SPI1, GTPASE-ACTIVATING PROTEIN,                                               GAP, RNA1P, RANGAP, LRR,                                               LEUCINE-2 RICH REPEAT PROTEIN,                                               TWINNING, HEMIHEDRAL                                               TWINNING, 3 MEROHEDRAL                                               TWINNING, MEROHEDRY       298   2bnh       113   223   1.4e−08   0.31   0.76       RIBONUCLEASE INHIBITOR;   ACETYLATION RNASE INHIBITOR,                                           CHAIN: NULL;   RIBONUCLEASE/ANGIOGENIN                                               INHIBITOR ACETYLATION,                                               LEUCINE-RICH REPEATS       298   2bnh       53   217   1e−10   0.32   1.00       RIBONUCLEASE INHIBITOR;   ACETYLATION RNASE INHIBITOR,                                           CHAIN: NULL;   RIBONUCLEASE/ANGIOGENIN                                               INHIBITOR ACETYLATION,                                               LEUCINE-RICH REPEATS               299   1brl   B   4   151   3.4e−44   0.91   1.00       MYOSIN; CHAIN: A, B, C, D, E, F,   MUSCLE PROTEIN MDE; MUSCLE                                           G, H;   PROTEIN       299   1brl   B   4   151   3.4e−44           219.13   MYOSIN; CHAIN: A, B, C, D, E, F,   MUSCLE PROTEIN MDE; MUSCLE                                           G, H;   PROTEIN       299   1cdm   A   4   149   1.7e−56   0.60   1.00       CALCIUM-BINDING PROTEIN                                           CALMODULIN COMPLEXED                                           WITH CALMODULIN-BINDING                                           DOMAIN OF 1CDM 3                                           CALMODULIN-DEPENDENT                                           PROTEIN KINASE II 1CDM 4       299   1cdm   A   4   149   1.7e−56           103.28   CALCIUM-BINDING PROTEIN                                           CALMODULIN COMPLEXED                                           WITH CALMODULIN-BINDING                                           DOMAIN OF 1CDM 3                                           CALMODULIN-DEPENDENT                                           PROTEIN KINASE II 1CDM 4       299   1cll       4   149   6.8e−62   0.49   1.00       CALCIUM-BINDING PROTEIN                                           CALMODULIN (VERTEBRATE)                                           1CLL 3       299   1cll       4   150   6.8e−62           113.59   CALCIUM-BINDING PROTEIN                                           CALMODULIN (VERTEBRATE)                                           1CLL 3       299   1exr   A   4   150   1.4e−59   0.40   1.00       CALMODULIN; CHAIN: A;   METAL TRANSPORT CALMODULIN,                                               HIGH RESOLUTION, DISORDER       299   1tcf       3   151   1.7e−48           89.97   TROPONIN C; CHAIN: NULL;   CALCIUM-REGULATED MUSCLE                                               CONTRACTION MUSCLE                                               CONTRACTION, CALCIUM-BINDING,                                               TROPONIN, E-F HAND, 2 OPEN                                               CONFORMATION REGULATORY                                               DOMAIN, CALCIUM-REGULATED 3                                               MUSCLE CONTRACTION       299   1tcf       4   148   1.7e−48   0.38   1.00       TROPONIN C; CHAIN: NULL;   CALCIUM-REGULATED MUSCLE                                               CONTRACTION MUSCLE                                               CONTRACTION, CALCIUM-BINDING,                                               TROPONIN, E-F HAND, 2 OPEN                                               CONFORMATION REGULATORY                                               DOMAIN, CALCIUM-REGULATED 3                                               MUSCLE CONTRACTION       299   1top       4   148   5.1e−49   0.57   1.00       CONTRACTILE SYSTEM PROTEIN                                           TROPONIN C 1TOP 3       299   1top       4   151   5.1e−49           83.80   CONTRACTILE SYSTEM PROTEIN                                           TROPONIN C 1TOP 3       299   1vrk   A   2   149   1.2e−60   0.72   1.00       CALMODULIN; CHAIN: A; RS20;   CALMODULIN, CALCIUM BINDING,                                           CHAIN: B;   HELIX-LOOP-HELIX, SIGNALLING, 2                                               COMPLEX(CALCIUM-BINDING                                               PROTEIN/PEPTIDE)       299   1vrk   A   2   151   1.2e−60           115.21   CALMODULIN; CHAIN: A; RS20;   CALMODULIN, CALCIUM BINDING,                                           CHAIN: B;   HELIX-LOOP-HELIX, SIGNALLING, 2                                               COMPLEX(CALCIUM-BINDING                                               PROTEIN/PEPTIDE)               300   1aox   A   36   215   1.7e−28   0.37   0.83       INTEGRIN ALPHA 2 BETA;   INTEGRIN INTEGRIN, CELL                                           CHAIN: A, B;   ADHESION, GLYCOPROTEIN       300   1atz   A   38   226   1.5e−23           72.47   VON WILLEBRAND FACTOR;   COLLAGEN-BINDING COLLAGEN-                                           CHAIN: A, B;   BINDING, HEMOSTASIS,                                               DINUCLEOTIDE BINDING FOLD       300   1atz   A   39   218   1.5e−23   0.88   1.00       VON WILLEBRAND FACTOR;   COLLAGEN-BINDING COLLAGEN-                                           CHAIN: A, B;   BINDING, HEMOSTASIS,                                               DINUCLEOTIDE BINDING FOLD       300   1auq       23   227   1.4e−35           62.36   A1 DOMAIN OF VON   WILLEBRAND WILLEBRAND, BLOOD                                           WILLEBRAND FACTOR; CHAIN:   COAGULATION, PLATELET,                                           NULL;   GLYCOPROTEIN       300   1auq       29   227   1.4e−35   0.57   1.00       A1 DOMAIN OF VON   WILLEBRAND WILLEBRAND, BLOOD                                           WILLEBRAND FACTOR; CHAIN:   COAGULATION, PLATELET,                                           NULL;   GLYCOPROTEIN       300   1ck4   A   39   217   5.1e−29   0.58   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN 1-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       300   1fns   A   36   227   5.1e−34   0.70   0.98       IMMUNOGLOBULIN NMC-4 IGG1;   IMMUNE SYSTEM VON                                           CHAIN: L; IMMUNOGLOBULIN   WILLEBRAND FACTOR,                                           NMC-4 IGG1; CHAIN: H; VON   GLYCOPROTEIN IBA (A; ALPHA)                                           WILLEBRAND FACTOR; CHAIN:   BINDING, 2 COMPLEX                                           A;   (WILLEBRAND/IMMUNOGLOBULIN),                                               BLOOD COAGULATION TYPE 3 2B                                               VON WILLEBRAND DISEASE       300   1ido       39   224   5.1e−31           59.31   INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       300   1ido       41   217   5.1e−31   0.61   1.00       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       300   1lfa   A   38   226   8.5e−23   0.53   0.99       CDI1A; ILFA 5 CHAIN: A, B; 1LFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       300   1lfa   A   38   227   8.5e−23           53.04   CDI1A; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-L ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       300   1qc5   A   37   217   1.4e−28   0.41   0.94       ALPHAI BETA1 INTEGRIN;   CELL ADHESION INTEGRIN, CELL                                           CHAIN: A; ALPHAI BETA1   ADHESION                                           INTEGRIN; CHAIN: B;               301   1bxe   A   13   153   1.7e−33   −0.14   0.71       RIBOSOMAL PROTEIN L22;   RNA BINDING PROTEIN RIBOSOMAL                                           CHAIN: A;   PROTEIN, PROTEIN SYNTHESIS, RNA                                               BINDING, 2 ANTIBIOTICS                                               RESISTANCE, RNA BINDING                                               PROTEIN       301   1flk   0   2   152   1.7e−44   0.02   1.00       23S RRNA; CHAIN: 0; 5S RRNA;   RIBOSOME 50S RIBOSOMAL                                           CHAIN: 9; RIBOSOMAL PROTEIN   PROTEIN L2P, HMAL2, HL4; 50S                                           L2; CHAIN: A; RIBOSOMAL   RIBOSOMAL PROTEIN L3P, HMAL3,                                           PROTEIN L3; CHAIN: B;   HL1; 50S RIBOSOMAL PROTEIN L4E,                                           RIBOSOMAL PROTEIN L4; CHAIN:   HMAL4, HL6; 50S RIBOSOMAL                                           C; RIBOSOMAL PROTEIN L5;   PROTEIN L5P, HMAL5, HL13; 30S                                           CHAIN: D; RIBOSOMAL PROTEIN   RIBOSOMAL PROTEIN HS6; 50S                                           L7AE; CHAIN: E; RIBOSOMAL   RIBOSOMAL PROTEIN L13P, HMAL13;                                           PROTEIN L10E; CHAIN: F;   50S RIBOSOMAL PROTEIN L14P,                                           RIBOSOMAL PROTEIN L13;   HMAL14, HL27; 50S RIBOSOMAL                                           CHAIN: G; RIBOSOMAL PROTEIN   PROTEIN L15P, HMAL15, HL9; 50S                                           L14; CHAIN: H; RIBOSOMAL   RIBOSOMAL PROTEIN L18P, HMAL18,                                           PROTEIN L15E; CHAIN: I;   HL12; 50S RIBOSOMAL PROTEIN                                           RIBOSOMAL PROTEIN L15;   L18E, HL29, L19; 50S RIBOSOMAL                                           CHAIN: J; RIBOSOMAL PROTEIN   PROTEIN L19E, HMAL19, HL24; 50S                                           L18; CHAIN: K; RIBOSOMAL   RIBOSOMAL PROTEIN L21E, HL31;                                           PROTEIN L18E; CHAIN: L;   50S RIBOSOMAL PROTEIN L22P,                                           RIBOSOMAL PROTEIN L19;   HMAL22, HL23; 50S RIBOSOMAL                                           CHAIN: M; RIBOSOMAL PROTEIN   PROTEIN L23P, HMAL23, HL25, L21;                                           L21E; CHAIN: N; RIBOSOMAL   50S RIBOSOMAL PROTEIN L24P,                                           PROTEIN L22; CHAIN: O;   HMAL24, HL16, HL15; 50S                                           RIBOSOMAL PROTEIN L23;   RIBOSOMAL PROTEIN L24E,                                           CHAIN: P; RIBOSOMAL PROTEIN   HL21/HL22; 50S RIBOSOMAL                                           L24; CHAIN: Q; RIBOSOMAL   PROTEIN L29P, HMAL29, HL33; 50S                                           PROTEIN L24E; CHAIN: R;   RIBOSOMAL PROTEIN L30P, HMAL30,                                           RIBOSOMAL PROTEIN L29;   HL20, HL16; 50S RIBOSOMAL                                           CHAIN: S; RIBOSOMAL PROTEIN   PROTEIN L31E, L34, HL30; 50S                                           L30; CHAIN: T; RIBOSOMAL   RIBOSOMAL PROTEIN L32E, HL5; 50S                                           PROTEIN L31E; CHAIN: U;   RIBOSOMAL PROTEIN L37E, L35E;                                           RIBOSOMAL PROTEIN L32E;   50S RIBOSOMAL PROTEINS L39E,                                           CHAIN: V; RIBOSOMAL PROTEIN   HL39E, HL46E; 50S RIBOSOMAL                                           L37AE; CHAIN: W; RIBOSOMAL   PROTEIN L44E, LA, HLA; 50S                                           PROTEIN L37E; CHAIN: X;   RIBOSOMAL PROTEIN L6P, HMAL6,                                           RIBOSOMAL PROTEIN L39E;   HL10 RIBOSOME ASSEMBLY, RNA-                                           CHAIN: Y; RIBOSOMAL PROTEIN   RNA, PROTEIN-RNA, PROTEIN-                                           L44E; CHAIN: Z; RIBOSOMAL   PROTEIN                                           PROTEIN L6; CHAIN: I;               302   1ahd   P   143   208   1e−33   −0.16   0.98       DNA-BINDING PROTEIN                                           ANTENNAPEDIA PROTEIN                                           (HOMEODOMAIN) MUTANT                                           WITH CYS 39 1AHD 3 REPLACED                                           BY SER (C39S) COMPLEX WITH                                           DNA (NMR, 1AHD 4.16                                           STRUCTURES) 1AHD 5       302   1ahd   P   143   209   1e−33           72.79   DNA-BINDING PROTEIN                                           ANTENNAPEDIA PROTEIN                                           (HOMEODOMAIN) MUTANT                                           WITH CYS 39 1AHD 3 REPLACED                                           BY SER (C39S) COMPLEX WITH                                           DNA (NMR, 1AHD 4.16                                           STRUCTURES) 1AHD 5       302   1b72   A   137   203   1.5e−30           69.28   HOMEOBOX PROTEIN HOX-B1;   PROTEIN/DNA HOMEODOMAIN,                                           CHAIN: A; PBX1; CHAIN: B; DNA   DNA, COMPLEX, DNA-BINDING                                           CHAIN: D; DNA CHAIN: E;   PROTEIN, PROTEIN/DNA       302   1b72   A   143   203   1.5e−30   −0.07   0.99       HOMEOBOX PROTEIN HOX-B1;   PROTEIN/DNA HOMEODOMAIN,                                           CHAIN: A; PBX1; CHAIN: B; DNA   DNA, COMPLEX, DNA-BINDING                                           CHAIN: D; DNA CHAIN: E;   PROTEIN, PROTEIN/DNA       302   1b72   A   147   204   1.7e−27   −0.29   1.00       HOMEOBOX PROTEIN HOX-B1;   PROTEIN/DNA HOMEODOMAIN,                                           CHAIN: A; PBX1; CHAIN: B; DNA   DNA, COMPLEX, DNA-BINDING                                           CHAIN: D; DNA CHAIN: E;   PROTEIN, PROTEIN/DNA       302   1b8i   A   143   202   4.5e−30           61.07   ULTRABITHORAX HOMEOTIC   TRANSCRIPTION/DNA                                           PROTEIN IV; CHAIN: A;   ULTRABITHORAX; PBX PROTEIN;                                           HOMEOBOX PROTEIN   DNA BINDING, HOMEODOMAIN,                                           EXTRADENTICLE; CHAIN: B; DNA   HOMEOTIC PROTEINS,                                           (5′-CHAIN: C; DNA (5′-CHAIN: D;   DEVELOPMENT, 2 SPECIFICITY       302   1b8i   A   144   201   4.5e−30   0.09   0.83       ULTRABITHORAX HOMEOTIC   TRANSCRIPTION/DNA                                           PROTEIN IV; CHAIN: A;   ULTRABITHORAX; PBX PROTEIN;                                           HOMEOBOX PROTEIN   DNA BINDING, HOMEODOMAIN,                                           EXTRADENTICLE; CHAIN: B; DNA   HOMEOTIC PROTEINS,                                           (5′-CHAIN: C; DNA (5′-CHAIN: D;   DEVELOPMENT, 2 SPECIFICITY       302   1ftz       142   210   1.2e−28           71.20   DNA-BINDING FUSHI TARAZU                                           PROTEIN (HOMEODOMAIN)                                           (NMR, 20 STRUCTURES) 1FTZ 3       302   1ftz       144   208   1.2e−28   −0.30   0.59       DNA-BINDING FUSHI TARAZU                                           PROTEIN (HOMEODOMAIN)                                           (NMR, 20 STRUCTURES) 1FTZ 3       302   1san       148   209   3.4e−31           69.53   DNA-BINDING PROTEIN                                           ANTENNAPEDIA PROTEIN                                           (HOMEODOMAIN) MUTANT                                           WITH CYS 39 1SAN 3 REPLACED                                           BY SER AND RESIDUES 1-6                                           DELETED (C39S,DEL 1-6) 1SAN 4                                           (NMR, 20 STRUCTURES) 1SAN 5       302   1san       149   208   3.4e−31   0.00   1.00       DNA-BINDING PROTEIN                                           ANTENNAPEDIA PROTEIN                                           (HOMEODOMAIN) MUTANT                                           WITH CYS 39 1SAN 3 REPLACED                                           BY SER AND RESIDUES 1-6                                           DELETED (C39S,DEL 1-6) 1SAN 4                                           (NMR, 20 STRUCTURES) 1SAN 5       302   9ant   A   147   202   5.1e−31   0.38   1.00       ANTENNAPEDIA PROTEIN;   COMPLEX (DNA-BINDING                                           CHAIN: A, B; DNA; CHAIN: C, D, E,   PROTEIN/DNA) HD; HOMEODOMAIN,                                           F;   COMPLEX (DNA-BINDING                                               PROTEIN/DNA)       302   9ant   A   147   202   5.1e−31           68.47   ANTENNAPEDIA PROTEIN;   COMPLEX (DNA-BINDING                                           CHAIN: A, B; DNA; CHAIN: C, D, E,   PROTEIN/DNA) HD; HOMEODOMAIN,                                           F;   COMPLEX (DNA-BINDING                                               PROTEIN/DNA)               307   1ddv   A   4   96   0.0003   0.48   0.46       GLGF-DOMAIN PROTEIN HOMER;   SIGNALING PROTEIN PROTEIN-                                           CHAIN: A; METABOTROPIC   LIGAND COMPLEX, POLYPROLINE                                           GLUTAMATE RECEPTOR   RECOGNITION, BETA TURN                                           MGLUR5; CHAIN: B;       307   1ddw   A   4   96   0.00015   0.62   0.69       GLGF-DOMAIN PROTEIN HOMER;   SIGNALING PROTEIN PLECKSTRIN                                           CHAIN: A;   HOMOLOGY DOMAIN FOLD       307   1rrp   B   7   101   1.5e−25   0.57   0.96       RAN; CHAIN: A, C; NUCLEAR   COMPLEX (SMALL                                           PORE COMPLEX PROTEIN   GTPASE/NUCLEAR PROTEIN)                                           NUP358; CHAIN: B, D;   COMPLEX (SMALL                                               GTPASE/NUCLEAR PROTEIN), SMALL                                               GTPASE, 2 NUCLEAR TRANSPORT               309   2ife   A   159   237   1.2e−16   0.62   0.89       TRANSLATION INITIATION   GENE REGULATION INITIATION                                           FACTOR IF3; CHAIN: A;   FACTOR               310   1f5n   A   107   167   0.0049   −0.27   0.03       INTERFERON-INDUCED   SIGNALING PROTEIN GBP, GTP                                           GUANYLATE-BINDING PROTEIN   HYDROLYSIS, GDP, GMP,                                           1; CHAIN: A;   INTERFERON INDUCED, DYNAMIN 2                                               RELATED, LARGE GTPASE FAMILY,                                               GMPPNP, GPPNHP,       310   1osm   A   9   99   1.5e−15   1.73   −0.20       OMPK36; CHAIN: A, B, C;   OUTER MEMBRANE PROTEIN                                               OSMOPORIN; OUTER MEMBRANE                                               PROTEIN, NON-SPECIFIC PORIN,                                               OSMOPORIN, 2 BETA-BARREL,                                               TRANSMEMBRANE       310   1qq4   A   14   119   1.2e−11   1.84   0.04       ALPHA-LYTIC PROTEASE;   HYDROLASE DOUBLE BETA                                           CHAIN: A;   BARREL, BACTERIAL SERINE                                               PROTEASE       310   1qq4   A   8   96   3e−09   1.29   −0.08       ALPHA-LYTIC PROTEASE;   HYDROLASE DOUBLE BETA                                           CHAIN: A;   BARREL, BACTERIAL SERINE                                               PROTEASE       310   1tal       14   119   1e−11   1.63   −0.06       ALPHA-LYTIC PROTEASE;   SERINE PROTEASE SERINE                                           CHAIN: NULL;   PROTEASE, LOW TEMPERATURE,                                               HYDROLASE, 2 SERINE PROTEINASE       310   1tal       8   99   1.2e−10   1.03   −0.20       ALPHA-LYTIC PROTEASE;   SERINE PROTEASE SERINE                                           CHAIN: NULL;   PROTEASE, LOW TEMPERATURE,                                               HYDROLASE, 2 SERINE PROTEINASE               311   1alh   A   116   195   8.5e−18   −0.02   0.27       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       311   1alh   A   339   448   1.2e−39   −0.24   0.11       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       311   1alh   A   619   728   6e−37   −0.46   0.12       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       311   1mey   C   105   195   3.4e−32   −0.06   0.22       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   142   223   1.7e−39   −0.08   0.95       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   170   251   1.7e−42   0.19   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   198   279   1.2e−44   0.17   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   226   307   3.4e−46   0.27   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   254   335   1.7e−46   −0.02   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   282   363   8.5e−47   −0.26   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   310   391   1.5e−46   −0.08   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   338   419   1.7e−46   0.07   0.98       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   366   447   3.4e−47   0.08   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   394   475   6.8e−49   0.32   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   422   503   1e−49   0.06   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   450   531   3.4e−49   0.18   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   478   559   1.2e−48   0.37   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   478   560   3.4e−49           108.14   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   506   587   8.5e−49   0.14   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   534   615   1.5e−48   0.14   0.99       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   562   643   6.8e−49   −0.00   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   590   671   6.8e−49   0.04   0.82       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   618   699   1.7e−49   −0.22   0.94       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   646   727   1.2e−50   −0.03   0.98       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   674   755   1.2e−50   0.23   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   702   783   6.8e−51   0.31   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   730   811   3.4e−50   0.08   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   758   839   1.7e−50   −0.03   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1mey   C   786   852   1.5e−40   −0.09   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       311   1tf6   A   199   345   1.7e−34   0.00   0.98       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   394   560   1.7e−37           116.05   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   395   540   1.7e−37   0.21   0.88       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   507   652   3.4e−36   −0.03   0.48       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   563   708   1.4e−36   −0.36   0.45       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   619   764   1.4e−36   −0.22   0.46       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1tf6   A   703   852   6.8e−38   0.19   0.98       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       311   1ubd   C   116   223   5.1e−25   −0.02   0.86       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   147   251   1.5e−41   −0.11   0.94       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   168   279   6e−51   −0.09   0.66       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   201   307   8.5e−32   0.06   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   203   307   6e−53   −0.15   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   224   336   3e−52   −0.10   0.72       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   308   447   1.5e−48   −0.40   0.54       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   371   476   3e−50   −0.17   0.86       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   374   475   1e−34   −0.10   0.80       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   394   503   1.5e−54   −0.13   0.69       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   420   559   7.5e−57   −0.17   0.46       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   430   531   1.7e−34   0.22   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   458   559   1.7e−33   −0.07   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   504   615   1.3e−51   0.16   0.80       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   598   699   1.7e−34   −0.42   0.21       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   616   755   3e−49   −0.41   0.21       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   626   727   1.7e−34   −0.33   0.45       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   672   784   3e−57           93.95   YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   682   783   1.7e−34   −0.02   0.89       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   700   811   3e−57   −0.12   0.90       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   728   839   1.5e−54   0.00   0.99       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   738   839   1.4e−34   −0.08   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   1ubd   C   756   852   1.2e−44   −0.20   0.51       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       311   2gli   A   119   250   1.4e−28   −0.17   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   143   281   6e−55   0.02   0.53       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   198   334   8.5e−32   −0.17   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   201   337   1.5e−65   0.34   0.86       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   226   365   4.5e−66   0.06   0.95       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   310   477   4.5e−64   0.04   0.60       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   346   474   5.1e−32   0.08   0.84       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   394   533   7.5e−72   0.06   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   422   561   7.5e−72           102.20   ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   430   558   3.4e−33   0.32   0.78       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   478   617   1.2e−68   −0.09   0.65       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   570   698   1.2e−33   −0.19   0.07       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   654   782   1.2e−33   0.17   0.55       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   674   841   4.5e−70   −0.08   0.63       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   682   810   5.1e−33   0.03   0.62       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   710   841   6.8e−34   −0.14   0.84       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   730   852   6e−60   0.12   0.80       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       311   2gli   A   738   851   3.4e−29   0.17   0.80       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               312   1b34   A   7   81   4.5e−23   0.29   0.30       SMALL NUCLEAR   RNA BINDING PROTEIN SNRNP,                                           RIBONUCLEOPROTEIN SM D1;   SPLICING, SPLICEOSOME, SM, CORE                                           CHAIN: A; SMALL NUCLEAR   SNRNP DOMAIN, 2 SYSTEMIC LUPUS                                           RIBONUCLEOPROTEIN SM D2;   ERYTHEMATOSUS, SLE                                           CHAIN: B;       312   1b34   A   9   71   3.4e−17   0.08   0.04       SMALL NUCLEAR   RNA BINDING PROTEIN SNRNP,                                           RIBONUCLEOPROTEIN SM D1;   SPLICING, SPLICEOSOME, SM, CORE                                           CHAIN: A; SMALL NUCLEAR   SNRNP DOMAIN, 2 SYSTEMIC LUPUS                                           RIBONUCLEOPROTEIN SM D2;   ERYTHEMATOSUS, SLE                                           CHAIN: B;       312   1b34   B   7   72   1.2e−12   0.46   0.18       SMALL NUCLEAR   RNA BINDING PROTEIN SNRNP,                                           RIBONUCLEOPROTEIN SM D1;   SPLICING, SPLICEOSOME, SM, CORE                                           CHAIN: A; SMALL NUCLEAR   SNRNP DOMAIN, 2 SYSTEMIC LUPUS                                           RIBONUCLEOPROTEIN SM D2;   ERYTHEMATOSUS, SLE                                           CHAIN: B;       312   1d3b   A   5   72   1.7e−14   0.28   0.07       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN       312   1d3b   A   7   76   1.1e−20   0.63   0.05       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN       312   1d3b   B   10   78   7.5e−18   0.34   −0.06       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN       312   1d3b   B   9   70   1.7e−15   −0.01   0.04       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN       312   1d3b   D   4   70   6.8e−16   0.76   −0.05       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN       312   1d3b   D   9   78   1.5e−17   0.11   −0.01       SMALL NUCLEAR   RNA BINDING PROTEIN D3 CORE                                           RIBONUCLEOPROTEIN SM D3;   SNRNP PROTEIN; B CORE SNRNP                                           CHAIN: A, C, E, G, I, K; SMALL   PROTEIN SNRNP, SPLICING, SM,                                           NUCLEAR RIBONUCLEOPROTEIN   CORE SNRNP DOMAIN, SYSTEMIC                                           ASSOCIATED CHAIN: B, D, F, H, J,   LUPUS 2 ERYTHEMATOSUS, SLE,                                           L;   RNA BINDING PROTEIN               314   1b8q   A   101   173   1.3e−06   0.08   0.15       NEURONAL NITRIC OXIDE   OXIDOREDUCTASE PDZ DOMAIN,                                           SYNTHASE; CHAIN: A;   NNOS, NITRIC OXIDE SYNTHASE                                           HEPTAPEPTIDE; CHAIN: B;       314   1be9   A   113   175   8.5e−05   0.19   0.99       PSD-95; CHAIN: A; CRIPT; CHAIN:   PEPTIDE RECOGNITION PEPTIDE                                           B;   RECOGNITION, PROTEIN                                               LOCALIZATION       314   1pdr       113   175   0.0012   0.13   0.90       HUMAN DISCS LARGE PROTEIN;   SIGNAL TRANSDUCTION HDLG,                                           CHAIN: NULL;   DHR3 DOMAIN; SIGNAL                                               TRANSDUCTION, SH3 DOMAIN,                                               REPEAT       314   1qlc   A   119   172   0.00034   0.27   0.99       POSTSYNAPTIC DENSITY   PEPTIDE RECOGNITION PSD-95; PDZ                                           PROTEIN 95; CHAIN: A;   DOMAIN, NEURONAL NITRIC OXIDE                                               SYNTHASE, NMDA RECEPTOR 2                                               BINDING       314   3pdz   A   109   190   3e−09   0.73   0.76       TYROSINE PHOSPHATASE (PTP-   HYDROLASE PDZ DOMAIN, HUMAN                                           BAS, TYPE 1); CHAIN: A;   PHOSPHATASE, HPTPIE, PTP-BAS,                                               SPECIFICITY 2 OF BINDING               316   1a4y   A   805   893   4.5e−05   0.52   0.60       RIBONUCLEASE INHIBITOR;   COMPLEX (INHIBITOR/NUCLEASE)                                           CHAIN: A, D; ANGIOGENIN;   COMPLEX (INHIBITOR/NUCLEASE),                                           CHAIN: B, E;   COMPLEX (RI-ANG), HYDROLASE 2                                               MOLECULAR RECOGNITION,                                               EPITOPE MAPPING LEUCINE-RICH 3                                               REPEATS       316   1a4y   A   815   877   7.5e−08   0.54   1.00       RIBONUCLEASE INHIBITOR;   COMPLEX (INHIBITOR/NUCLEASE)                                           CHAIN: A, D; ANGIOGENIN;   COMPLEX (INHIBITOR/NUCLEASE),                                           CHAIN: B, E;   COMPLEX (RI-ANG), HYDROLASE 2                                               MOLECULAR RECOGNITION,                                               EPITOPE MAPPING, LEUCINE-RICH 3                                               REPEATS       316   1aoj   A   590   647   6e−16   −0.80   0.30       EPS8; CHAIN: A, B;   SIGNAL TRANSDUCTION SRC                                               HOMOLOGY DOMAIN; SIGNAL                                               TRANSDUCTION, SH3 DOMAIN, EPS8,                                               PROLINE RICH PEPTIDE       316   1tud       577   627   1.1e−07   −0.30   0.64       ALPHA-SPECTRIN; CHAIN: NULL;   CYTOSKELETON CAPPING PROTEIN,                                               CALCIUM-BINDING, DUPLICATION,                                               REPEAT, 2 SH3 DOMAIN,       316   2nmb   A   155   263   9e−14   −0.13   0.10       NUMB PROTEIN; CHAIN: A; GPPY   CELL CYCLE/GENE REGULATION                                           PEPTIDE; CHAIN: B;   COMPLEX, SIGNAL TRANSDUCTION,                                               PHOSPHOTYROSINE BINDING 2                                               DOMAIN (PTB), ASYMETR IC CELL                                               DIVISION, CELL CYCLE/GENE 3                                               REGULATION               318   1a5f   H   38   246   1.4e−20           69.16   MONOCLONAL ANTI-E-SELECTIN   IMMUNOGLOBULIN                                           7A9 ANTIBODY; CHAIN: L, H;   IMMUNOGLOBULIN, FAB,                                               ANTIBODY, ANTI-E-SELECTIN       318   1adq   L   41   241   6.8e−29   0.18   0.35       IGG4 REA; CHAIN: A; RF-AN   COMPLEX                                           IGM/LAMBDA; CHAIN: H, L;   (IMMUNOGLOBULIN/AUTOANTIGEN)                                               COMPLEX                                               (IMMUNOGLOBULIN/AUTOANTIGEN),                                               RHEUMATOID FACTOR 2 AUTO-                                               ANTIBODY COMPLEX       318   1ac6   H   38   255   1.7e−22           64.20   ANTIBODY CTM01; CHAIN: L, H;   IMMUNOGLOBULIN                                               IMMUNOGLOBULIN, FAB                                               FRAGMENT, HUMANISATION       318   1afv   H   38   236   1.7e−23   0.11   1.00       HUMAN IMMUNODEFICIENCY   COMPLEX (VIRAL                                           VIRUS TYPE 1 CAPSID CHAIN: A,   CAPSID/IMMUNOGLOBULIN) HIV-I                                           B; ANTIBODY FAB25.3   CA, HIV CA, HIV P24, P24; FAB, FAB                                           FRAGMENT; CHAIN: H, K, L, M;   LIGHT CHAIN, FAB HEAVY CHAIN                                               COMPLEX (VIRAL                                               CAPSID/IMMUNOGLOBULIN), HIV,                                               CAPSID PROTEIN, 2 P24       318   1aqk   H   39   247   3.4e−20           65.54   FAB B7-15A2; CHAIN: L, H;   IMMUNOGLOBULIN HUMAN FAB,                                               ANTI-TETANUS TOXOID, HIGH                                               AFFINITY, CRYSTAL 2 PACKING                                               MOTIF, PROGRAMMING                                               PROPENSITY TO CRYSTALLIZE, 3                                               IMMUNOGLOBULIN       318   1aqk   L   40   260   1.7e−26           64.54   FAB B7-15A2; CHAIN: L, H;   IMMUNOGLOBULIN HUMAN FAB,                                               ANTI-TETANUS TOXOID, HIGH                                               AFFINITY, CRYSTAL 2 PACKING                                               MOTIF, PROGRAMMING                                               PROPENSITY TO CRYSTALLIZE, 3                                               IMMUNOGLOBULIN       318   1aqk   L   41   241   1.7e−26   0.21   0.74       FAR B7-15A2; CHAIN: L, H;   IMMUNOGLOBULIN HUMAN FAB,                                               ANTI-TETANUS TOXOID, HIGH                                               AFFINITY, CRYSTAL 2 PACKING                                               MOTIF, PROGRAMMING                                               PROPENSITY TO CRYSTALLIZE, 3                                               IMMUNOGLOBULIN       318   1ay1   H   50   236   8.5e−23   −0.10   0.28       TP7 FAB; CHAIN: L, H;   IMMUNOGLOBULIN                                               IMMUNOGLOBULIN, ANTBODY,                                               FAB, ENZYME INHIBITOR, PCR, 2                                               HOT START       318   1b2w   H   39   247   1.2e−19           63.67   ANTIBODY (LIGHT CHAIN);   IMMUNE SYSTEM                                           CHAIN: L; ANTIBODY (HEAVY   IMMUNOGLOBULIN;                                           CHAIN); CHAIN: H;   IMMUNOGLOBULIN ANTIBODY                                               ENGINEERING, HUMANIZED AND                                               CHIMERIC ANTIBODY, FAB, 2 X-RAY                                               STRUCTURE, THREE-DIMENSIONAL,                                               STRYCTURE, GAMMA-3                                               INTERFERON, IMMUNE SYSTEM       318   1b2w   L   38   259   1.5e−23           64.13   ANTIBODY (LIGHT CHAIN):   IMMUNE SYSTEM                                           CHAIN: L; ANTIBODY (HEAVY   IMMUNOGLOBULIN;                                           CHAIN): CHAIN: H;   IMMUNOGLOBULIN ANTIBODY                                               ENGINEERING, HUMANIZED AND                                               CHIMERIC ANTIBODY, FAB, 2 X-RAY                                               STRUCTURE, THREE-DIMENSIONAL                                               STRYCTURE, GAMMA-3                                               INTERFERON, IMMUNE SYSTEM       318   1b2w   L   39   232   1.5e−23   −0.00   0.07       ANTIBODY (LIGHT CHAIN);   IMMUNE SYSTEM                                           CHAIN: L; ANTIBODY (HEAVY   IMMUNOGLOBULIN;                                           CHAIN); CHAIN: H;   IMMUNOGLOBULIN ANTIBODY                                               ENGINEERING, HUMANIZED AND                                               CHIMERIC ANTIBODY, FAB, 2 X-RAY                                               STRUCTURE, THREE-DIMENSIONAL                                               STRYCTURE, GAMMA-3                                               INTERFERON, IMMUNE SYSTEM       318   1b4j   H   39   247   1.2e−19           67.97   ANTIBODY; CHAIN: L, H;   ANTIBODY ENGINEERING                                               ANTIBODY ENGINEERING,                                               HUMANIZED AND CHIMERIC                                               ANTIBODIES, 2 FAB, X-RAY                                               STRUCTURES, GAMMA-INTERFERON       318   1baf   H   37   259   8.5e−21           65.16   IMMUNOGLOBULIN FAB                                           FRAGMENT OF MURINE                                           MONOCLONAL ANTIBODY AN02                                           COMPLEX 1BAF 3 WITH ITS                                           HAPTEN (2,2,6,6-TETRAMETHYL-                                           1-PIPERIDINYLOXY-1BAF 4                                           DINITROPHENYL) 1BAF 5       318   1bih   A   90   246   8.5e−20   0.30   0.41       HEMOLIN; CHAIN: A, B;   INSECT IMMUNITY INSECT                                               IMMUNITY, LPS-BINDING,                                               HOMOPHILIC ADHESION       318   1bjl   L   39   232   1e−22   0.22   0.11       FAB FRAGMENT; CHAIN: L, H, J,   COMPLEX (ANTIBODY/ANTIGEN)                                           K; VASCULAR ENDOTHELIAL   FAB-12; VEGF; COMPLEX                                           GROWTH FACTOR; CHAIN: V, W;   (ANTIBODY/ANTIGEN), ANGIOGENIC                                               FACTOR       318   1bjm   A   40   241   1.7e−26   0.07   0.11       LOC-LAMBDA I TYPE LIGHT-   IMMUNOGLOBULIN BENCE-JONES                                           CHAIN DIMER; 1BJM 6 CHAIN: A,   PROTEIN; 1BJM 8 BENCE JONES,                                           B; 1BJM 7   ANTIBODY, MULTIPLE                                               QUATERNARY STRUCTURES 1BJM 13       318   1bm3   H   37   259   6.8e−21           68.28   IMMUNOGLOBULIN OPG2 FAB,   IMMUNE SYSTEM                                           CONSTANT DOMAIN; CHAIN: L;   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN OPG2 FAB,                                           VARIABLE DOMAIN; CHAIN: H;       318   1ct8   H   37   254   5.1e−22           64.09   CATALYTIC ANTIBODY 19A4   CATALYTIC ANTIBODY CATALYTIC                                           (LIGHT CHAIN); CHAIN: L;   ANTIBODY, TERPENOID SYNTHASE,                                           CATALYTIC ANTIBODY 19A4   CARBOCATION, 2 CYCLIZATION                                           (HEAVY CHAIN); CHAIN: H;   CASCADE       318   1cic   B   38   257   5.1e−22           67.07   IG HEAVY CHAIN V REGIONS;   IMMUNOGLOBULIN                                           CHAIN: A; IG HEAVY CHAIN V   IMMUNOGLOBULIN, FAB COMPLEX,                                           REGIONS; CHAIN: B; IG HEAVY   IDIOTOPE, ANTI-IDIOTOPE                                           CHAIN V REGIONS; CHAIN: C; IG                                           HEAVY CHAIN V REGIONS;                                           CHAIN D;       318   1cs6   A   45   247   1.7e−32   0.03   0.77       AXONIN-I; CHAIN: A;   CELL ADHESION NEURAL CELL                                               ADHESION       318   1ct8   B   38   259   3.4e−22           64.34   7C8 FAB FRAGMENT; SHORT   IMMUNE SYSTEM ABZYME                                           CHAIN; CHAIN: A, C; 7C8 FAB   TRANSITION STATE ANALOG,                                           FRAGMENT; LONG CHAIN;   IMMUNE SYSTEM                                           CHAIN: B, D       318   1cvs   C   174   249   1.7e−12   0.27   0.34       FIBROBLAST GROWTH FACTOR   GROWTH FACTOR/GROWTH FACTOR                                           2; CHAIN: A, B; FIBROBLAST   RECEPTOR FGF, FGFR,                                           GROWTH FACTOR RECEPTOR 1;   IMMUNOGLOBULIN-LIKE, SIGNAL                                           CHAIN: C, D;   TRANSDUCTION, 2 DIMERIZATION,                                               GROWTH FACTOR/GROWTH FACTOR                                               RECEPTOR       318   1cvs   D   174   249   1.7e−12   0.22   0.34       FIBROBLAST GROWTH FACTOR   GROWTH FACTOR/GROWTH FACTOR                                           2; CHAIN: A, B; FIBROBLAST   RECEPTOR FGF, FGFR,                                           GROWTH FACTOR RECEPTOR 1;   IMMUNOGLOBULIN-LIKE, SIGNAL                                           CHAIN: C, D;   TRANSDUCTION, 2 DIMERIZATION,                                               GROWTH FACTOR/GROWTH FACTOR                                               RECEPTOR       318   1dee   A   39   232   3.4e−23   0.15   0.06       IGM RF 2A2; CHAIN: A, C, E; IGM   IMMUNE SYSTEM FAB-IBP COMPLEX                                           RF 2A2; CHAIN: B, D, F;   CRYSTAL STRUCTURE 2.7A                                           IMMUNOGLOBULIN G BINDING   RESOLUTION BINDING 2 OUTSIDE                                           PROTEIN A; CHAIN: G, H;   THE ANTIGEN COMBINING SITE                                               SUPERANTIGEN FAB VH3 3                                               SPECIFICITY       318   1ev2   E   173   249   1.7e−13   0.13   0.25       FIBROBLAST GROWTH FACTOR   GROWTH FACTOR/GROWTH FACTOR                                           2; CHAIN: A, B, C, D; FIBROBLAST   RECEPTOR FGF2; FGFR2;                                           GROWTH FACTOR RECEPTOR 2;   IMMUNOGLOBULIN (IG)LIKE                                           CHAIN: E, F, G, H;   DOMAINS BELONGING TO THE I-SET                                               2 SUBGROUP WITHIN IG-LIKE                                               DOMAINS, B-TREFOIL FOLD       318   1evl   C   174   249   1.7e−12   0.37   0.13       FIBROBLAST GROWTH FACTOR   GROWTH FACTOR/GROWTH FACTOR                                           1; CHAIN: A, B; FIBROBLAST   RECEPTOR FGFI; EGERI;                                           GROWTH FACTOR RECEPTOR 1;   IMMUNOGLOBULIN (IG) LIKE                                           CHAIN: C, D;   DOMAINS BELONGING TO THE I-SET                                               2 SUBGROUP WITHIN IG-LIKE                                               DOMAINS, B-TREFOIL FOLD       318   1fai   H   38   254   3.4e−19           63.84   IMMUNOGLOBULIN FAB                                           FRAGMENT FROM A                                           MONOCLONAL ANTI-ARSONATE                                           ANTIBODY, R19.9 1FAI 3                                           (IGG2B,KAPPA) 1FAI 4       318   1thg   A   154   247   1.5e−08   0.27   0.16       TELOKIN; CHAIN: A   CONTRACTILE PROTEIN                                               IMMUNOGLOBULIN FOLD, BETA                                               BARREL       318   1fvd   B   37   247   5.1e−21           66.24   IMMUNOGLOBULIN FAB                                           FRAGMENT OF HUMANIZED                                           ANTIBODY 4D5, VERSION 4 IFVD 3       318   1hnf       43   232   1.3e−23   0.02   0.10       TLYMPHOCYTE ADHESION                                           GLYCOPROTEIN CD2 (HUMAN)                                           IHNF 3       318   1iai   H   38   254   5.1e−20           65.01   IDIOTYPIC FAB 730.1.4 (IGG1) OF   COMPLEX (IMMUNOGLOBULIN                                           VIRUS IIAI 5 CHAIN: L, H; 1IAI 7   IGG1/IGG2A)                                           ANTI-IDIOTYPIC FAB 409.5.3                                           (IGG2A); IIAI 9 CHAIN: M, I 1IAI                                           10       318   1lil   A   40   241   1.7e−25   0.18   0.13       LAMBDA III BENCE JONES   IMMUNOGLOBULIN                                           PROTEIN CLE; CHAIN: A, B   IMMUNOGLOBULIN, BENCE JONES                                               PROTEIN       318   1nca   H   38   254   1.5e−21           67.34   HYDROLASE(O-GLYCOSYL) N9                                           NEURAMINIDASE-NC41                                           (E.C.3.2.1.18) COMPLEX WITH FAB                                           1NCA 3       318   1nsn   H   37   254   1.4e−22           65.27   IGG FAB (IGG1, KAPPA): 1NSN 4   COMPLEX                                           CHAIN: L, H; 1NSN 5   (IMMUNOGLOBULIN/HYDROLASE)                                           STAPHYLOCOCCAL NUCLEASE:   N10 FAB IMMUNOGLOBULIN: 1NSN 7                                           1NSN 9 CHAIN: S; 1NSN 10   STAPHYLOCOCCAL NUCLEASE                                               RIBONUCLEATE, 1NSN 11                                               IMMUNOGLOBULIN.                                               STAPHYLOCOCCAL NUCLEASE 1NSN                                               25       318   1wio   A   47   262   7.5e−28   0.19   0.29       T-CELL SURFACE   GLYCOPROTEIN CD4;                                           GLYCOPROTEIN CD4; CHAIN: A,   IMMUNOGLOBULIN FOLD.                                           B;   TRANSMEMBRANE, GLYCOPROTEIN,                                               T-CELL, 2 MHC LIPOPROTEIN,                                               POLYMORPHISM       318   25c8   H   38   255   5.1e−23           64.25   IGG 5C8; CHAIN: L, H;   CATALYTIC ANTIBODY CATALYTIC                                               ANTIBODY, FAB, RING CLOSURE                                               REACTION       318   25c8   H   50   236   5.1e−23   0.12   0.19       IGG 5C8; CHAIN: L, H;   CATALYTIC ANTIBODY CATALYTIC                                               ANTIBODY, FAB, RING CLOSURE                                               REACTION       318   2cgr   H   37   254   1.2e−17           65.11   IMMUNOGLOBULIN IGG2B                                           (KAPPA) FAB FRAGMENT                                           COMPLEXED WITH ANTIGEN                                           2CGR 3 N-(P-CYANOPHENYL)-N′-                                           (DIPHENYLEMETHYL)                                           GUANIDINEACETIC ACID 2CGR 4       318   2tb4   L   40   241   1.5e−25   0.29   0.37       IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB 2FB4 4       318   2fgw   L   39   232   1.2e−23   0.27   0.01       IMMUNOGLOBULIN FAB                                           FRAGMENT OF A HUMANIZED                                           VERSION OF THE ANTI-CD18                                           2FGW 3 ANTIBODY ‘H52’ (HUH52-                                           OZ FAB) 2FGW 4       318   2mcg   I   40   241   1.2e−27   0.14   0.30       IMMUNOGLOBULIN                                           IMMUNOGLOBULIN LAMBDA                                           LIGHT CHAIN DIMER (/MCG$)                                           2MCG 3 (TRIGONAL FORM) 2MCG 4       318   2pcp   B   38   255   3.4e−21           68.25   IMMUNOGLOBULIN; CHAIN: A, B,   IMMUNOGLOBULIN                                           C, D;   IMMUNOGLOBULIN       318   32c2   B   50   236   3.4e−23   0.21   0.13       IGG1 ANTIBODY 32C2; CHAIN: A;   IMMUNE SYSTEM FAB, ANTIBODY,                                           IGG1 ANTIBODY 32C2; CHAIN: B;   AROMATASE, P450       318   3fct   B   37   247   8.5e−19           66.99   METAL CHELATASE CATALYTIC   IMMUNE SYSTEM METAL                                           ANTIBODY; CHAIN: A, C; METAL   CHELATASE, CATALYTIC                                           CHELATASE CATALYTIC   ANTIBODY, FAB FRAGMENT,                                           ANTIBODY; CHAIN: B, D;   IMMUNE 2 SYSTEM       318   3ncm   A   168   245   4.5e−09   0.09   −0.14       NEURAL CELL ADHESION   CELL ADHESION PROTEIN NCAM                                           MOLECULE, LARGE ISOFORM;   MODULE 2; CELL ADHESION.                                           CHAIN: A;   GLYCOPROTEIN, HEPARIN-BINDING,                                               GPI-ANCHOR, 2 NEURAL ADHESION                                               MOLECULE, IMMUNOGLOBULIN                                               FOLD, HOMOPHILIC 3 BINDING,                                               CELL ADHESION PROTEIN       318   7fab   L   40   241   1.7e−26   0.00   0.17       IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB&#39; NEW                                           (LAMBDA LIGHT CHAIN) 7FAB 3       318   8fab   A   43   241   1.4e−26   0.39   0.18       IMMUNOGLOBULIN FAB                                           FRAGMENT FROM HUMAN                                           IMMUNOGLOBULIN IGG1                                           (LAMBDA, HIL) 8FAB 3               319   1cly   A   8   171   1.4e−63           109.08   RAS-RELATED PROTEIN RAP-1A;   SIGNALING PROTEIN GTP-BINDING                                           CHAIN: A; PROTO-ONKOGENE   PROTEINS, PROTEIN-PROTEIN                                           SERINE/THREONINE PROTEIN   COMPLEX, EFFECTORS                                           KINASE CHAIN: B;       319   1cly   A   9   171   1.4e−63   0.82   1.00       RAS-RELATED PROTEIN RAP-1A;   SIGNALING PROTEIN GTP-BINDING                                           CHAIN: A; PROTO-ONKOGENE   PROTEINS, PROTEIN-PROTEIN                                           SERINE/THREONINE PROTEIN   COMPLEX, EFFECTORS                                           KINASE CHAIN: B;       319   1ctq   A   8   172   6.8e−65           108.57   TRANSFORMING PROTEIN P21/H-   SIGNALING PROTEIN G PROTEIN,                                           RAS-1; CHAIN: A;   GTP HYDROLYSIS, KINETIC                                               CRYSTALLOGRAPHY, 2 SIGNALING                                               PROTEIN       319   1ctq   A   9   171   6.8e−65   0.88   1.00       TRANSFORMING PROTEIN P21/H-   SIGNALING PROTEIN G PROTEIN,                                           RAS-1; CHAIN: A;   GTP HYDROLYSIS, KINETIC                                               CRYSTALLOGRAPHY, 2 SIGNALING                                               PROTEIN       319   1cxz   A   3   172   3.4e−55           108.33   HIS-TAGGED TRANSFORMING   SIGNALING PROTEIN PROTEIN-                                           PROTEIN RHOA(0-181); CHAIN: A;   PROTEIN COMPLEX, ANTIPARALLEL                                           PKN; CHAIN: B;   COILED-COIL       319   1d5c   A   9   165   6e−67   0.83   1.00       RAB6 GTPASE; CHAIN: A;   ENDOCYTOSIS/EXOCYTOSIS G-                                               PROTEIN, GTPASE, RAB6,                                               VESICULAR TRAFFICKING       319   1d5c   A   9   169   5.1e−63   0.87   1.00       RAB6 GTPASE; CHAIN: A;   ENDOCYTOSIS/EXOCYTOSIS G-                                               PROTEIN, GTPASE, RAB6,                                               VESICULAR TRAFFICKING       319   1ds6   A   9   170   1.5e−55   0.73   1.00       RAS-RELATED C3 BOTULINUM   SIGNALING PROTEIN P21-RAC2; RHO                                           TOXIN SUBSTRATE 2; CHAIN: A;   GDI 2, RHO-GDI BETA, LY-GDI; BETA                                           RHO GDP-DISSOCIATION   SANDWHICH, PROTEIN-PROTEIN                                           INHIBITOR 2; CHAIN: B;   COMPLEX, G-DOMAIN, 2                                               IMMUNOGLOBULIN FOLD, WALKER                                               FOLD, GTP-BINDING PROTEIN       319   1ek0   A   9   169   5.1e−61   0.93   1.00       GTP-BINDING PROTEIN YPT51;   ENDOCYTOSIS/EXOCYTOSIS G                                           CHAIN: A;   PROTEIN, VESICULAR TRAFFIC, GTP                                               HYDROLYSIS, YPT/RAB 2 PROTEIN,                                               ENDOCYTOSIS, HYDROLASE       319   1kao       8   172   1.2e−59           109.78   RAP2A; CHAIN: NULL;   GTP-BINDING PROTEIN GTP-                                               BINDING PROTEIN, SMALL G                                               PROTEIN, RAP2, GDP, RAS       319   1kao       9   169   1.2e−59   0.96   1.00       RAP2A; CHAIN: NULL;   GTP-BINDING PROTEIN GTP-                                               BINDING PROTEIN, SMALL G                                               PROTEIN, RAP2, GDP, RAS       319   1tx4   B   6   170   1.1e−56           97.67   P50-RHOGAP; CHAIN: A;   COMPLEX(GTPASE                                           TRANSFORMING PROTEIN RHOA;   ACTIVATN/PROTO-ONCOGENE)                                           CHAIN: B;   GTPASE-ACTIVATING PROTEIN                                               RHOGAP; COMPLEX (GTPASE                                               ACTIVATION/PROTO-ONCOGENE).                                               GTPASE, 2 TRANSITION STATE. GAP       319   1tx4   B   7   170   1.1e−56   0.65   1.00       P50-RHOGAP; CHAIN: A;   COMPLEX(GTPASE                                           TRANSFORMING PROTEIN RHOA;   ACTIVATN/PROTO-ONCOGENE)                                           CHAIN: B;   GTPASE-ACTIVATING PROTEIN                                               RHOGAP; COMPLEX (GTPASE                                               ACTIVATION/PROTO-ONCOGENE),                                               GTPASE, 2 TRANSITION STATE, GAP       319   1zbd   A   3   178   5.1e−70           154.65   RAB-3A; CHAIN: A; RABPHILIN-   COMPLEX (GTP-BINDING/EFFECTOR)                                           3A; CHAIN: B;   RAS-RELATED PROTEIN RAB3A;                                               COMPLEX (GTP-                                               BINDING/EFFECTOR), G PROTEIN,                                               EFFECTOR, RABCDR, 2 SYNAPTIC                                               EXOCYTOSIS, RAB PROTEIN, RAB3A,                                               RABPHILIN       319   1zbd   A   5   175   5.1e−70   0.92   1.00       RAB-3A; CHAIN: A; RABPHILIN-   COMPLEX (GTP-BINDING/EFFECTOR)                                           3A; CHAIN: B;   RAS-RELATED PROTEIN RAB3A;                                               COMPLEX (GTP-                                               BINDING/EFFECTOR), G PROTEIN,                                               EFFECTOR, RABCDR, 2 SYNAPTIC                                               EXOCYTOSIS, RAB PROTEIN, RAB3A,                                               RABPHILIN       319   3rab   A   4   172   1.5e−70   0.71   1.00       RAB3A; CHAIN: A;   HYDROLASE G PROTEIN,                                               VESICULAR TRAFFICKING, GTP                                               HYDROLYSIS, RAB 2 PROTEIN,                                               NEUROTRANSMITTER RELEASE,                                               HYDROLASE       319   3rab   A   4   172   1.5e−70           170.48   RAB3A; CHAIN: A;   HYDROLASE G PROTEIN,                                               VESICULAR TRAFFICKING, GTP                                               HYDROLYSIS, RAB 2 PROTEIN,                                               NEUROTRANSMITTER RELEASE,                                               HYDROLASE               321   1b0x   A   227   287   1.5e−05   1.26   0.99       EPHA4 RECEPTOR TYROSINE   TRANSFERASE RECEPTOR                                           KINASE; CHAIN: A;   TYROSINE KINASE, PROTEIN                                               INTERACTION MODULE, 2                                               DIMERIZATION DOMAIN,                                               TRANSFERASE       321   1b4f   A   226   297   1.2e−13   0.85   0.74       EPHB2; CHAIN: A, B, C, D, E, F, G,   SIGNAL TRANSDUCTION SAM                                           H;   DOMAIN, EPH RECEPTOR, SIGNAL                                               TRANSDUCTION, OLIGOMER       321   1sgg       226   287   3e−06   0.84   0.92       EPHRIN TYPE-B RECEPTOR 2;   TYROSINE-PROTEIN KINASE NMR,                                           CHAIN: NULL;   RECEPTOR OLIGOMERIZATION, EPH                                               RECEPTORS, TYROSINE 2                                               PHOSPHORYLATION, SIGNAL                                               TRANSDUCTION, TYROSINE-                                               PROTEIN 3 KINASE               323   1a17       114   266   3.4e−12   0.15   0.43       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1a17       130   279   4.5e−14   0.30   −0.01       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1a17       157   318   6e−08   0.17   −0.02       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1a17       246   380   6.8e−13   0.22   0.22       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1a17       293   400   1.7e−13   0.34   −0.12       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1a17       4   143   5.1e−16   0.43   0.07       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       323   1b89   A   11   275   0.00017   0.05   0.04       CLATHRIN HEAVY CHAIN:   CLATHRIN CLATHRIN, TRISKELION,                                           CHAIN: A;   COATED VESICLES, ENDOCYTOSIS,                                               SELF-2 ASSEMBLY, ALPHA-ALPHA                                               SUPERHELIX       323   1e96   B   162   318   6.8e−11   0.31   0.11       RAS-RELATED C3 BOTULINUM   SIGNALLING COMPLEX RAC1:                                           TOXIN SUBSTRATE 1; CHAIN: A;   P67PHOX; SIGNALLING COMPLEX,                                           NEUTROPHIL CYTOSOL FACTOR   GTPASE, NADPH OXIDASE, PROTEIN-                                           2 (NCF-2) CHAIN: B;   PROTEIN 2 COMPLEX, TPR MOTIF       323   1e96   B   2   109   6.8e−10   0.31   −0.06       RAS-RELATED C3 BOTULINUM   SIGNALLING COMPLEX RAC1;                                           TOXIN SUBSTRATE 1; CHAIN: A;   P67PHOX; SIGNALLING COMPLEX,                                           NEUTROPHIL CYTOSOL FACTOR   GTPASE, NADPH OXIDASE, PROTEIN-                                           2 (NCF-2) CHAIN: B;   PROTEIN 2 COMPLEX, TPR MOTIF       323   1e96   B   245   392   1.2e−08   0.16   −0.14       RAS-RELATED C3 BOTULINUM   SIGNALLING COMPLEX RAC1;                                           TOXIN SUBSTRATE 1; CHAIN: A;   P67PHOX; SIGNALLING COMPLEX,                                           NEUTROPHIL CYTOSOL FACTOR   GTPASE, NADPH OXIDASE, PROTEIN-                                           2 (NCF-2) CHAIN: B;   PROTEIN 2 COMPLEX, TPR MOTIF       323   1e96   B   82   232   1.2e−10   0.27   −0.02       RAS-RELATED C3 BOTULINUM   SIGNALLING COMPLEX RAC1;                                           TOXIN SUBSTRATE 1; CHAIN: A;   P67PHOX; SIGNALLING COMPLEX,                                           NEUTROPHIL CYTOSOL FACTOR   GTPASE, NADPH OXIDASE, PROTEIN-                                           2 (NCF-2) CHAIN: B;   PROTEIN 2 COMPLEX, TPR MOTIF       323   1elr   A   11   114   1.7e−15   0.50   0.90       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   121   233   1.2e−12   0.42   0.22       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   169   274   3.4e−13   0.04   0.06       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN.                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   1   74   1e−09   0.40   −0.01       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN.                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   212   313   1.2e−15   0.58   −0.05       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   252   356   1.2e−13   0.05   0.05       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   332   411   1e−11   0.04   −0.18       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   56   157   1.5e−07   −0.03   0.21       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elr   A   88   194   1.7e−13   0.19   0.28       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A: HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       323   1elw   A   126   244   3.4e−11   0.18   0.81       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN.                                           B: HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       323   1elw   A   249   366   1e−11   0.20   0.19       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN.                                           B: HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       323   1elw   A   293   393   3.4e−11   0.29   −0.08       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN,                                           B; HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       323   1elw   A   4   121   3.4e−14   0.56   0.62       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN,                                           B; HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       323   1elw   A   81   208   1.2e−08   0.18   −0.11       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN,                                           B; HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       323   1fch   A   104   410   1e−31   0.02   −0.02       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTS1-CONTAINING PEPTIDE;   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       323   1fch   A   11   317   1.2e−29   0.37   0.87       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTSI-CONTAINING PEPTIDE;   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       323   1fch   A   2   263   3.4e−23   0.36   0.99       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTS1-CONTAINING PEPTIDE;   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       323   1qqe   A   120   375   3.4e−10   0.14   0.58       VESICULAR TRANSPORT   PROTEIN TRANSPORT HELIX-TURN-                                           PROTEIN SEC17; CHAIN: A;   HELIX TPR-LIKE REPEAT, PROTEIN                                               TRANSPORT       323   1qqe   A   221   388   3.4e−10   0.01   −0.09       VESICULAR TRANSPORT   PROTEIN TRANSPORT HELIX-TURN-                                           PROTEIN SEC17; CHAIN: A;   HELIX TPR-LIKE REPEAT, PROTEIN                                               TRANSPORT       323   1qqe   A   3   188   1e−11   0.48   0.19       VESICULAR TRANSPORT   PROTEIN TRANSPORT HELIX-TURN-                                           PROTEIN SEC17; CHAIN: A;   HELIX TPR-LIKE REPEAT, PROTEIN                                               TRANSPORT       323   1qqe   A   68   359   3.4e−10           54.55   VESICULAR TRANSPORT   PROTEIN TRANSPORT HELIX-TURN-                                           PROTEIN SEC17; CHAIN: A;   HELIX TPR-LIKE REPEAT, PROTEIN                                               TRANSPORT               324   1b4f   A   28   74   0.00045   0.19   0.90       EPHB2; CHAIN: A, B, C, D, E, F, G,   SIGNAL TRANSDUCTION SAM                                           H;   DOMAIN, EPH RECEPTOR, SIGNAL                                               TRANSDUCTION, OLIGOMER               329   1b7f   A   421   559   5.1e−20   −0.15   0.98       SXL-LETHAL PROTEIN; CHAIN: A,   RNA-BINDING PROTEIN/RNA TRA                                           B; RNA (5′-   PRE-MRNA; SPLICING REGULATION,                                           R(P*GP*UP*UP*GP*UP*UP*UP*UP   RNP DOMAIN, RNA COMPLEX                                           *UP*UP*UP*U)- CHAIN: P, Q;       329   1cvj   A   423   547   1.7e−21   0.00   0.52       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       329   1cvj   B   423   535   3.4e−20   0.09   0.63       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       329   1cvj   F   423   502   3.4e−17   054   0.87       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       329   1cvj   H   423   535   1.4e−17   −0.03   0.49       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       329   1d8z   A   418   496   6.8e−19   012   0.82       HU ANTIGEN C; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       329   1hal       416   544   1.7e−17   −0.01   0.03       HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       329   2sxl       421   496   1.2e−16   0.37   0.96       SEX-LETHAL PROTEIN; CHAIN:   RNA-BINDING DOMAIN RNA-                                           NULL;   BINDING DOMAIN, ALTERNATIVE                                               SPLICING       329   2upl   A   415   550   1e−17   −0.04   0.05       HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN A1;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   A1, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA).                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN A1       329   3sxl   A   421   559   1.7e−19   0.05   0.89       SEX-LETHAL; CHAIN: A, B, C,   RNA BINDING DOMAIN RNA                                               BINDING DOMAIN, RBD, RNA                                               RECOGNITION MOTIF, RRM, 2                                               SPLICING INHIBITOR,                                               TRANSLATIONAL INHIBITOR, SEX 3                                               DETERMINATION, X CHROMOSOME                                               DOSAGE COMPENSATION               332   1adq   L   57   268   6e−98   0.86   1.00       IGG4 REA; CHAIN: A; RF-AN   COMPLEX                                           IGM/LAMBDA; CHAIN: H, L;   (IMMUNOGLOBULIN/AUTOANTIGEN)                                               COMPLEX                                               (IMMUNOGLOBULIN/AUTOANTIGEN),                                               RHEUMATOID FACTOR 2 AUTO-                                               ANTIBODY COMPLEX       332   1adq   L   57   268   6e−98           301.73   IGG4 REA; CHAIN: A; RF-AN   COMPLEX                                           IGM/LAMBDA; CHAIN: H, L;   (IMMUNOGLOBULIN/AUTOANTIGEN)                                               COMPLEX                                               (IMMUNOGLOBULIN/AUTOANTIGEN),                                               RHEUMATOID FACTOR 2 AUTO-                                               ANTIBODY COMPLEX       332   1aqk   L   56   268   6.8e−88           318.27   FAB B7-15A2; CHAIN: L, H;   IMMUNOGLOBULIN HUMAN FAB,                                               ANTI-TETANUS TOXOID, HIGH                                               AFFINITY, CRYSTAL 2 PACKING                                               MOTIF, PROGRAMMING                                               PROPENSITY TO CRYSTALLIZE. 3                                               IMMUNOGLOBULIN       332   1b2w   L   55   267   5.1e−90   0.76   1.00       ANTIBODY (LIGHT CHAIN);   IMMUNE SYSTEM                                           CHAIN: L; ANTIBODY (HEAVY   IMMUNOGLOBULIN;                                           CHAIN); CHAIN: H;   IMMUNOGLOBULIN ANTIBODY                                               ENGINEERING, HUMANIZED AND                                               CHIMERIC ANTIBODY, FAB, 2 X-RAY                                               STRUCTURE, THREE-DIMENSIONAL                                               STRYCTURE, GAMMA-3                                               INTERFERON, IMMUNE SYSTEM       332   1bjm   A   55   268   3.4e−85           322.11   LOC-LAMBDA 1 TYPE LIGHT-   IMMUNOGLOBULIN BENCE-JONES                                           CHAIN DIMER; 1BJM 6 CHAIN: A,   PROTEIN; 1BJM 8 BENCE JONES,                                           B; 1BJM 7   ANTIBODY, MULTIPLE                                               QUATERNARY STRUCTURES 1BJM 13       332   1bwm   A   7   161   3.4e−21   −0.07   0.33       ALPHA-BETA T CELL RECEPTOR   IMMUNE SYSTEM                                           (TCR) (D10); CHAIN: A;   IMMUNOGLOBULIN,                                               IMMUNORECEPTOR, IMMUNE                                               SYSTEM       332   1dee   A   55   267   1e−90   0.84   1.00       IGM RF 2A2; CHAIN: A, C, E; IGM   IMMUNE SYSTEM FAB-IBP COMPLEX                                           RF 2A2; CHAIN: B, D, F;   CRYSTAL STRUCTURE 2.7A                                           IMMUNOGLOBULIN G BINDING   RESOLUTION BINDING 2 OUTSIDE                                           PROTEIN A; CHAIN: G, H;   THE ANTIGEN COMBINING SITE                                               SUPERANTIGEN FAB VH3 3                                               SPECIFICITY       332   1dzb   A   1   162   5.1e−60   0.09   0.46       SCFV FRAGMENT IF9; CHAIN: A,   COMPLEX (ANTIBODY ANTIGEN) 1,4-                                           B; TURKEY EGG-WHITE   BETA-N-ACETYLMURAMIDASE C;                                           LYSOZYME C; CHAIN: X, Y;   SINGLE-DOMAIN ANTIBODY,                                               TURKEY EGG-WHITE LYSOZYME, 2                                               ANTIBODY-PROTEIN COMPLEX,                                               SINGLE-CHAIN FV FRAGMENT       332   1f3r   B   1   164   1.4e−61   0.14   0.98       ACETYLCHOLINE RECEPTOR   IMMUNE SYSTEM IG-FOLD, IMMUNO                                           ALPHA: CHAIN: A; FV ANTIBODY   COMPLEX, ANTIBODY-ANTIGEN.                                           FRAGMENT; CHAIN: B;   BETA-TURN       332   1igl   A   55   267   1.2e−89   0.68   1.00       IGG2A INTACT ANTIBODY-   IMMUNOGLOBULIN INTACT                                           MAB231; CHAIN: A, B, C, D   IMMUNOGLOBULIN V REGION C                                               REGION, IMMUNOGLOBULIN       332   1lil   A   57   268   4.5e−99   086   1.00       LAMBDA III BENCE JONES   IMMUNOGLOBULIN                                           PROTEIN CLE; CHAIN: A, B   IMMUNOGLOBULIN, BENCE JONES                                               PROTEIN       332   1lil   A   58   268   4.5e−99           299.68   LAMBDA III BENCE JONES   IMMUNOGLOBULIN                                           PROTEIN CLE; CHAIN: A, B   IMMUNOGLOBULIN, BENCE JONES                                               PROTEIN       332   1lmk   A   1   162   3.4e−59   0.12   0.92       IMMUNOGLOBULIN ANTI-                                           PHOSPHATIDYLINOSITOL                                           SPECIFIC PHOSPHOLIPASE C                                           DIABODY 1LMK 3 SYNONYMS:                                           L5MK16 DIABODY, SINGLE-                                           CHAIN FV DIMER 1LMK 4       332   1mcp   L   55   267   3.4e−91   0.79   1.00       IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB                                           FRAGMENT (MC/PC$603) 1MCP 4       332   1mcp   L   55   267   3.4e−91           202.00   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB                                           FRAGMENT (MC/PC$603) 1MCP 4       332   1mcw   W   55   268   1e−82           294.22   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN                                           HETEROLOGOUS LIGHT CHAIN                                           DIMER IMCW 3 (/MCG$-/WEIR$                                           HYBRID) 1MCW 4       332   1mfa       1   161   3.4e−21   −0.34   0.01       IMMUNOGLOBULIN FV                                           FRAGMENT (MURINE SE155-4)                                           COMPLEX WITH THE                                           TRISACCHARIDE: 1MFA 3                                           ALPHA-D-GALACTOSE(1-2)                                           [ALPHA-D-ABEQUOSE(1-3)]                                           ALPHA-1MFA 4 D-MANNOSE                                           (PI-OME) (PART OF THE CELL-                                           SURFACE CARBOHYDRATE                                           1MFA 5 OF PATHOGENIC                                           SALMONELLA) 1MFA 6       332   1nca   L   55   267   5.1e−91   0.78   1.00       HYDROLASE(O-GLYCOSYL)N9                                           NEURAMINIDASE-NC4I                                           (E.C.3.2.1.18) COMPLEX WITH FAB                                           1NCA 3       332   1nqb   A   1   163   5.1e−61   0.17   0.53       SINGLE-CHAIN ANTIBODY   IMMUNOGLOBULIN VARIABLE                                           FRAGMENT; CHAIN: A, C;   HEAVY (VH) DOMAIN, VARIABLE                                               LIGHT (VL) ANTIBODY FRAGMENT,                                               MULTIVALENT ANTIBODY,                                               DIABODY, DOMAIN 2 SWAPPING,                                               IMMUNOGLOBULIN       332   1qlr   A   55   267   1.5e−89   0.65   1.00       IGM KAPPA CHAIN V-III (KAU   IMMUNOGLOBULIN                                           COLD AGGLUTININ); CHAIN: A,   IMMUNOGLOBULIN,                                           C; IGM FAB REGION IV-J(H4)-C   AUTOANTIBODY, COLD                                           (KAU COLD AGGLUTININ);   AGGLUTININ, HUMAN IGM 2 FAB                                           CHAIN: B, D;   FRAGMENT       332   1qok   A   1   162   1.7e−61   0.45   0.42       MFE-23 RECOMBINANT   IMMUNOGLOBULIN                                           ANTIBODY FRAGMENT; CHAIN:   IMMUNOGLOBULIN, SINGLE-CHAIN                                           A;   FV, ANTI-CARCINOEMBRYONIC 2                                               ANTIGEN       332   1sbs   L   55   267   3.4e−92   0.89   1.00       MONOCLONAL ANTIBODY 3A2;   MONOCLONAL ANTIBODY                                           CHAIN: H, L;   MONOCLONAL ANTIBODY, FAB-                                               FRAGMENT, REPRODUCTION       332   2fb4   L   55   268   6.8e−87           326.11   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB 2FB4 4       332   2mcg   L   55   268   1.7e−86           304.84   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN LAMBDA                                           LIGHT CHAIN DIMER (/MCG$)                                           2MCG 3 (TRIGONAL FORM) 2MCG 4       332   7fab   L   55   264   3e−95           290.47   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB&#39; NEW                                           (LAMBDA LIGHT CHAIN) 7FAB 3       332   7fab   L   56   264   3e−95   0.85   1.00       IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB&#39; NEW                                           (LAMBDA LIGHT CHAIN) 7FAB 3       332   8fab   A   58   264   5.1e−87           291.96   IMMUNOGLOBULIN FAB                                           FRAGMENT FROM HUMAN                                           IMMUNOGLOBULIN IGGI                                           (LAMBDA, HIL) 8FAB 3               338   1fl3   L   39   117   0.00034   −0.04   0.22       BLUE FLUORESCENT ANTIBODY   IMMUNE SYSTEM                                           (19G2)-HEAVY CHAIN; CHAIN: H,   IMMUNOGLOBULIN FOLD                                           A; BLUE FLUORESCENT                                           ANTIBODY (19G2)-LIGHT CHAIN;                                           CHAIN: L, B;               342   1ekl   A   225   349   3.4e−14   −0.04   0.19       EPOXIDE HYDROLASE; CHAIN: A,   HYDROLASE HOMODIMER,                                           B;   ALPHA/BETA HYDROLASE FOLD,                                               DISUBSTITUTED UREA 2 INHIBITOR       342   1ek1   B   132   349   1.5e−17   0.25   0.54       EPOXIDE HYDROLASE; CHAIN: A,   HYDROLASE HOMODIMER,                                           B;   ALPHA/BETA HYDROLASE FOLD,                                               DISUBSTITUTED UREA 2 INHIBITOR       342   1fez   A   130   330   4.5e−29   0.37   0.82       PHOSPHONOACETALDEHYDE   HYDROLASE HAD-FAMILY                                           HYDROLASE; CHAIN: A, B, C, D;   ALPHA/BETA CORE DOMAIN, MG(II)                                               BINDING SITE, 5-2 HELIX BUNDLE       342   1fez   A   130   366   1.5e−23   0.56   1.00       PHOSPHONOACETALDEHYDE   HYDROLASE HAD-FAMILY                                           HYDROLASE; CHAIN: A, B, C, D;   ALPHA/BETA CORE DOMAIN, MG(II)                                               BINDING SITE, 5-2 HELIX BUNDLE       342   1qq5   A   130   386   3.4e−26           51.58   L-2-HALOACID DEHALOGENASE;   HYDROLASE L-2-HALOACID                                           CHAIN: A, B;   DEHALOGENASE, HYDROLASE       342   1qq5   A   131   362   3.4e−26   0.32   0.65       L-2-HALOACID DEHALOGENASE;   HYDROLASE L-2-HALOACID                                           CHAIN: A, B;   DEHALOGENASE, HYDROLASE       342   1zrn       130   362   1.7e−28           57.26   L-2-HALOACID DEHALOGENASE;   DEHALOGENASE DEHALOGENASE,                                           CHAIN: NULL;   HYDROLASE       342   1zrn       131   361   1.7e−28   0.29   0.76       L-2-HALOACID DEHALOGENASE;   DEHALOGENASE DEHALOGENASE,                                           CHAIN: NULL;   HYDROLASE               343   1alh   A   129   213   8.5e−24   0.05   −0.05       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       343   1alh   A   161   241   3.4e−30   0.13   0.12       QGSR ZINC FINGER PEPTlDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       343   1mey   C   145   213   3.4e−38   −0.21   0.10       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN: CHAIN; C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   160   241   6.8e−50   0.09   0.54       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   188   269   5.1e−50   −0.08   0.89       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   216   297   5.1e−50   0.20   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   244   325   3.4e−50   0.22   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   272   353   1.4e−49   0.47   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G:   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   272   354   3.4e−50           103.55   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   300   357   3.4e−33   0.42   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   C   39   142   5.1e−43   −0.12   0.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   G   158   185   1.2e−12   0.50   0.71       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1mey   G   37   64   1.7e−11   −0.39   0.13       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       343   1tf6   A   161   313   8.5e−38   −0.20   0.66       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       343   1tf6   A   187   353   8.5e−38           89.34   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       343   1tf6   A   217   355   3.4e−35   0.13   1.00       TFIIIA: CHAIN: A, D: 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE: CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       343   1ubd   C   168   269   5.1e−35   −0.19   0.69       YY1: CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1:                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       343   1ubd   C   214   325   1.2e−52   −0.09   0.93       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       343   1ubd   C   242   353   6e−53   0.03   0.99       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       343   1ubd   C   244   354   6e−53           86.36   YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       343   1ubd   C   252   353   6.8e−34   0.09   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       343   2gli   A   157   268   1.2e−31   0.00   0.27       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       343   2gli   A   188   327   1.2e−61   0.41   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       343   2gli   A   216   353   1.5e−67   0.42   0.99       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       343   2gli   A   216   355   1.5e−67           95.61   ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       343   2gli   A   224   352   3.4e−33   0.43   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       343   2gli   A   40   243   3e−23   −0.10   0.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A: DNA: CHAIN: C. D:   PROTEIN/DNA) FIVE-FINGER GL1;                                               GL1, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               345   1bbz   A   7   63   4.5e−15   −0.10   0.72       ABL TYROSINEKINASE; CHAIN:   COMPLEX (TRANSFERASE/PEPTIDE)                                           A, C, E, G; PEPTIDE P41; CHAIN: B,   COMPLEX (TRANSFERASE/PEPTIDE),                                           D, F, H;   SIGNAL TRANSDUCTION, 2 SH3                                               DOMAIN       345   1gbq   A   8   63   3e−16   −0.22   0.88       GRB2; CHAIN: A; SOS-1; CHAIN: B;   COMPLEX (SIGNAL                                               TRANSDUCTION/PEPTIDE) COMPLEX                                               (SIGNAL TRANSDUCTION/PEPTIDE),                                               SH3 DOMAIN       345   1gbr   A   8   65   3e−16   −0.04   0.98       SIGNAL TRANSDUCTION                                           PROTEIN GROWTH FACTOR                                           RECEPTOR-BOUND PROTEIN 2                                           (GRB2, N-TERMINAL 1GBR 3 SH3                                           DOMAIN) COMPLEXED WITH                                           SOS-A PEPTIDE 1GBR 4 (NMR, 29                                           STRUCTURES) 1GBR 5       345   1gfc       8   63   3e−15   0.27   0.89       ADAPTOR PROTEIN CONTAINING                                           SH2 AND SH3 GROWTH FACTOR                                           RECEPTOR-BOUND PROTEIN 2                                           (GRB2) 1GFC 3 (C-TERMINAL SH3                                           DOMAIN) (NMR, MINIMIZED                                           MEAN STRUCTURE) 1GFC 4       345   1pht       8   71   1.2e−15   −0.32   0.33       PHOSPHATIDYLINOSITOL 3-   PHOSPHOTRANSFERASE P13K SH3;                                           KINASE P85-ALPHA SUBUNIT;   1PHT 9 PHOSPHATIDYLINOSITOL 3-                                           1PHT 6 CHAIN: NULL; 1PHT 7   KINASE, P85-ALPHA SUBUNIT, SH3                                               DOMAIN 1PHT 21       345   1pks       8   63   1.5e−14   −0.24   0.30       PHOSPHOTRANSFERASE                                           PHOSPHATIDYLINOSITOL 3-                                           KINASE (E.C.2.7.1.137) (P13K) 1PKS                                           3 (SH3 DOMAIN) (NMR,                                           MINIMIZED AVERAGE                                           STRUCTURE) 1PKS 4       345   1pwt       1   63   7.5e−16   −0.09   0.99       ALPHA SPECTRIN; CHAIN: NULL;   CIRCULAR PERMUTANT PWT;                                               CIRCULAR PERMUTANT, SH3                                               DOMAIN, CYTOSKELETON       345   1qkw   A   8   63   7.5e−16   0.13   0.98       ALPHA II SPECTRIN; CHAIN: A;   CYTOSKELETON CYTOSKELETON,                                               MEMBRANE, SH3 DOMAIN       345   1sem   A   8   58   6e−15   0.30   0.92       SEM-5; 1SEM 3 CHAIN: A, B; 1SEM   SIGNAL TRANSDUCTION PROTEIN                                           5 10-RESIDUE PROLINE-RICH   SRC-HOMOLOGY 3 (SH3) DOMAIN,                                           PEPTIDE FROM MSOS 1SEM 8   PEPTIDE-BINDING PROTEIN, 1SEM 18                                           CHAIN: C, D 1SEM 10   2 GUANINE NUCLEOTIDE                                               EXCHANGE FACTOR 1SEM 19               348   2occ   K   30   78   8.5e−27   −0.76   0.60       CYTOCHROME C OXIDASE;   OXIDOREDUCTASE                                           CHAIN: A, B, C, D, E, F, G, H, I, J, K,   FERROCYTOCHROME C\:OXYGEN                                           L, M, N, O, P, Q,   OXIDOREDUCTASE;                                               OXIDOREDUCTASE,                                               CYTOCHROME(C)-OXYGEN,                                               CYTOCHROME C 2 OXIDASE       348   2occ   K   30   78   8.5e−27           69.07   CYTOCHROME C OXIDASE;   OXIDOREDUCTASE                                           CHAIN: A, B, C, D, E, F, G, H, I, J, K,   FERROCYTOCHROME C\:OXYGEN                                           L, M, N, O, P, Q,   OXIDOREDUCTASE;                                               OXIDOREDUCTASE,                                               CYTOCHROME(C)-OXYGEN,                                               CYTOCHROME C 2 OXIDASE               355   1bxe   A   66   175   5.1e−43   0.90   1.00       RIBOSOMAL PROTEIN L22;   RNA BINDING PROTEIN RIBOSOMAL                                           CHAIN: A:   PROTEIN, PROTEIN SYNTHESIS, RNA                                               BINDING, 2 ANTIBIOTICS                                               RESISTANCE, RNA BINDING                                               PROTEIN       355   1ffk   O   54   174   3.4e−23   0.21   0.60       23S RRNA; CHAIN: 0; 5S RRNA;   RIBOSOME 50S RIBOSOMAL                                           CHAIN: 9; RIBOSOMAL PROTEIN   PROTEIN L2P, HMAL2, HL4: 50S                                           L2; CHAIN: A; RIBOSOMAL   RIBOSOMAL PROTEIN L3P, HMAL3.                                           PROTEIN L3; CHAIN: B;   HL1; 50S RIBOSOMAL PROTEIN L4E,                                           RIBOSOMAL PROTEIN L4; CHAIN:   HMAL4, HL6; 50S RIBOSOMAL                                           C: RIBOSOMAL PROTEIN L5;   PROTEIN L5P, HMAL5, HL13; 30S                                           CHAIN: D; RIBOSOMAL PROTEIN   RIBOSOMAL PROTEIN HS6; 50S                                           L7AE; CHAIN: E; RIBOSOMAL   RIBOSOMAL PROTEIN L13P, HMAL13;                                           PROTEIN L10E; CHAIN: F;   50S RIBOSOMAL PROTEIN L14P,                                           RIBOSOMAL PROTEIN L13;   HMAL14, HL27; 50S RIBOSOMAL                                           CHAIN: G; RIBOSOMAL PROTEIN   PROTEIN L15P, HMAL15, HL9; 50S                                           L14; CHAIN: H; RIBOSOMAL   RIBOSOMAL PROTEIN L18P, HMAL18,                                           PROTEIN L15E, CHAIN: I;   HL12; 50S RIBOSOMAL PROTEIN                                           RIBOSOMAL PROTEIN L15;   L18E, HL29, L19; 50S RIBOSOMAL                                           CHAIN: J; RIBOSOMAL PROTEIN   PROTEIN L19E, HMAL19, HL24; 50S                                           L18; CHAIN: K; RIBOSOMAL   RIBOSOMAL PROTEIN L21E, HL31;                                           PROTEIN L18E; CHAIN: L;   50S RIBOSOMAL PROTEIN L22P,                                           RIBOSOMAL PROTEIN L19;   HMAL22, HL23; 50S RIBOSOMAL                                           CHAIN: M; RIBOSOMAL PROTEIN   PROTEIN L23P, HMAL23, HL25, L21;                                           L21E; CHAIN: N; RIBOSOMAL   50S RIBOSOMAL PROTEIN L24P,                                           PROTEIN L22; CHAIN: O;   HMAL24, HL16, HL15; 50S                                           RIBOSOMAL PROTEIN L23;   RIBOSOMAL PROTEIN L24E,                                           CHAIN: P; RIBOSOMAL PROTEIN   HL21/HL22; 50S RIBOSOMAL                                           L24; CHAIN: Q; RIBOSOMAL   PROTEIN L29P, HMAL29, HL33; 50S                                           PROTEIN L24E; CHAIN: R;   RIBOSOMAL PROTEIN L30P, HMAL30,                                           RIBOSOMAL PROTEIN L29;   HL20, HL16; 50S RIBOSOMAL                                           CHAIN: S; RIBOSOMAL PROTEIN   PROTEIN L31E, L34, HL30; 50S                                           L30; CHAIN: T; RIBOSOMAL   RIBOSOMAL PROTEIN L32E, HL5; 50S                                           PROTEIN L31E; CHAIN: U;   RIBOSOMAL PROTEIN L37E, L35E;                                           RIBOSOMAL PROTEIN L32E;   50S RIBOSOMAL PROTEINS L39E,                                           CHAIN: V; RIBOSOMAL PROTEIN   HL39E, HL46E; 50S RIBOSOMAL                                           L37AE; CHAIN: W; RIBOSOMAL   PROTEIN L44E, LA, HLA; 50S                                           PROTEIN L37E; CHAIN: X;   RIBOSOMAL PROTEIN L6P, HMAL6,                                           RIBOSOMAL PROTEIN L39E;   HL10 RIBOSOME ASSEMBLY, RNA-                                           CHAIN: Y; RIBOSOMAL PROTEIN   RNA, PROTEIN-RNA, PROTEIN-                                           L44E; CHAIN: Z; RIBOSOMAL   PROTEIN                                           PROTEIN L6; CHAIN: 1;               369   1d2h   A   70   190   1.2e−14   0.20   0.17       GLYCINE N-   TRANSFERASE                                           METHYLTRANSFERASE; CHAIN:   METHYLTRANSFERASE                                           A, B, C, D;       369   2adm   A   66   209   6.8e−13   0.14   −0.11       ADENINE-N6-DNA-   METHYLTRANSFERASE                                           METHYLTRANSFERASE TAQ1;   TRANSFERASE,                                           CHAIN: A, B;   METHYLTRANSFERASE,                                               RESTRICTION SYSTEM               371   1a02   F   108   160   4.5e−13   −0.36   0.17       NFAT; CHAIN: N; C-FOS; CHAIN:   COMPLEX                                           F; C-JUN; CHAIN: J; DNA; CHAIN:   (TRANSCRIPTION/NUCLEAR/NUCLEAR)                                           A, B;   AR) NF-AT; TRANSCRIPTION                                               FACTOR, PROTEIN-DNA COMPLEX,                                               NFAT, NF-AT, 2 AP-I, FOS-JUN,                                               QUATERNARY PROTEIN-DNA                                               COMPLEX, CRYSTAL 3 STRUCTURE,                                               TRANSCRIPTION SYNERGY,                                               COMBINATORIAL GENE 4                                               REGULATION, COMPLEX                                               (TRANSCRIPTION/NUCLEAR/NUCLEAR)       371   1a02   F   108   160   4.5e−13           62.39   NFAT; CHAIN: N; C-FOS; CHAIN:   COMPLEX                                           F; C-JUN; CHAIN: J; DNA; CHAIN:   (TRANSCRIPTION/NUCLEAR/NUCLEAR)                                           A, B;   NF-AT; TRANSCRIPTION                                               FACTOR, PROTEIN-DNA COMPLEX,                                               NFAT, NF-AT, 2 AP-1, FOS-JUN,                                               QUATERNARY PROTEIN-DNA                                               COMPLEX, CRYSTAL 3 STRUCTURE,                                               TRANSCRIPTION SYNERGY,                                               COMBINATORIAL GENE 4                                               REGULATION, COMPLEX                                               (TRANSCRIPTION/NUCLEAR/NUCLEAR)       371   1a02   F   115   146   3.4e−10   −0.05   0.69       NFAT; CHAIN: N; C-FOS; CHAIN;   COMPLEX                                           F; C-JUN; CHAIN: J; DNA; CHAIN:   (TRANSCRIPTION/NUCLEAR/NUCLEAR)                                           A, B;   NF-AT; TRANSCRIPTION                                               FACTOR, PROTEIN-DNA COMPLEX,                                               NFAT, NF-AT, 2 AP-1, FOS-JUN.                                               QUATERNARY PROTEIN-DNA                                               COMPLEX, CRYSTAL 3 STRUCTURE,                                               TRANSCRIPTION SYNERGY,                                               COMBINATORIAL GENE 4                                               REGULATION, COMPLEX                                               (TRANSCRIPTION/NUCLEAR/NUCLEAR)       371   1fos   E   107   166   3.4e−10           70.24   COMPLEX (GENE-REGULATORY                                           PROTEIN/DNA) C-JUN PROTO-                                           ONCOGENE (TRANSCRIPTION                                           FACTOR AP-1) DIMERIZED IFOS 4                                           WITH C-FOS AND COMPLEXED                                           WITH DNA IFOS 5 COILED-COIL,                                           DNA-BINDING PROTEIN,                                           HETERODIMER 1FOS 19       371   1fos   E   115   146   3.4e−10   −0.39   0.76       COMPLEX(GENE-REGULATORY                                           PROTEIN/DNA) C-JUN PROTO-                                           ONCOGENE (TRANSCRIPTION                                           FACTOR AP-1) DIMERIZED 1FOS 4                                           WITH C-FOS AND COMPLEXED                                           WITH DNA 1FOS 5 COILED-COIL,                                           DNA-BINDlNG PROTEIN,                                           HETERODIMER IFOS 19               373   1d5t   A   166   598   0   0.32   1.00       GUANINE NUCLEOTIDE   HYDROLASE INHIBITOR ULTRA-                                           DISSOCIATION INHIBITOR:   HIGH RESOLUTION                                           CHAIN: A;       373   1qo8   A   8   46   0.0045   0.01   0.17       FLAVOCYTOCHROME C3   OXIDOREDUCTASE                                           FUMARATE REDUCTASE; CHAIN:   OXIDOREDUCTASE                                           A, D;       373   3lad   A   8   48   0.006   −0.12   0.36       OXIDOREDUCTASE                                           DIHYDROLIPOAMIDE                                           DEHYDROGENASE (E.C.1.8.1.4)                                           3LAD 3               374   1alh   A   168   252   5.1e−15   0.00   0.05       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   188   280   6.8e−22   −0.03   0.30       QGSR ZINC FINGER PEPTIDE:   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   228   304   3.4e−23   0.60   0.12       QGSR ZINC FINGER PEPTIDE:   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   308   388   1.2e−29   −0.01   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   308   389   1.2e−32   −0.32   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   336   416   1e−30   0.03   0.92       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   393   472   1.2e−37   0.64   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   420   502   1.2e−37           86.81   QGSR ZINC FINGER PEPTIDE:   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   476   556   1.2e−34   0.57   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1alh   A   476   556   1.7e−31   0.43   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       374   1mey   C   186   280   3.4e−38   0.45   0.75       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   227   304   8.5e−41   0.40   0.84       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   255   360   1e−43   −0.15   0.35       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN: CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   307   388   1e−48   0.06   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN: CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   335   416   5.1e−50   −0.05   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   363   444   1e−50   0.39   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   391   472   1.7e−51   0.48   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   419   500   6.8e−51   0.55   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   447   528   1.2e−50   0.51   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   447   529   6.8e−51           106.37   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   C   475   556   1.7e−50   0.37   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1mey   G   225   252   1.5e−10   −0.12   0.69       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       374   1tf3   A   187   276   6.8e−14   0.06   −0.06       TRANSCRIPTION FACTOR IIIA;   COMPLEX (TRANSCRIPTION                                           CHAIN: A; 5S RNA GENE; CHAIN:   REGULATION/DNA) TFIIIA; 5S GENE;                                           E, F;   NMR, TFIIIA, PROTEIN, DNA,                                               TRANSCRIPTION FACTOR, 5S RNA 2                                               GENE, DNA BINDING PROTEIN, ZINC                                               FINGER, COMPLEX 3                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1tf6   A   187   341   5.1e−29   0.05   −0.07       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN;   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1tf6   A   307   470   8.5e−39           117.85   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1tf6   A   308   453   6.8e−38   0.01   0.98       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1tf6   A   336   481   1.7e−38   0.12   1.00       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1tf6   A   392   538   8.5e−39   0.13   0.96       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1tf6   A   448   556   3.4e−30   0.18   0.46       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE: CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       374   1ubd   C   166   280   8.5e−25   0.10   0.05       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   190   304   3.4e−27   0.28   0.60       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   263   360   8.5e−29   −0.15   0.19       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   287   388   5.1e−34   0.12   0.94       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   312   444   9e−41   0.13   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   315   416   1.5e−34   0.01   0.99       YY1; CHAIN: C: ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   343   444   1.5e−34   0.30   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   399   500   5.1e−36   0.23   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   418   529   1.5e−51   0.18   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   421   529   1.5e−51           98.87   YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   445   556   1.5e−46   0.20   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1ubd   C   455   556   1.5e−34   0.21   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       374   1zfd       532   558   6.8e−05   0.06   0.30       SWI5; CHAIN: NULL;   ZINC FINGER DNA BINDING DOMAIN                                               DNA BINDING MOTIF, ZINC FINGER                                               DNA BINDING DOMAIN       374   2adr       189   254   3.4e−11   −0.04   0.06       ADR1; CHAIN: NULL;   TRANSCRIPTION REGULATION                                               TRANSCRIPTION REGULATION,                                               ADRI, ZINC FINGER, NMR       374   2gli   A   161   303   8.5e−24   0.07   −0.11       ZINC FINGER PROTEIN GLII;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA: CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       374   2gli   A   287   415   1.2e−34   0.18   0.87       ZINC FINGER PROTEIN GLII;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       374   2gli   A   335   474   1.2e−61           106.08   ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       374   2gli   A   393   530   1.2e−61   0.49   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       374   2gli   A   420   557   4.5e−58   0.36   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C. D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               375   1c3t   A   1   76   1e−31   0.68   1.00       ID8 UBIQUITIN; CHAIN: A;   DE NOVO PROTEIN PROTEIN                                               DESIGN, HYDROPHOBIC CORE,                                               PACKING, ROTAMERS, ROC, 2                                               UBIQUITIN, DE NOVO PROTEIN,                                               UBIQUITIN       375   1c3t   A   1   76   1e−31           102.61   ID8 UBIQUITIN; CHAIN: A;   DE NOVO PROTEIN PROTEIN                                               DESIGN, HYDROPHOBIC CORE,                                               PACKING, ROTAMERS, ROC, 2                                               UBIQUITIN, DE NOVO PROTEIN,                                               UBIQUITIN       375   1tbe   B   1   72   1.2e−32   0.97   1.00       UBIQUITIN TETRAUBIQUITIN                                           1TBE 3       375   1tbe   B   1   72   1.2e−32           97.63   UBIQUITIN TETRAUBIQUITIN                                           1TBE 3       375   1ubi       1   76   1e−33   1.07   1.00       CHROMOSOMAL PROTEIN                                           UBIQUITIN 1UBI 3       375   1ubi       1   76   7.5e−36           105.89   CHROMOSOMAL PROTEIN                                           UBIQUITIN 1UBI 3       375   1ubi       1   76   7.5e−36   1.07   1.00       CHROMOSOMAL PROTEIN                                           UBIQUITIN 1UBI 3       375   1ud7   A   1   76   1.2e−32   0.96   1.00       UBIQUITIN CORE MUTANT ID7:   UBIQUITIN UBIQUITIN, DESIGNED                                           CHAIN: A;   CORE MUTANT       375   1ud7   A   1   76   1.2e−32           102.60   UBIQUITIN CORE MUTANT ID7:   UBIQUITIN UBIQUITIN, DESIGNED                                           CHAIN: A;   CORE MUTANT               377   1cdm   A   5   144   1.2e−62   0.90   1.00       CALCIUM-BINDING PROTEIN                                           CALMODULIN COMPLEXED                                           WITH CALMODULIN-BINDING                                           DOMAIN OF 1CDM 3                                           CALMODULIN-DEPENDENT                                           PROTEIN KINASE II 1CDM 4       377   1cdm   A   5   144   1.2e−62           149.72   CALCIUM-BINDING PROTEIN                                           CALMODULIN COMPLEXED                                           WITH CALMODULIN-BINDING                                           DOMAIN OF ICDM 3                                           CALMODULIN-DEPENDENT                                           PROTEIN KINASE II 1CDM 4       377   1cll       5   144   3.4e−66   1.07   1.00       CALCIUM-BINDING PROTEIN                                           CALMODULIN (VERTEBRATE)                                           1CLL 3       377   1cll       5   145   3.4e−66           156.05   CALCIUM-BINDING PROTEIN                                           CALMODULIN (VERTEBRATE)                                           1CLL 3       377   1cmf       74   146   1.5e−23           79.20   CALMODULIN (VERTEBRATE);   CALCIUM-BINDING PROTEIN                                           1CMF 6 CHAIN: NULL; 1CMF 7   CALMODULIN APO TR2C-DOMAIN;                                               1CMF 9       377   1cmf       81   143   1.5e−23   0.90   1.00       CALMODULIN (VERTEBRATE);   CALCIUM-BINDING PROTEIN                                           1CMF 6 CHAIN: NULL; 1CMF 7   CALMODULIN APO TR2C-DOMAIN;                                               1CMF 9       377   1exr   A   3   143   5.1e−64   0.96   1.00       CALMODULIN; CHAIN: A;   METAL TRANSPORT CALMODULIN,                                               HIGH RESOLUTION, DISORDER       377   1t71   A   81   143   1.5e−23   1.14   1.00       CALMODULIN; CHAIN: A;   TRANSPORT PROTEIN CALCIUM                                               BINDING, EF HAND, FOUR-HELIX                                               BUNDLE       377   1tnx       1   143   3.4e−50           127.27   TROPONIN C; 1TNX 4 CHAIN:   CALCIUM-BINDING PROTEIN EF-                                           NULL; 1TNX 5   HAND 1TNX 14       377   1tnx       5   143   3.4e−50   0.85   1.00       TROPONIN C; 1TNX 4 CHAIN:   CALCIUM-BINDING PROTEIN EF-                                           NULL; 1TNX 5   HAND 1TNX 14       377   1vrk   A   2   146   1.5e−66   1.08   1.00       CALMODULIN; CHAIN: A; RS20;   CALMODULIN, CALCIUM BINDING,                                           CHAIN: B;   HELIX-LOOP-HELIX, SIGNALLING, 2                                               COMPLEX(CALCIUM-BINDING                                               PROTEIN/PEPTIDE)       377   1vrk   A   2   146   1.5e−66           156.22   CALMODULIN; CHAIN: A; RS20;   CALMODULIN, CALCIUM BINDING,                                           CHAIN: B;   HELIX-LOOP-HELIX, SIGNALLING, 2                                               COMPLEX(CALCIUM-BINDING                                               PROTEIN/PEPTIDE)               384   1b7f   A   2   113   1.7e−21   0.43   0.99       SXL-LETHAL PROTEIN; CHAIN: A,   RNA-BINDING PROTEIN/RNA TRA                                           B; RNA (5′-   PRE-MRNA; SPLICING REGULATION,                                           R(P*GP*UP*UP*GP*UP*UP*UP*UP   RNP DOMAIN, RNA COMPLEX                                           *UP*UP*UP*U)-CHAIN: P, Q:       384   1b7f   A   33   205   3.4e−43   1.07   1.00       SXL-LETHAL PROTEIN; CHAIN: A,   RNA-BINDING PROTEIN/RNA TRA                                           B; RNA (5′-   PRE-MRNA; SPLICING REGULATION,                                           R(P*GP*UP*UP*GP*UP*UP*UP*UP   RNP DOMAIN, RNA COMPLEX                                           *UP*UP*UP*U)-CHAIN: P, Q;       384   1b7f   A   33   205   3.4e−43           84.87   SXL-LETHAL PROTEIN; CHAIN: A,   RNA-BINDING PROTEIN/RNA TRA                                           B; RNA (5′-   PRE-MRNA; SPLICING REGULATION,                                           R(P*GP*UP*UP*GP*UP*UP*UP*UP   RNP DOMAIN, RNA COMPLEX                                           *UP*UP*UP*U)-CHAIN: P, Q;       384   1cvj   A   2   119   1.5e−31   0.42   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   A   37   211   1.4e−43   0.72   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   A   378   500   3.4e−23   0.16   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H: RNA(5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   B   2   99   6.8e−26   0.31   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   B   37   188   1.7e−37   0.57   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   F   37   178   8.5e−28   0.33   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1cvj   H   37   181   1.4e−28   0.46   1.00       POLYDENYLATE BINDING   GENE REGULATION/RNA POLY(A)                                           PROTEIN 1; CHAIN: A, B, C, D, E,   BINDING PROTEIN 1, PABP 1; RRM,                                           F, G, H; RNA (5′-   PROTEIN-RNA COMPLEX, GENE                                           R(*AP*AP*AP*AP*AP*AP*AP*AP*   REGULATION/RNA                                           AP*AP*A)-3′); CHAIN: M, N, O, P,                                           Q, R, S, T;       384   1d8z   A   32   117   5.1e−22   0.61   1.00       HU ANTIGEN C; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       384   1d8z   A   419   501   4.5e−24   0.83   1.00       HU ANTIGEN C; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       384   1d9a   A   36   120   1.5e−17   0.77   1.00       HU ANTIGEN C; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       384   1d9a   A   418   501   4.5e−23   0.72   1.00       HU ANTIGEN C; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       384   1hal       30   205   1.7e−51   0.70   1.00       HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       384   1hal       31   204   1.7e−51           74.92   HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       384   1hal       376   494   1e−23   0.63   −0.05       HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       384   1hal       4   113   6.8e−22   0.33   0.63       HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       384   1hal       413   498   3.4e−28   0.70   1.00       HNRNP A1; CHAIN: NULL;   NUCLEAR PROTEIN                                               HETEROGENEOUS NUCLEAR                                               RIBONUCLEOPROTEIN A1, NUCLEAR                                               PROTEIN, HNRNP, RBD, RRM, RNP,                                               RNA BINDING, 2                                               RIBONUCLEOPROTEIN       384   1hdl   A   36   113   1e−22   0.91   1.00       HETEROGENEOUS NUCLEAR   RNA BINDING PROTEIN RNA-                                           RIBONUCLEOPROTEIN D0;   BINDING DOMAIN                                           CHAIN: A;       384   1hdl   A   419   494   8.5e−24   1.02   0.99       HETEROGENEOUS NUCLEAR   RNA BINDING PROTEIN RNA-                                           RIBONUCLEOPROTEIN D0;   BINDING DOMAIN                                           CHAIN: A;       384   1sxl       406   501   6e−25   0.48   0.99       RNA-BINDING PROTEIN SEX-                                           LETHAL PROTEIN (C-TERMINUS,                                           OR SECOND RNA-BINDING                                           DOMAIN 1SXL 3 (RBD-2),                                           RESIDUES 199-294 PLUS N-                                           TERMINAL MET) 1SXL 4 (NMR, 17                                           STRUCTURES) ISXL 5       384   2mss   A   36   113   6.8e−18   0.50   0.58       MUSASHI1; CHAIN: A;   RNA BINDING PROTEIN RNA-                                               BINDING DOMAIN       384   2sxl       33   118   3.4e−20   0.63   1.00       SEX-LETHAL PROTEIN; CHAIN:   RNA-BINDING DOMAIN RNA-                                           NULL;   BINDING DOMAIN, ALTERNATIVE                                               SPLICING       384   2upl   A   29   210   1.4e−53   0.69   1.00       HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN A1;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   AI, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA),                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN A1       384   2upl   A   30   213   1.4e−53           77.86   HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN A1;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   AI, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA),                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN A1       384   2upl   A   376   499   1e−24   −0.07   0.06       HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN A1;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   AI, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA),                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN A1       384   2upl   A   4   119   5.1e−23   0.44   0.63       HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN A1;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   AI, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA),                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN AI       384   2up1   A   412   501   1.5e−29   0.87   1.00       HETEROGENEOUS NUCLEAR   COMPLEX                                           RIBONUCLEOPROTEIN AI;   (RIBONUCLEOPROTEIN/DNA) HNRNP                                           CHAIN: A; 12-NUCLEOTIDE   AI, UPI; COMPLEX                                           SINGLE-STRANDED TELOMETRIC   (RIBONUCLEOPROTEIN/DNA),                                           DNA; CHAIN: B;   HETEROGENEOUS NUCLEAR 2                                               RIBONUCLEOPROTEIN AI       384   3sx1   A   2   106   1.2e−20   0.47   0.99       SEX-LETHAL; CHAIN: A, B, C;   RNA BINDING DOMAIN RNA                                               BINDING DOMAIN, RBD, RNA                                               RECOGNITION MOTIF, RRM, 2                                               SPLICING INHIBITOR,                                               TRANSLATIONAL INHIBITOR, SEX 3                                               DETERMINATION, X CHROMOSOME                                               DOSAGE COMPENSATION       384   3sx1   A   35   189   3.4e−41   0.72   1.00       SEX-LETHAL; CHAIN: A, B, C;   RNA BINDING DOMAIN RNA                                               BINDING DOMAIN, RBD, RNA                                               RECOGNITION MOTIF, RRM, 2                                               SPLICING INHIBITOR,                                               TRANSLATIONAL INHIBITOR, SEX 3                                               DETERMINATION, X CHROMOSOME                                               DOSAGE COMPENSATION               391   1a06       1   327   1.7e−63           98.83   CALCIUM/CALMODULIN-   KINASE KINASE, SIGNAL                                           DEPENDENT PROTEIN KINASE;   TRANSDUCTION,                                           CHAIN: NULL;   CALCIUM/CALMODULIN       391   1a6o       1   296   1.2e−81           153.21   PROTEIN KINASE CK2/ALPHA-   TRANSFERASE TRANSFERASE,                                           SUBUNIT; CHAIN: NULL;   SERINE/THREONINE-PROTEIN                                               KINASE, CASEIN KINASE, 2 SER/THR                                               KINASE       391   1a6o       3   295   1.2e−81   0.30   1.00       PROTEIN KINASE CK2/ALPHA-   TRANSFERASE TRANSFERASE,                                           SUBUNIT; CHAIN: NULL;   SERINE/THREONINE-PROTEIN                                               KINASE, CASEIN KINASE, 2 SER/THR                                               KINASE       391   1apm   E   1   324   6e−55           116.50   TRANSFERASE(PHOSPHOTRANSFERASE)                                           $C-/AMP$-DEPENDENT                                           PROTEIN KINASE (E.C.2.7.1.37)                                           ($C/APK$) 1APM 3 (CATALYTIC                                           SUBUNIT) ALPHA ISOENZYME                                           MUTANT WITH SER 139 1APM 4                                           REPLACED BY ALA (/S139A$)                                           COMPLEX WITH THE PEPTIDE                                           1APM 5 INHIBITOR PKI(5-24) AND                                           THE DETERGENT MEGA-8 1APM 6       391   1apm   E   2   288   1e−53   0.45   1.00       TRANSFERASE(PHOSPHOTRANSFERASE)                                           $C-/AMP$-DEPENDENT                                           PROTEIN KINASE (E.C.2.7.1.37)                                           ($C/APK$) 1APM 3 (CATALYTIC                                           SUBUNIT) ALPHA ISOENZYME                                           MUTANT WITH SER 139 1APM 4                                           REPLACED BY ALA (/S139A$)                                           COMPLEX WITH THE PEPTIDE                                           1APM 5 INHIBITOR PKI(5-24) AND                                           THE DETERGENT MEGA-8 1APM 6       391   1apm   E   2   304   6e−55   0.31   1.00       TRANSFERASE(PHOSPHOTRANSFERASE)                                           $C-/AMP$-DEPENDENT                                           PROTElN KINASE (E.C.2.7.1.37)                                           ($C/APK$) 1APM 3 (CATALYTIC                                           SUBUNIT) ALPHA ISOENZYME                                           MUTANT WITH SER 139 1APM 4                                           REPLACED BY ALA (/S139A$)                                           COMPLEX WITH THE PEPTIDE                                           1APM 5 INHIBITOR PKI(5-24) AND                                           THE DETERGENT MEGA-8 1APM 6       391   1aql       2   294   0   0.37   1.00       CYCLIN-DEPENDENT PROTEIN   PROTEIN KINASE CDK2; PROTEIN                                           KINASE 2; CHAIN: NULL;   KINASE, CELL CYCLE,                                               PHOSPHORYLATION,                                               STAUROSPORINE, 2 CELL DIVISION,                                               MITOSIS, INHIBITION       391   1aql       2   298   0           212.68   CYCLIN-DEPENDENT PROTEIN   PROTEIN KINASE CDK2; PROTEIN                                           KINASE 2; CHAIN: NULL;   KINASE, CELL CYCLE,                                               PHOSPHORYLATION,                                               STAUROSPORINE, 2 CELL DIVISION,                                               MITOSIS, INHIBITION       391   1bi8   A   3   289   3.4e−91           182.71   CYCLIN-DEPENDENT KINASE 6;   COMPLEX (KINASE/INHIBITOR)                                           CHAIN: A, C; CYCLIN-   CDK6; P19INK4D; CYCLIN                                           DEPENDENT KINASE INHIBITOR;   DEPENDENT KINASE, CYCLIN                                           CHAIN: B, D;   DEPENDENT KINASE INHIBITORY 2                                               PROTEIN, CDK, INK4, CELL CYCLE,                                               COMPLEX (KINASE/INHIBITOR)                                               HEADER HELIX       391   1bi8   A   4   289   3.4e−91   0.04   1.00       CYCLIN-DEPENDENT KINASE 6;   COMPLEX (KINASE/INHIBITOR)                                           CHAIN: A, C; CYCLIN-   CDK6; P19INK4D; CYCLIN                                           DEPENDENT KINASE INHIBITOR;   DEPENDENT KINASE, CYCLIN                                           CHAIN: B, D;   DEPENDENT KINASE INHIBITORY 2                                               PROTEIN, CDK, INK4, CELL CYCLE,                                               COMPLEX (KINASE/INHIBITOR)                                               HEADER HELIX       391   1blx   A   1   296   1.7e−99           202.88   CYCLIN-DEPENDENT KINASE 6;   COMPLEX (INHIBITOR                                           CHAIN: A; P19INK4D; CHAIN: B;   PROTEIN/KINASE) INHIBITOR                                               PROTEIN, CYCLIN-DEPENDENT                                               KINASE, CELL CYCLE 2 CONTROL,                                               ALPHA/BETA, COMPLEX (INHIBITOR                                               PROTEIN/KINASE)       391   1blx   A   4   291   1.7e−99   0.27   1.00       CYCLIN-DEPENDENT KINASE 6;   COMPLEX (INHIBITOR                                           CHAIN: A; P19INK4D; CHAIN: B;   PROTEIN/KINASE) INHIBITOR                                               PROTEIN, CYCLIN-DEPENDENT                                               KINASE, CELL CYCLE 2 CONTROL,                                               ALPHA/BETA, COMPLEX (INHIBITOR                                               PROTEIN/KINASE)       391   1byg   A   1   303   3e−34           74.19   C-TERMINAL SRC KINASE;   TRANSFERASE CSK; PROTEIN                                           CHAIN: A;   KINASE, C-TERMINAL SRC KINASE,                                               PHOSPHORYLATION, 2                                               STAUROSPORINE, TRANSFERASE       391   1cki   A   2   281   3e−55           68.61   CASEIN KINASE 1 DELTA; 1CKI 6   PHOSPHOTRANSFERASE PROTEIN                                           CHAIN: A, B; 1CKI 7   KINASE 1CKI 18       391   1cki   A   4   288   3e−55   0.17   0.89       CASEIN KINASE 1 DELTA; 1CKI 6   PHOSPHOTRANSFERASE PROTEIN                                           CHAIN: A, B; 1CKI 7   KINASE 1CKI 18       391   1cm8   A   1   326   0   0.42   1.00       PHOSPHORYLATED MAP KINASE   TRANSFERASE STRESS-ACTIVATED                                           P38-GAMMA; CHAIN: A, B;   PROTEIN KINASE-3, ERK6, ERK5: P38-                                               GAMMA, GAMMA,                                               PHOSPHORYLATION, MAP KINASE       391   1cmk   E   1   324   6.8e−56           111.92   PHOSPHOTRANSFERASE CAMP-                                           DEPENDENT PROTEIN KINASE                                           CATALYTIC SUBUNIT 1CMK 3                                           (E.C.2.7.1.37) 1CMK 4       391   1cmk   E   2   288   6.8e−56   0.46   1.00       PHOSPHOTRANSFERASE CAMP-                                           DEPENDENT PROTEIN KINASE                                           CATALYTIC SUBUNIT 1CMK 3                                           (E.C.2.7.1.37) 1CMK 4       391   1csn       1   284   5.1e−18           77.16   CASEIN KINASE-1; 1CSN 4   PHOSPHOTRANSFERASE       391   1ctp   E   1   311   1.5e−56           109.28   TRANSFERASE(PHOSPHOTRANSFERASE)                                           CAMP-DEPENDENT                                           PROTEIN KINASE (E.C.2.7.1.37)                                           (CAPK) 1CTP 3 (CATALYTIC                                           SUBUNIT) 1CTP 4       391   1f3m   C   3   297   7.5e−67   0.41   1.00       SERINE/THREONINE-PROTEIN   TRANSFERASE KINASE DOMAIN,                                           KINASE PAK-ALPHA; CHAIN: A,   AUTOINHIBITORY FRAGMENT,                                           B; SERINE/THREONINE-PROTEIN   HOMODIMER                                           KINASE PAK-ALPHA; CHAIN: C,                                           D;       391   1fgk   A   1   299   1.5e−38           95.41   FGF RECEPTOR I; CHAIN: A, B;   PHOSPHOTRANSFERASE FGFRIK,                                               FIBROBLAST GROWTH FACTOR                                               RECEPTOR 1; TRANSFERASE,                                               TYROSINE-PROTEIN KINASE, ATP-                                               BINDING, 2 PHOSPHORYLATION,                                               RECEPTOR, PHOSPHOTRANSFERASE       391   1fgk   B   1   298   7.5e−37           101.29   FGF RECEPTOR 1; CHAIN: A, B;   PHOSPHOTRANSFERASE FGFRIK,                                               FIBROBLAST GROWTH FACTOR                                               RECEPTOR 1; TRANSFERASE,                                               TYROSINE-PROTEIN KINASE, ATP-                                               BINDING, 2 PHOSPHORYLATION,                                               RECEPTOR, PHOSPHOTRANSFERASE       391   1hcl       2   294   0   0.67   1.00       HUMAN CYCLIN-DEPENDENT   PROTEIN KINASE CDK2;                                           KINASE 2; CHAIN: NULL;   TRANSFERASE, SERINE/THREONINE                                               PROTEIN KINASE, ATP-BINDING, 2                                               CELL CYCLE, CELL DIVISION,                                               MITOSIS, PHOSPHORYLATION       391   1hcl       2   298   0           239.66   HUMAN CYCLIN-DEPENDENT   PROTEIN KINASE CDK2;                                           KINASE 2; CHAIN: NULL;   TRANSFERASE, SERINE/THREONINE                                               PROTEIN KINASE, ATP-BINDING, 2                                               CELL CYCLE, CELL DIVISION,                                               MITOSIS, PHOSPHORYLATION       391   1ian       1   328   0   0.12   1.00       P38 MAP KINASE; CHAIN: NULL;   SERINE/THREONINE-PROTEIN                                               KINASE CSBP, RK, P38; PROTEIN                                               SER/THR-KINASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE       391   1ian       1   328   0           163.36   P38 MAP KINASE; CHAIN: NULL;   SERINE/THREONINE-PROTEIN                                               KINASE CSBP, RK, P38; PROTEIN                                               SER/THR-KINASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE       391   1ir3   A   1   275   4.5e−37           79.01   INSULIN RECEPTOR; CHAIN: A;   COMPLEX                                           PEPTIDE SUBSTRATE; CHAIN: B;   (TRANSFERASE/SUBSTRATE)                                               TYROSINE KINASE, SIGNAL                                               TRANSDUCTION,                                               PHOSPHOTRANSFERASE, 2                                               COMPLEX (KINASE/PEPTIDE                                               SUBSTRATE/ATP ANALOG),                                               ENZYME, 3 COMPLEX                                               (TRANSFERASE/SUBSTRATE)       391   1jnk       1   323   0   0.46   1.00       C-JUN N-TERMINAL KINASE;   TRANSFERASE JNK3; TRANSFERASE,                                           CHAIN: NULL;   JNK3 MAP KINASE,                                               SERINE/THREONINE PROTEIN 2                                               KINASE       391   1jnk       1   331   0           161.78   C-JUN N-TERMINAL KINASE;   TRANSFERASE JNK3; TRANSFERASE,                                           CHAIN: NULL;   JNK3 MAP KINASE,                                               SERINE/THREONINE PROTEIN 2                                               KINASE       391   1koa       1   302   1e−57   0.26   1.00       TWITCHIN; CHAIN: NULL;   KINASE KINASE, TWITCHIN,                                               INTRASTERIC REGULATION       391   1koa       1   358   1e−57           86.80   TWITCHIN; CHAIN: NULL;   KINASE KINASE, TWITCHIN,                                               INTRASTERIC REGULATION       391   1kob   A   1   292   1.7e−57   0.26   1.00       TWITCHIN: CHAIN: A, B;   KINASE KINASE, TWITCHIN,                                               INTRASTERIC REGULATION       391   1kob   A   1   357   1.7e−57           124.22   TWITCHIN; CHAIN: A, B;   KINASE KINASE, TWITCHIN,                                               INTRASTERIC REGULATION       391   1p38       1   328   0   0.47   1.00       MAP KINASE P38; CHAIN: NULL;   TRANSFERASE MITOGEN                                               ACTIVATED PROTEIN KINASE;                                               TRANSFERASE, MAP KINASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE, 2 P38       391   1p38       1   332   0           191.19   MAP KINASE P38; CHAIN: NULL;   TRANSFERASE MITOGEN                                               ACTIVATED PROTEIN KINASE;                                               TRANSFERASE, MAP KINASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE, 2 P38       391   1phk       1   291   1.7e−66           123.81   PHOSPHORYLASE KINASE;   KINASE RABBIT MUSCLE                                           CHAIN: NULL;   PHOSPHORYLASE KINASE;                                               GLYCOGEN METABOLISM,                                               TRANSFERASE, SERINE/THREONINE-                                               PROTEIN, 2 KINASE, ATP-BINDING,                                               CALMODULIN-BINDING       391   1phk       3   291   1.7e−66   0.37   1.00       PHOSPHORYLASE KINASE;   KINASE RABBIT MUSCLE                                           CHAIN: NULL;   PHOSPHORYLASE KINASE;                                               GLYCOGEN METABOLISM,                                               TRANSFERASE, SERINE/THREONINE-                                               PROTEIN, 2 KINASE, ATP-BINDING,                                               CALMODULIN-BINDING       391   1pme       1   330   0   0.53   1.00       ERK2: CHAIN: NULL;   TRANSFERASE MAP KINASE,                                               SERINE/THREONINE PROTEIN                                               KINASE, TRANSFERASE       391   1pme       1   331   0           183.19   ERK2; CHAIN: NULL;   TRANSFERASE MAP KINASE,                                               SERINE/THREONINE PROTEIN                                               KINASE, TRANSFERASE       391   1tki   A   1   358   1.7e−45           114.84   TITIN; CHAIN: A, B;   SERINE KINASE SERINE KINASE,                                               TITIN, MUSCLE, AUTOINHIBITION       391   3erk       1   325   0           187.32   EXTRACELLULAR REGULATED   TRANSFERASE MITOGEN                                           KINASE 2; CHAIN: NULL;   ACTIVATED PROTEIN KINASE, MAP                                               2, ERK2; TRANSFERASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE, MAP KINASE, 2 ERK2       391   3erk       1   326   0   0.54   1.00       EXTRACELLULAR REGULATED   TRANSFERASE MITOGEN                                           KINASE 2; CHAIN: NULL;   ACTIVATED PROTEIN KINASE, MAP                                               2, ERK2; TRANSFERASE,                                               SERINE/THREONINE-PROTEIN                                               KINASE, MAP KINASE, 2 ERK2               393   1apq       120   154   1.5e−11   −0.02   1.00       COMPLEMENT PROTEASE CIR:   COMPLEMENT COMPLEMENT, EGF,                                           CHAIN: NULL;   CALCIUM BINDING, SERINE                                               PROTEASE       393   1ek4   A   5   111   6e−25   0.51   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       393   1ek4   A   527   709   1e−46   1.12   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       393   1dan   L   116   205   4.5e−20   −0.44   0.65       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   124   246   3e−32   −0.30   0.10       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   168   287   4.5e−31   −0.15   0.55       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   207   328   6e−31   −0.25   0.57       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   248   369   3e−25   −0.40   0.11       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   276   358   6.8e−16   −0.17   0.84       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   317   397   3.4e−16   −0.32   0.47       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   332   451   9e−25   −0.23   0.17       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   336   447   1.7e−18   −0.42   0.00       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   372   492   9e−26   −0.12   0.05       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   412   535   1.2e−30   0.20   0.22       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   439   528   1.7e−17   −0.09   0.94       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   (GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dqb   A   438   525   7.5e−17   0.40   0.98       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       393   1dva   L   317   397   3.4e−16   −0.62   0.58       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       393   1dva   L   439   528   1.7e−17   0.21   0.84       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       393   1dx5   I   121   233   1e−23   0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   153   274   3e−25   0.09   0.55       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   195   315   4.5e−27   0.30   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   235   346   1.2e−17   0.02   0.99       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   236   356   1.5e−26   −0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   318   438   1.5e−22   0.19   0.93       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   359   479   3e−24   0.41   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   401   520   3e−24   0.61   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   79   188   6.8e−15   −0.40   0.05       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1emn       273   347   5.1e−19   0.06   0.78       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       317   388   3.4e−18   −0.20   0.99       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       440   511   5.1e−18   0.32   1.00       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1fak   L   150   246   7.5e−22   −0.23   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   192   287   1.5e−21   −0.05   0.24       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   232   328   3e−23   0.08   0.80       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   273   369   3e−18   −0.27   0.15       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   276   358   6.8e−16   0.01   0.90       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   317   397   3.4e−16   −0.41   0.35       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   355   451   6e−19   0.35   0.23       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   396   492   4.5e−19   0.09   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   437   527   3e−21   0.44   0.76       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   439   528   1.7e−17   0.22   0.98       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1ido       1   109   4.5e−24   0.33   0.84       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1ido       527   707   4.5e−46           98.35   INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1ido       529   706   4.5e−46   1.04   1.00       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1jia   A   205   321   1.5e−19   0.01   −0.02       PHOSPHOLIPASE A2; CHAIN: A, B;   PHOSPHOLIPASE PHOSPHOLIPASE                                               A2, AGKISTRODON HALYS PALLAS                                               CRYSTAL 2 STRUCTURE       393   1lfa   A   1   112   1.5e−24   0.01   0.89       CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               1LFA 8       393   1lfa   A   526   711   1.5e−53           93.64   CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               1LFA 8       393   1lfa   A   526   713   1.5e−53   1.12   1.00       CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               1LFA 8       393   1pfx   L   157   301   4.5e−30   −0.01   0.07       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   197   341   3e−29   −0.15   0.81       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   286   423   3e−23   −0.10   0.06       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   403   527   6e−25   0.06   0.41       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   440   538   1.2e−15   −0.13   0.11       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1qfk   L   444   528   1.7e−16   0.30   0.86       COAGULATION FACTOR VIIA   SERINE PROTEASE FVIIA; FVIIA;                                           (LIGHT CHAIN); CHAIN: L;   BLOOD COAGULATION, SERINE                                           COAGULATION FACTOR VIIA   PROTEASE                                           (HEAVY CHAIN); CHAIN: H;                                           TRIPEPTIDYL INHIBITOR; CHAIN:                                           C;       393   1xka   L   444   528   1.7e−14   0.33   0.64       BLOOD COAGULATION FACTOR   BLOOD COAGULATION FACTOR                                           XA; CHAIN: L, C;   STUART FACTOR; BLOOD                                               COAGULATION FACTOR, SERINE                                               PROTEINASE, EPIDERMAL 2                                               GROWTH FACTOR LIKE DOMAIN       393   1apq       120   154   1.5e−11   −0.02   1.00       COMPLEMENT PROTEASE CIR;   COMPLEMENT COMPLEMENT, EGF,                                           CHAIN: NULL;   CALCIUM BINDING, SERINE                                               PROTEASE       393   1aut   L   80   151   1.2e−10   −0.62   0.05       ACTIVATED PROTEIN C; CHAIN:   COMPLEX (BLOOD                                           C, L; D-PHE-PRO-MAI; CHAIN: P;   COAGULATION/INHIBITOR)                                               AUTOPROTHROMBIN IIA;                                               HYDROLASE, SERINE PROTEINASE),                                               PLASMA CALCIUM BINDING, 2                                               GLYCOPROTEIN, COMPLEX (BLOOD                                               COAGULATION/INHIBITOR)       393   1ck4   A   5   111   6e−25   0.51   1.00       INTEGRIN ALPHA-I; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       393   1ck4   A   527   709   1e−46   1.12   1.00       INTEGRIN ALPHA-I; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       393   1dan   L   116   205   4.5e−20   −0.44   0.65       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   124   246   3e−32   −0.30   0.10       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA, CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   168   287   4.5e−31   −0.15   0.55       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   207   328   6e−31   −0.25   0.57       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   248   369   3e−25   −0.40   0.11       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   273   365   1.2e−16   0.02   0.23       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   332   451   9e−25   −0.23   0.17       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   372   492   9e−26   −0.12   0.05       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   412   535   1.2e−30   0.20   0.22       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dan   L   439   528   1.7e−18   0.18   0.89       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINI:                                           VIIA: CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       393   1dqb   A   315   401   1.1e−15   0.05   0.69       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       393   1dqb   A   438   525   7.5e−17   0.40   0.98       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       393   1dva   L   273   365   1.2e−16   −0.09   0.63       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       393   1dva   L   439   528   1.7e−18   0.32   0.92       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, 1; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D: PEPTIDE E-76;                                           CHAIN: X, Y;       393   1dx5   I   121   233   1e−23   0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN: EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   153   274   3e−25   0.09   0.55       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   195   315   4.5e−27   0.30   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   236   356   1.5e−26   −0.04   1.00       THROMBIN LIGHT CHAIN:   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D: THROMBIN   FACTOR II: COAGULATION FACTOR                                           HEAVY CHAIN: CHAIN: M, N, O, P:   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   316   438   3.4e−17   −0.08   0.99       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   318   438   1.5e−22   0.19   0.93       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   359   479   3e−24   0.41   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   401   520   3e−24   0.61   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D: THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   442   525   1.5e−13   0.45   0.78       THROMBIN LIGHT CHAIN:   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II: FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L: THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1dx5   I   77   188   3.4e−15   −0.52   0.18       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       393   1emn       112   187   3.4e−16   0.12   0.96       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING.                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       235   306   1.7e−18   0.27   0.81       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       273   347   1.7e−17   0.10   0.88       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       317   392   1e−17   −0.34   0.80       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1emn       710   779   6.8e−15   0.06   −0.19       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       393   1fak   L   107   164   6e−11   −0.12   0.31       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX (SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   150   246   7.5e−22   −0.23   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   192   287   1.5e−21   −0.05   0.24       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND).                                               BLOOD CLOTTING       393   1fak   L   232   328   3e−23   0.08   0.80       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA:   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   273   365   1.2e−16   −0.05   0.21       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND).                                               BLOOD CLOTTING       393   1fak   L   273   369   3e−18   −0.27   0.15       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA:   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T: 5LI5; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   355   451   6e−19   0.35   0.23       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   396   492   4.5e−19   0.09   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   437   527   3e−21   0.44   0.76       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA: CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H: SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1fak   L   439   528   1.7e−18   0.13   0.94       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR.                                           1;   RECEPTOR ENZYME, 3 INHIBITOR.                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       393   1ido       1   109   4.5e−24   0.33   0.84       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1ido       527   707   4.5e−46           98.35   INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1ido       529   706   4.5e−46   1.04   1.00       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       393   1jia   A   205   321   1.5e−19   0.01   −0.02       PHOSPHOLIPASE A2; CHAIN: A, B;   PHOSPHOLIPASE PHOSPHOLIPASE                                               A2, AGKISTRODON HALYS PALLAS                                               CRYSTAL 2 STRUCTURE       393   1lfa   A   1   112   1.5e−24   0.01   0.89       CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       393   1lfa   A   526   711   1.5e−53           93.74   CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       393   1lfa   A   526   713   1.5e−53   1.12   1.00       CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               1LFA 8       393   1pfx   L   157   301   4.5e−30   −0.01   0.07       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   197   341   3e−29   −0.15   0.81       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   286   423   3e−23   −0.10   0.06       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   403   527   6e−25   0.06   0.41       FACTOR IXA: CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1pfx   L   440   536   8.5e−15   0.30   0.94       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       393   1qfk   L   444   528   3.4e−17   0.06   0.92       COAGULATION FACTOR VIIA   SERINE PROTEASE FVIIA; FVIIA;                                           (LIGHT CHAIN); CHAIN: L;   BLOOD COAGULATION, SERINE                                           COAGULATION FACTOR VIIA   PROTEASE                                           (HEAVY CHAIN); CHAIN: H;                                           TRIPEPTIDYL INHIBITOR; CHAIN:                                           C;       393   1xka   L   444   528   1.5e−14   0.33   0.64       BLOOD COAGULATION FACTOR   BLOOD COAGULATION FACTOR                                           XA; CHAIN: L, C;   STUART FACTOR; BLOOD                                               COAGULATION FACTOR, SERINE                                               PROTEINASE, EPIDERMAL 2                                               GROWTH FACTOR LIKE DOMAIN               394   1apq       120   154   1.5e−11   −0.02   1.00       COMPLEMENT PROTEASE CIR;   COMPLEMENT COMPLEMENT, EGF,                                           CHAIN: NULL;   CALCIUM BINDING, SERINE                                               PROTEASE       394   1ck4   A   5   111   6e−25   0.51   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN 1-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       394   1ck4   A   527   709   1e−46   1.12   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN 1-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       394   1dan   L   116   205   4.5e−20   −0.44   0.65       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           DFFRCMK) WITH CHAIN: C;       394   1dan   L   124   246   3e−32   −0.30   0.10       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR: CHAIN: T, U: D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   168   287   4.5e−31   −0.15   0.55       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   207   328   6e−31   −0.25   0.57       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   248   369   3e−25   −0.40   0.11       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   276   358   6.8e−16   −0.17   0.84       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   317   397   3.4e−16   −0.32   0.47       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   332   451   9e−25   −0.23   0.17       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   336   447   1.7e−18   −0.42   0.00       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   372   492   9e−26   −0.12   0.05       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   412   535   1.2e−30   0.20   0.22       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   439   528   1.7e−17   −0.09   0.94       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dqb   A   438   525   7.5e−17   0.40   0.98       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       394   1dva   L   317   397   3.4e−16   −0.62   0.58       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       394   1dva   L   439   528   1.7e−17   0.21   0.84       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN): CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       394   1dx5   I   121   233   1e−23   0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   153   274   3e−25   0.09   0.55       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, 0, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   195   315   4.5e−27   0.30   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F;   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   235   346   1.2e−17   0.02   0.99       THROMBIN LIGHT CHAIN:   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   236   356   1.5e−26   −0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   318   438   1.5e−22   0.19   0.93       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   359   479   3e−24   0.41   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN: EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS.                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   401   520   3e−24   0.61   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   79   188   6.8e−15   −0.40   0.05       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CDI41                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1emn       273   347   5.1e−19   0.06   0.78       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-1 FRAGMENT,                                               MATRIX PROTEIN       394   1emn       317   388   3.4e−18   −0.20   0.99       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-1 FRAGMENT,                                               MATRIX PROTEIN       394   1emn       440   511   5.1e−18   0.32   1.00       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-1 FRAGMENT,                                               MATRIX PROTEIN       394   1fak   L   150   246   7.5e−22   −0.23   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   192   287   1.5e−21   −0.05   0.24       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   232   328   3e−23   0.08   0.80       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   273   369   3e−18   −0.27   0.15       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   276   358   6.8e−16   0.01   0.90       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   317   397   3.4e−16   −0.41   0.35       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   355   451   6e−19   0.35   0.23       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1 fak   L   396   492   4.5e−19   0.09   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   437   527   3e−21   0.44   0.76       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   439   528   1.7e−17   0.22   0.98       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           1;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1ido       1   109   4.5e−24   0.33   0.84       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1ido       527   707   4.5e−46           98.35   INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1ido       529   706   4.5e−46   1.04   1.00       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1jia   A   205   321   1.5e−19   0.01   −0.02       PHOSPHOLIPASE A2; CHAIN: A, B;   PHOSPHOLIPASE PHOSPHOLIPASE                                               A2, AGKISTRODON HALYS PALLAS                                               CRYSTAL 2 STRUCTURE       394   1lfa   A   1   112   1.5e−24   0.01   0.89       CD11A; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1lfa   A   526   711   1.5e−53           93.64   CD11A; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1lfa   A   526   713   1.5e−53   1.12   1.00       CD11A; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-1, ALPHA-                                               L\, BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1pfx   L   157   301   4.5e−30   −0.01   0.07       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   197   341   3e−29   −0.15   0.81       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   286   423   3e−23   −0.10   0.06       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   403   527   6e−25   0.06   0.41       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   440   538   1.2e−15   −0.13   0.11       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: 1;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1qfk   L   444   528   1.7e−16   0.30   0.86       COAGULATION FACTOR VIIA   SERINE PROTEASE FVIIA; FVIIA;                                           (LIGHT CHAIN); CHAIN: L;   BLOOD COAGULATION, SERINE                                           COAGULATION FACTOR VIIA   PROTEASE                                           (HEAVY CHAIN); CHAIN: H;                                           TRIPEPTIDYL INHIBITOR; CHAIN:                                           C;       394   1xka   L   444   528   1.7e−14   0.33   0.64       BLOOD COAGULATION FACTOR   BLOOD COAGULATION FACTOR                                           XA; CHAIN: L, C;   STUART FACTOR; BLOOD                                               COAGULATION FACTOR, SERINE                                               PROTEINASE, EPIDERMAL 2                                               GROWTH FACTOR LIKE DOMAIN       394   1apq       120   154   1.5e−11   −0.02   1.00       COMPLEMENT PROTEASE CIR;   COMPLEMENT COMPLEMENT, EGF,                                           CHAIN: NULL;   CALCIUM BINDING, SERINE                                               PROTEASE       394   1aut   L   80   151   1.2e−10   −0.62   0.05       ACTIVATED PROTEIN C; CHAIN:   COMPLEX (BLOOD                                           C, L; D-PHE-PRO-MAI; CHAIN: P;   COAGULATION/INHIBITOR)                                               AUTOPROTHROMBIN IIA;                                               HYDROLASE, SERINE PROTEINASE).                                               PLASMA CALCIUM BINDING, 2                                               GLYCOPROTEIN, COMPLEX (BLOOD                                               COAGULATION/INHIBITOR)       394   1ck4   A   5   111   6e−25   0.51   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       394   1ck4   A   527   709   1e−46   1.12   1.00       INTEGRIN ALPHA-1; CHAIN: A, B;   STRUCTURAL PROTEIN I-DOMAIN,                                               METAL BINDING, COLLAGEN,                                               ADHESION       394   1dan   L   116   205   4.5e−20   −0.44   0.65       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   124   246   3e−32   −0.30   0.10       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   168   287   4.5e−31   -0.15   0.55       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H: SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   207   328   6e−31   −0.25   0.57       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   248   369   3e−25   −0.40   0.11       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   273   365   1.2e−16   0.02   0.23       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   332   451   9e−25   −0.23   0.17       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   372   492   9e−26   −0.12   0.05       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   412   535   1.2e−30   0.20   0.22       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dan   L   439   528   1.7e−18   0.18   0.89       BLOOD COAGULATION FACTOR   BLOOD COAGULATION, SERINE                                           VIIA; CHAIN: L, H; SOLUBLE   PROTEASE, COMPLEX, CO-FACTOR,                                           TISSUE FACTOR; CHAIN: T, U; D-   2 RECEPTOR ENZYME, INHIBITOR,                                           PHE-PHE-ARG-   GLA, EGF, 3 COMPLEX (SERINE                                           CHLOROMETHYLKETONE   PROTEASE/COFACTOR/LIGAND)                                           (DFFRCMK) WITH CHAIN: C;       394   1dqb   A   315   401   1.1e−15   0.05   0.69       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       394   1dqb   A   438   525   7.5e−17   0.40   0.98       THROMBOMODULIN; CHAIN: A;   MEMBRANE PROTEIN NMR,                                               THROMBIN, EGF MODULE,                                               ANTICOAGULANT,                                               GLYCOSYLATION       394   1dva   L   273   365   1.2e−16   −0.09   0.63       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, 1; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       394   1dva   L   439   528   1.7e−18   0.32   0.92       DES-GLA FACTOR VIIA (HEAVY   HYDROLASE/HYDROLASE                                           CHAIN); CHAIN: H, I; DES-GLA   INHIBITOR PROTEIN-PEPTIDE                                           FACTOR VIIA (LIGHT CHAIN);   COMPLEX                                           CHAIN: L, M; (DPN)-PHE-ARG;                                           CHAIN: C, D; PEPTIDE E-76;                                           CHAIN: X, Y;       394   1dx5   I   121   233   1e−23   0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   153   274   3e−25   0.09   0.55       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   195   315   4.5e−27   0.30   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   236   356   1.5e−26   −0.04   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   316   438   3.4e−17   −0.08   0.99       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATlON FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P:   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   318   438   1.5e−22   0.19   0.93       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   359   479   3e−24   0.41   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   401   520   3e−24   0.61   1.00       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   442   525   1.5e−13   0.45   0.78       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1dx5   I   77   188   3.4e−15   −0.52   0.18       THROMBIN LIGHT CHAIN;   SERINE PROTEINASE COAGULATION                                           CHAIN: A, B, C, D; THROMBIN   FACTOR II; COAGULATION FACTOR                                           HEAVY CHAIN; CHAIN: M, N, O, P;   II; FETOMODULIN, TM, CD141                                           THROMBOMODULIN; CHAIN: I, J,   ANTIGEN; EGR-CMK SERINE                                           K, L; THROMBIN INHIBITOR L-   PROTEINASE, EGF-LIKE DOMAINS,                                           GLU-L-GLY-L-ARM; CHAIN: E, F,   ANTICOAGULANT COMPLEX, 2                                           G, H;   ANTIFIBRINOLYTIC COMPLEX       394   1emn       112   187   3.4e−16   0.12   0.96       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       394   1emn       235   306   1.7e−18   0.27   0.81       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       394   1emn       273   347   1.7e−17   0.10   0.88       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       394   1emn       317   392   1e−17   −0.34   0.80       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALClUM-BINDlNG,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       394   1emn       710   779   6.8e−15   0.06   −0.19       FIBRILLIN; CHAIN: NULL;   MATRIX PROTEIN EXTRACELLULAR                                               MATRIX, CALCIUM-BINDING,                                               GLYCOPROTEIN, 2 REPEAT, SIGNAL,                                               MULTIGENE FAMILY, DISEASE                                               MUTATION, 3 EGF-LIKE DOMAIN,                                               HUMAN FIBRILLIN-I FRAGMENT,                                               MATRIX PROTEIN       394   1fak   L   107   164   6e−11   −0.12   0.31       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   150   246   7.5e−22   −0.23   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   192   287   1.5e−21   −0.05   0.24       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   232   328   3e−23   0.08   0.80       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   273   365   1.2e−16   −0.05   0.21       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   273   369   3e−18   −0.27   0.15       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   355   451   6e−19   0.35   0.23       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   396   492   4.5e−19   0.09   0.10       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   437   527   3e−21   0.44   0.76       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1fak   L   439   528   1.7e−18   0.13   0.94       BLOOD COAGULATION FACTOR   BLOOD CLOTTING                                           VIIA; CHAIN: L; BLOOD   COMPLEX(SERINE                                           COAGULATION FACTOR VIIA;   PROTEASE/COFACTOR/LIGAND),                                           CHAIN: H; SOLUBLE TISSUE   BLOOD COAGULATION, 2 SERINE                                           FACTOR; CHAIN: T; 5L15; CHAIN:   PROTEASE, COMPLEX, CO-FACTOR,                                           I;   RECEPTOR ENZYME, 3 INHIBITOR,                                               GLA, EGF, COMPLEX (SERINE 4                                               PROTEASE/COFACTOR/LIGAND),                                               BLOOD CLOTTING       394   1ido       1   109   4.5e−24   0.33   0.84       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1ido       527   707   4.5e−46           98.35   INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1ido       529   706   4.5e−46   1.04   1.00       INTEGRIN; CHAIN: NULL;   CELL ADHESION PROTEIN A-                                               DOMAIN INTEGRIN, CELL ADHESION                                               PROTEIN, GLYCOPROTEIN,                                               EXTRACELLULAR 2 MATRIX,                                               CYTOSKELETON       394   1jia   A   205   321   1.5e−19   0.01   −0.02       PHOSPHOLIPASE A2; CHAIN: A, B;   PHOSPHOLIPASE PHOSPHOLIPASE                                               A2, AGKISTRODON HALYS PALLAS                                               CRYSTAL 2 STRUCTURE       394   1lfa   A   1   112   1.5e−24   0.01   0.89       CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-I, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1lfa   A   526   711   1.5e−53           93.74   CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-I, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1lfa   A   526   713   1.5e−53   1.12   1.00       CDIIA; ILFA 5 CHAIN: A, B; ILFA 6   CELL ADHESION LFA-I, ALPHA-                                               L\,BETA-2 INTEGRIN, A-DOMAIN;                                               ILFA 8       394   1pfx   L   157   301   4.5e−30   −0.01   0.07       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   197   341   3e−29   −0.15   0.81       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   286   423   3e−23   −0.10   0.06       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   403   527   6e−25   0.06   0.41       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1pfx   L   440   536   8.5e−15   0.30   0.94       FACTOR IXA; CHAIN: C, L,; D-   COMPLEX (BLOOD                                           PHE-PRO-ARG; CHAIN: I;   COAGULATION/INHIBITOR)                                               CHRISTMAS FACTOR; COMPLEX,                                               INHIBITOR, HEMOPHILIA/EGF,                                               BLOOD COAGULATION, 2 PLASMA,                                               SERINE PROTEASE, CALCIUM-                                               BINDING, HYDROLASE, 3                                               GLYCOPROTEIN       394   1qfk   L   444   528   3.4e−17   0.06   0.92       COAGULATION FACTOR VIIA   SERINE PROTEASE FVIIA; FVIIA;                                           (LIGHT CHAIN); CHAIN: L;   BLOOD COAGULATION, SERINE                                           COAGULATION FACTOR VIIA   PROTEASE                                           (HEAVY CHAIN); CHAIN: H;                                           TRIPEPTIDYL INHIBITOR; CHAIN:                                           C;       394   1xka   L   444   528   1.5e−14   0.33   0.64       BLOOD COAGULATION FACTOR   BLOOD COAGULATION FACTOR                                           XA; CHAIN: L, C;   STUART FACTOR; BLOOD                                               COAGULATION FACTOR, SERINE                                               PROTEINASE, EPIDERMAL 2                                               GROWTH FACTOR LIKE DOMAIN               399   1aip   A   183   403   3.4e−67   −0.15   0.17       ELONGATION FACTOR TU;   COMPLEX OF TWO ELONGATION                                           CHAIN: A, B, E, F; ELONGATION   FACTORS EF-TU; EF-TS;                                           FACTOR TS; CHAIN: C, D, G, H;   ELONGATION FACTOR,                                               NUCLEOTIDE EXCHANGE, GTP-                                               BINDING, 2 COMPLEX OF TWO                                               ELONGATION FACTORS       399   1efc   A   183   403   3.4e−71   −0.23   0.01       ELONGATION FACTOR; CHAIN:   RNA BINDING PROTEIN EFTU;                                           A, B;   TRANSPORT AND PROTECTION                                               PROTEIN, RNA BINDING PROTEIN       399   1efu   A   183   403   5.1e−65   −0.21   0.09       ELONGATION FACTOR TU;   COMPLEX (TWO ELONGATION                                           CHAIN: A, C; ELONGATION   FACTORS) ELONGATION FACTOR                                           FACTOR TS; CHAIN: B, D;   FOR TRANSFER, HEAT UNSTABLE,                                               ELONGATION FACTOR FOR                                               TRANSFER, HEAT STABLE,                                               ELONGATION FACTOR, COMPLEX                                               (TWO ELONGATION FACTORS)       399   1ega   A   184   388   6.8e−38   −0.11   0.13       GTP-BINDING PROTEIN ERA;   HYDROLASE ERA, GTPASE, RNA-                                           CHAIN: A, B;   BINDING, RAS-LIKE, HYDROLASE       399   1etu       183   343   5.1e−47   0.07   0.41       TRANSPORT AND PROTECTION                                           PROTEIN ELONGATION FACTOR                                           TU (DOMAIN I) —*GUANOSINE                                           DIPHOSPHATE IETU 4 COMPLEX                                           IETU 5       399   1exm   A   183   403   1.7e−73   −0.28   0.10       ELONGATION FACTOR TU (EF-   TRANSLATION EF-TU; GTPASE,                                           TU); CHAIN: A;   MOLECULAR SWITCH, TRNA,                                               RIBOSOME, Q-BETA REPLICASE, 2                                               CHAPERONE, DISULFIDE                                               ISOMERASE       399   1f60   A   183   400   1e−73   −0.34   0.07       ELONGATION FACTOR EEFIA;   TRANSLATION PROTEIN-PROTEIN                                           CHAIN: A; ELONGATION FACTOR   COMPLEX                                           EEFIBA; CHAIN: B;       399   1kao       184   342   1.7e−05   −0.06   0.13       RAP2A; CHAIN: NULL;   GTP-BINDING PROTEIN GTP-                                               BINDING PROTEIN, SMALL G                                               PROTEIN, RAP2, GDP, RAS               402   1alh   A   167   239   1.5e−20   −0.09   0.27       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       402   1alh   A   186   271   1.5e−20           58.92   QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       402   1alh   A   243   310   3.4e−24   0.08   1.00       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       402   1mey   C   166   239   5.1e−37   −0.10   0.30       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       402   1mey   C   185   269   1.4e−44   −0.23   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       402   1mey   C   214   300   1.4e−44           67.85   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       402   1mey   C   242   310   1e−37   −0.09   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       402   1spl       273   301   0.00015   −0.17   0.99       SPIF3; CHAIN: NULL;   ZINC FINGER TRANSCRIPTION                                               FACTOR SPI; ZINC FINGER,                                               TRANSCRIPTION ACTIVATION, SPI       402   1tf3   A   214   303   3.4e−20           67.04   TRANSCRIPTION FACTOR IIIA;   COMPLEX (TRANSCRIPTION                                           CHAIN: A; 5S RNA GENE; CHAIN:   REGULATION/DNA) TFIIIA; 5S GENE;                                           E, F;   NMR, TFIIIA, PROTEIN, DNA,                                               TRANSCRIPTION FACTOR, 5S RNA 2                                               GENE, DNA BINDING PROTEIN, ZINC                                               FINGER, COMPLEX 3                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   1tf3   A   243   307   3.4e−20   0.06   0.48       TRANSCRIPTION FACTOR IIIA;   COMPLEX (TRANSCRIPTION                                           CHAIN: A; 5S RNA GENE; CHAIN:   REGULATION/DNA) TFIIIA; 5S GENE;                                           E, F;   NMR, TFIIIA, PROTEIN, DNA,                                               TRANSCRIPTION FACTOR, 5S RNA 2                                               GENE, DNA BINDING PROTEIN, ZINC                                               FINGER, COMPLEX 3                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   1tf6   A   108   295   5.1e−39           78.75   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       402   1tf6   A   167   306   5.1e−39   −0.11   0.39       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       402   1ubd   C   167   269   1.7e−33   −0.23   0.31       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   1ubd   C   187   300   5.1e−49           165.14   YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   1ubd   C   190   299   5.1e−49   0.13   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   1ubd   C   222   310   1.7e−30   −0.28   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       402   2gli   A   149   301   8.5e−38           82.64   ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       402   2gli   A   167   298   8.5e−38   −0.15   0.94       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GL1, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               404   1fjg   Q   71   147   1.5e−28   0.12   0.99       16S RIBOSOMAL RNA; CHAIN: A;   RIBOSOME 30S RIBOSOMAL                                           FRAGMENT OF MESSENGER   SUBUNIT, RIBOSOME, ANTIBIOTIC,                                           RNA; CHAIN: X; 30S RIBOSOMAL   STREPTOMYCIN, 2 SPECTINOMYCIN,                                           PROTEIN S2; CHAIN: B; 30S   PAROMOMYCIN                                           RIBOSOMAL PROTEIN S3; CHAIN:                                           C; 30S RIBOSOMAL PROTEIN S4;                                           CHAIN: D; 30S RIBOSOMAL                                           PROTEIN S5; CHAIN: E; 30S                                           RIBOSOMAL PROTEIN S6; CHAIN:                                           F; 30S RIBOSOMAL PROTEIN S7;                                           CHAIN: G; 30S RIBOSOMAL                                           PROTEIN S8; CHAIN: H; 30S                                           RIBOSOMAL PROTEIN S9; CHAIN:                                           I; 30S RIBOSOMAL PROTEIN S10;                                           CHAIN: J; 30S RIBOSOMAL                                           PROTEIN S11; CHAIN: K; 30S                                           RIBOSOMAL PROTEIN S12;                                           CHAIN: L; 30S RIBOSOMAL                                           PROTEIN S13; CHAIN: M; 30S                                           RIBOSOMAL PROTEIN S14;                                           CHAIN: N; 30S RIBOSOMAL                                           PROTEIN S15; CHAIN: O; 30S                                           RIBOSOMAL PROTEIN S16;                                           CHAIN: P; 30S RIBOSOMAL                                           PROTEIN S17; CHAIN: Q; 30S                                           RIBOSOMAL PROTEIN S18;                                           CHAIN: R; 30S RIBOSOMAL                                           PROTEIN S19; CHAIN: S; 30S                                           RIBOSOMAL PROTEIN S20;                                           CHAIN: T; 30S RIBOSOMAL                                           PROTEIN THX; CHAIN: V       404   1qd7   I   69   151   3.4e−32   −0.76   0.00       CENTRAL FRAGMENT OF 16S   RIBOSOME 30S RIBOSOMAL                                           RNA; CHAIN: A; END FRAGMENT   SUBUNIT, LOW RESOLUTION MODEL                                           OF 16 S RNA; CHAIN: B; S4                                           RIBOSOMAL PROTEIN; CHAIN: C;                                           S5 RIBOSOMAL PROTEIN; CHAIN:                                           D; S6 RIBOSOMAL PROTEIN;                                           CHAIN: E; S7 RIBOSOMAL                                           PROTEIN; CHAIN: F; S8                                           RIBOSOMAL PROTEIN; CHAIN: G;                                           S15 RIBOSOMAL PROTEIN;                                           CHAIN: H; S17 RIBOSOMAL                                           PROTEIN; CHAIN: I; S20                                           RIBOSOMAL PROTEIN; CHAIN: J               406   1aps       2   98   1.4e−33   0.96   1.00       HYDROLASE(ACTING ON ACID                                           ANHYDRIDES)                                           ACYLPHOSPHATASE (E.C.3.6.1.7)                                           (NMR, 5 STRUCTURES) 1APS 3       406   1aps       2   99   1.4e−33           102.47   HYDROLASE(ACTING ON ACID                                           ANHYDRIDES)                                           ACYLPHOSPHATASE (E.C.3.6.1.7)                                           (NMR, 5 STRUCTURES) 1APS 3       406   2acy       2   99   3.4e−33   0.79   1.00       ACYLPHOSPHATASE; CHAIN:   ACYLPHOSPHATASE ACP;                                           NULL;   ACYLPHOSPHATASE, PHOSPHORIC                                               MONOESTER HYDROLASE       406   2acy       2   99   3.4e−33           139.55   ACYLPHOSPHATASE; CHAIN:   ACYLPHOSPHATASE ACP;                                           NULL;   ACYLPHOSPHATASE, PHOSPHORIC                                               MONOESTER HYDROLASE               407   1a17       622   730   1.5e−11   0.15   0.77       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       407   1a17       661   728   5.1e−06   0.09   0.98       SERINE/THREONINE PROTEIN   HYDROLASE TETRATRICOPEPTIDE,                                           PHOSPHATASE 5; CHAIN: NULL;   TRP; HYDROLASE, PHOSPHATASE,                                               PROTEIN-PROTEIN INTERACTIONS,                                               TPR, 2 SUPER-HELIX, X-RAY                                               STRUCTURE       407   1elr   A   263   376   1.2e−07   −0.04   0.12       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       407   1elr   A   620   727   9e−10   −0.47   0.00       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       407   1elr   A   660   733   6.8e−05   −0.38   0.40       TPR2A-DOMAIN OF HOP; CHAIN:   CHAPERONE HOP, TPR-DOMAIN,                                           A; HSP90-PEPTIDE MEEVD;   PEPTIDE-COMPLEX, HELICAL                                           CHAIN: B;   REPEAT, HSP90, 2 PROTEIN BINDING       407   1elw   A   658   758   1.2e−07   −0.23   0.21       TPR1-DOMAIN OF HOP; CHAIN: A,   CHAPERONE HOP, TPR-DOMAIN,                                           B; HSC70-PEPTIDE; CHAIN: C, D;   PEPTIDE-COMPLEX, HELICAL                                               REPEAT, HSC70, 2 HSP70, PROTEIN                                               BINDING       407   1fch   A   192   386   6e−12   −0.22   0.24       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTS1-CONTAINING PEPTIDE:   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       407   1fch   A   510   749   5.1e−12   −0.31   0.09       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTS1-CONTAINING PEPTIDE;   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       407   1fch   A   550   840   5.1e−15   −0.44   0.07       PEROXISOMAL TARGETING   SIGNALING PROTEIN PEROXISMORE                                           SIGNAL 1 RECEPTOR; CHAIN: A,   RECEPTOR 1, PTS1-BP, PEROXIN-5,                                           B; PTS1-CONTAINING PEPTIDE;   PTS1 PROTEIN-PEPTIDE COMPLEX,                                           CHAIN: C, D;   TETRATRICOPEPTIDE REPEAT, TPR,                                               2 HELICAL REPEAT       407   4hb1       703   744   0.0036   −0.01   0.10       DHP1; CHAIN: NULL;   DESIGNED HELICAL BUNDLE                                               DESIGNED HELICAL BUNDLE               414   1a5j       112   146   0.00075   −0.08   0.62       B-MYB; CHAIN: NULL;   DNA-BINDING PROTEIN DNA-                                               BINDING PROTEIN,                                               PROTOONCOGENE PRODUCT       414   1ak2       749   973   1.7e−52           304.37   ADENYLATE KINASE   PHOSPHOTRANSFERASE ATP\;AMP                                           ISOENZYME-2; CHAIN: NULL;   PHOSPHOTRANSFERASE,                                               MYOKINASE; NUCLEOSIDE                                               MONOPHOSPHATE KINASE,                                               PHOSPHOTRANSFERASE       414   1ak2       756   972   1.7e−52   0.84   1.00       ADENYLATE KINASE   PHOSPHOTRANSFERASE ATP\:AMP                                           ISOENZYME-2; CHAIN: NULL;   PHOSPHOTRANSFERASE,                                               MYOKINASE; NUCLEOSIDE                                               MONOPHOSPHATE KINASE,                                               PHOSPHOTRANSFERASE       414   1aky       751   971   4.5e−78           212.52   ADENYLATE KINASE; 1AKY 4   TRANSFERASE                                           CHAIN: NULL; 1AKY 5   (PHOSPHOTRANSFERASE) ATP\:AMP                                               PHOSPHOTRANSFERASE,                                               MYOKINASE; 1AKY 6 ATP:AMP                                               PHOSPHOTRANSFERASE,                                               MYOKINASE 1AKY 15       414   1aky       767   970   4.5e−78   0.66   1.00       ADENYLATE KINASE; 1AKY 4   TRANSFERASE                                           CHAIN: NULL; 1AKY 5   (PHOSPHOTRANSFERASE) ATP\:AMP                                               PHOSPHOTRANSFERASE,                                               MYOKINASE; 1AKY 6 ATP:AMP                                               PHOSPHOTRANSFERASE,                                               MYOKINASE 1AKY 15       414   1e4v   A   767   967   1.5e−74   0.13   1.00       ADENYLATE KINASE; CHAIN: A;   TRANSFERASE(PHOSPHOTRANSFERASE)                                               TRANSFERASE(PHOSPHOTRANSFERASE)       414   1mbj       113   146   7.5e−05   −0.18   0.51       MYB PROTO-ONCOGENE   DNA BINDING PROTEIN                                           PROTEIN; 1MBJ 4   PROTOONCOGENE PRODUCT 1MBJ                                               12       414   1mse   C   113   146   0.0015   −0.06   0.55       COMPLEX (BINDING                                           PROTEIN/DNA) C-MYB DNA-                                           BINDING DOMAIN COMPLEXED                                           WITH DNA 1MSE 3 (NMR,                                           MINIMIZED AVERAGE                                           STRUCTURE) 1MSE 4 1MSE 84               415   1e7u   A   3501   3986   1e−68   0.10   0.86       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K, P1 3K; PHOSPHOINOSITIDE 3-                                               KINASE GAMMA, SECONDARY                                               MESSENGER 2 GENERATION, P13K, P1                                               3K, WORTMANNIN       415   1e8y   A   3501   3986   3.4e−68   0.02   1.00       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K; PHOSPHOINOSITIDE 3-KINASE                                               GAMMA, SECONDARY MESSENGER 2                                               GENERATION, P13K, P1 3K       415   3fap   B   3581   3674   1.4e−24   0.05   −0.18       FK506-BINDING PROTEIN; CHAIN:   CELL CYCLE FKBP12; FRAP FKBP12,                                           A; FKBP12-RAPAMYCIN   FRAP, RAPAMYCIN, COMPLEX, GENE                                           ASSOCIATED PROTEIN; CHAIN:   THERAPY                                           B;       415   1e7u   A   3480   4043   8.5e−83   −0.12   0.37       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K, P1 3K; PHOSPHOINOSITIDE 3-                                               KINASE GAMMA, SECONDARY                                               MESSENGER 2 GENERATION, P13K, P1                                               3K, WORTMANNIN       415   1e8y   A   3480   4043   1e−77   0.13   0.94       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K; PHOSPHOINOSITIDE 3-KINASE                                               GAMMA, SECONDARY MESSENGER 2                                               GENERATION, P13K, P1 3K       415   3fap   B   3581   3673   1.5e−21   0.07   −0.18       FK506-BINDING PROTEIN; CHAIN:   CELL CYCLE FKBP12; FRAP FKBP12,                                           A; FKBP12-RAPAMYCIN   FRAP, RAPAMYCIN, COMPLEX, GENE                                           ASSOCIATED PROTEIN; CHAIN:   THERAPY                                           B;               416   1e7u   A   3501   3986   1e−68   0.10   0.86       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K, P1 3K; PHOSPHOINOSITIDE 3-                                               KINASE GAMMA, SECONDARY                                               MESSENGER 2 GENERATION, P13K, P1                                               3K, WORTMANNIN       416   1e8y   A   3501   3986   3.4e−68   0.02   1.00       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K; PHOSPHOINOSITIDE 3-KINASE                                               GAMMA, SECONDARY MESSENGER 2                                               GENERATION, P13K, P1 3K       416   3fap   B   3581   3674   1.4e−24   0.05   −0.18       FK506-BINDING PROTEIN; CHAIN:   CELL CYCLE FKBP12; FRAP FKBP12,                                           A; FKBP12-RAPAMYCIN   FRAP, RAPAMYCIN, COMPLEX, GENE                                           ASSOCIATED PROTEIN; CHAIN:   THERAPY                                           B;       416   1e7u   A   3480   4043   8.5e−83   −0.12   0.37       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K, P1 3K; PHOSPHOINOSITIDE 3-                                               KINASE GAMMA, SECONDARY                                               MESSENGER 2 GENERATION, P13K, P1                                               3K, WORTMANNIN       416   1e8y   A   3480   4043   1e−77   0.13   0.94       PHOSPHATIDYLINOSITOL 3-   PHOSPHOINOSITIDE 3-KINASE                                           KINASE CATALYTIC SUBUNIT;   GAMMA PTDINS-3-KINASE P110,                                           CHAIN: A;   P13K; PHOSPHOINOSITIDE 3-KINASE                                               GAMMA, SECONDARY MESSENGER 2                                               GENERATION, P13K, P1 3K       416   3fap   B   3581   3673   1.5e−21   0.07   −0.18       FK506-BINDING PROTEIN; CHAIN:   CELL CYCLE FKBP12; FRAP FKBP12,                                           A; FKBP12-RAPAMYCIN   FRAP, RAPAMYCIN, COMPLEX GENE                                           ASSOCIATED PROTEIN; CHAIN:   THERAPY                                           B;               418   1aip   A   181   384   1.7e−46   0.07   −0.15       ELONGATION FACTOR TU;   COMPLEX OF TWO ELONGATION                                           CHAIN: A, B, E, F; ELONGATION   FACTORS EF-TU; EF-TS;                                           FACTOR TS; CHAIN: C, D, G, H;   ELONGATION FACTOR,                                               NUCLEOTIDE EXCHANGE, GTP-                                               BINDING, 2 COMPLEX OF TWO                                               ELONGATION FACTORS       418   1d2e   A   181   386   1.7e−44   0.32   −0.17       ELONGATION FACTOR TU (EF-   RNA BINDING PROTEIN G-PROTEIN,                                           TU); CHAIN: A, B, C, D   BETA-BARREL       418   1e0s   A   185   312   3e−05   0.05   0.07       ADP-RIBOSYLATION FACTOR 6;   G PROTEIN G PROTEIN, RAS, ARF,                                           CHAIN: A;   ARF6, MEMBRANE TRAFFIC       418   1efe   A   181   386   3.4e−50   0.20   −0.17       ELONGATION FACTOR; CHAIN:   RNA BINDING PROTEIN EFTU;                                           A, B;   TRANSPORT AND PROTECTION                                               PROTEIN, RNA BINDING PROTEIN       418   1efu   A   181   386   5.1e−46   0.15   −0.17       ELONGATION FACTOR TU;   COMPLEX (TWO ELONGATION                                           CHAIN: A, C; ELONGATION   FACTORS) ELONGATION FACTOR                                           FACTOR TS; CHAIN: B, D;   FOR TRANSFER, HEAT UNSTABLE,                                               ELONGATION FACTOR FOR                                               TRANSFER, HEAT STABLE,                                               ELONGATION FACTOR, COMPLEX                                               (TWO ELONGATION FACTORS)       418   1ega   A   186   381   3.4e−36   0.10   0.01       GTP-BINDING PROTEIN ERA;   HYDROLASE ERA, GTPASE, RNA-                                           CHAIN: A, B;   BINDING, RAS-LIKE, HYDROLASE       418   1ega   A   34   185   8.5e−13   0.23   −0.19       GTP-BINDING PROTEIN ERA;   HYDROLASE ERA, GTPASE, RNA-                                           CHAIN: A, B;   BINDING, RAS-LIKE, HYDROLASE       418   1exm   A   179   384   5.1e−52   0.23   −0.17       ELONGATION FACTOR TU (EF-   TRANSLATION EF-TU; GTPASE,                                           TU); CHAIN: A;   MOLECULAR SWITCH, TRNA,                                               RIBOSOME, Q-BETA REPLICASE, 2                                               CHAPERONE, DISULFIDE                                               ISOMERASE       418   1f60   A   179   386   3.4e−31   0.23   −0.12       ELONGATION FACTOR EEFIA;   TRANSLATION PROTEIN-PROTEIN                                           CHAIN: A; ELONGATION FACTOR   COMPLEX                                           EEFIBA; CHAIN: B;       418   1hur   A   185   312   9e−05   0.06   0.12       HUMAN ADP-RIBOSYLATION   PROTEIN TRANSPORT GDP-BINDING,                                           FACTOR 1; 1HUR 5 CHAIN: A, B;   MEMBRANE TRAFFICKIN, NON-                                           1HUR 7   MYRISTOYLATED 1HUR 16               421   1afh   A   201   281   1.2e−26   −0.10   0.99       QGSR ZINC FINGER PEPTIDE;   COMPLEX (ZINC FINGER/DNA)                                           CHAIN: A; DUPLEX   COMPLEX (ZINC FINGER/DNA), ZINC                                           OLIGONUCLEOTIDE BINDING   FINGER, DNA-BINDING PROTEIN                                           SITE; CHAIN: B, C;       421   1c2a   A   396   513   1e−09   0.14   −0.15       BOWMAN-BIRK TRYPSIN   HYDROLASE INHIBITOR ALL-BETA                                           INHIBITOR; CHAIN: A   STRUCTURE, HYDROLASE                                               INHIBITOR       421   1mey   C   172   253   6.8e−41   −0.21   0.58       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   200   281   6.8e−44   0.09   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   228   309   3.4e−46   0.64   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   256   337   1.4e−47   0.60   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   284   365   1.7e−48   0.55   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   312   393   3.4e−49   0.50   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   340   421   6.8e−49   0.61   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   368   449   5.1e−50   0.34   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   396   477   3.4e−51   0.56   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   424   505   5.1e−51   0.53   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   452   533   6.8e−51   0.42   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   452   534   5.1e−51           108.34   DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   480   561   1.7e−50   0.40   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   508   589   8.5e−51   0.63   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   536   617   1.5e−50   0.31   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1mey   C   564   641   5.1e−46   0.13   1.00       DNA; CHAIN: A, B, D, E;   COMPLEX (ZINC FINGER/DNA) ZINC                                           CONSENSUS ZINC FINGER   FINGER, PROTEIN-DNA                                           PROTEIN; CHAIN: C, F, G;   INTERACTION, PROTEIN DESIGN, 2                                               CRYSTAL STRUCTURE, COMPLEX                                               (ZINC FINGER/DNA)       421   1tf6   A   201   346   5.1e−35   0.01   0.96       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       421   1tf6   A   257   402   1.4e−36   0.24   1.00       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       421   1tf6   A   369   514   1.7e−38   0.25   1.00       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       421   1tf6   A   396   559   1.7e−38           118.07   TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       421   1tf6   A   481   627   5.1e−38   0.04   1.00       TFIIIA; CHAIN: A, D; 5S   COMPLEX (TRANSCRIPTION                                           RIBOSOMAL RNA GENE; CHAIN:   REGULATION/DNA) COMPLEX                                           B, C, E, F;   (TRANSCRIPTION                                               REGULATION/DNA), RNA                                               POLYMERASE III, 2 TRANSCRIPTION                                               INITIATION, ZINC FINGER PROTEIN       421   1ubd   C   182   309   3e−26   −0.20   0.18       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION lNITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   203   309   3.4e−31   0.06   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   228   337   3e−51   0.33   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   282   393   4.5e−53   0.48   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   284   394   4.5e−53           92.65   YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   320   421   1.2e−33   0.29   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   348   449   1.7e−34   0.15   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   366   477   3e−53   0.23   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   376   477   3.4e−36   0.36   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   401   505   8.5e−36   0.16   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   422   533   6e−56   0.28   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   450   562   3e−55   0.16   0.96       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   460   561   1.7e−35   0.13   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTElN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   478   589   3e−53   0.04   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   506   617   3e−53   0.20   1.00       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   516   617   5.1e−34   0.34   0.96       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPTION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INTIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   1ubd   C   534   641   1.1e−39   0.17   0.98       YY1; CHAIN: C; ADENO-   COMPLEX (TRANSCRIPlION                                           ASSOCIATED VIRUS P5   REGULATION/DNA) YING-YANG 1;                                           INITIATOR ELEMENT DNA;   TRANSCRIPTION INITIATION,                                           CHAIN: A, B;   INITIATOR ELEMENT, YY1, ZINC 2                                               FINGER PROTEIN, DNA-PROTEIN                                               RECOGNITION, 3 COMPLEX                                               (TRANSCRIPTION                                               REGULATION/DNA)       421   2gli   A   172   308   1.5e−31   −0.27   0.78       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   192   311   3e−41   0.06   0.98       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   228   367   1.4e−63   0.72   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER (GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   264   392   1.7e−33   0.54   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   284   423   1.4e−63           110.65   ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   312   535   1.5e−67   −0.12   0.75       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   320   448   3.4e−34   0.31   0.99       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GL1, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   404   532   3.4e−34   0.47   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   452   591   1.5e-70   0.39   1.00       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)       421   2gli   A   508   626   7.5e−55   0.24   0.94       ZINC FINGER PROTEIN GLI1;   COMPLEX (DNA-BINDING                                           CHAIN: A; DNA; CHAIN: C, D;   PROTEIN/DNA) FIVE-FINGER GLI;                                               GLI, ZINC FINGER, COMPLEX (DNA-                                               BINDING PROTEIN/DNA)               423   1bcc   A   24   459   0   0.90   1.00       UBIQUINOL CYTOCHROME C   OXIDOREDUCTASE CYTOCHROME                                           OXIDOREDUCTASE; CHAIN: A, B,   BCI COMPLEX, COMPLEX III;                                           C, D, E, F, G, H, I, J;   UBIQUINONE, OXIDOREDUCTASE,                                               REDOX ENZYME, MEMBRANE                                               PROTEIN, 2 RESPIRATORY CHAIN,                                               ELECTRON TRANSPORT       423   1bcc   A   49   459   0           457.94   UBIQUINOL CYTOCHROME C   OXIDOREDUCTASE CYTOCHROME                                           OXIDOREDUCTASE; CHAIN: A, B,   BCI COMPLEX, COMPLEX III;                                           C, D, E, F, C, H, I, J;   UBIQUINONE, OXIDOREDUCTASE,                                               REDOX ENZYME, MEMBRANE                                               PROTEIN, 2 RESPIRATORY CHAIN,                                               ELECTRON TRANSPORT       423   1qcr   A   24   459   0   0.41   1.00       UBIQUINOL CYTOCHROME C   OXIDOREDUCTASE CYTOCHROME                                           OXIDOREDUCTASE; CHAIN: A, B,   BC1, QCR; BCI, QCR, MEMBRANE                                           C, D, E, F, G, H, I, J, K;   PROTEIN, PROTON                                               TRANSLOCATION, ELECTRON 2                                               TRANSFER, PROTEASE, MPP,                                               MITOCHONDRIAL PROCESSING 3                                               PEPTIDASE, STRUCTURE,                                               CYTOCHROME CI, CYTOCHROME B,                                               RIESKE, 4 IRON SULFER PROTEIN,                                               OXIDOREDUCTASE               426   1deq   B   122   285   1.4e−52   −0.25   0.62       FIBRINOGEN (ALPHA CHAIN);   BLOOD CLOTTING COILED-COIL                                           CHAIN: A, D, N, Q; FIBRINOGEN                                           (BETA CHAIN); CHAIN: B, E, O, R;                                           FIBRINOGEN (GAMMA CHAIN);                                           CHAIN: C, F, P, S; FIBRINOGEN;                                           CHAIN: M, Z;       426   1deq   C   53   276   4.2e−89   −0.52   1.00       FIBRINOGEN (ALPHA CHAIN);   BLOOD CLOTTING COIELD-COIL                                           CHAIN: A, D, N, Q; FIBRINOGEN                                           (BETA CHAIN); CHAIN: B, E, O, R;                                           FIBRINOGEN (GAMMA CHAIN);                                           CHAIN: C, F, P, S; FIBRINOGEN;                                           CHAIN: M, Z;       426   1deq   C   53   286   8.5e−45   −0.58   1.00       FIBRINOGEN (ALPHA CHAIN);   BLOOD CLOTTING COILED-COIL                                           CHAIN: A, D, N, Q; FIBRINOGEN                                           (BETA CHAIN); CHAIN: B, E, O, R;                                           FIBRINOGEN (GAMMA CHAIN);                                           CHAIN: C, F, P, S; FIBRINOGEN;                                           CHAIN: M, Z;       426   1ei3   C   29   286   3.4e−52   −0.58   1.00       FIBRINOGEN; CHAIN: A, D;   BLOOD CLOTTING COILED COILS,                                           FIBRINOGEN; CHAIN: B, E;   DISULFIDE RINGS, FIBRIN FORMING                                           FIBRINOGEN; CHAIN: C, F;   ENTITIES       426   1fzc   C   123   286   3.4e−39   0.19   1.00       FIBRIN; CHAIN: A, B, C, D, E, F, G,   BLOOD COAGULATION BLOOD                                           H, I, J;   COAGULATION, PLASMA PROTEIN,                                               CROSSLINKING       426   1fzc   C   123   288   3.4e−39           175.96   FIBRIN; CHAIN: A, B, C, D, E, F, G,   BLOOD COAGULATION BLOOD                                           H, I, J;   COAGULATION, PLASMA PROTEIN,                                               CROSSLINKING       426   1fzg   C   128   288   1e−38           174.90   FIBRINOGEN; CHAIN: A, B, C, D,   BLOOD COAGULATION BLOOD                                           E, F, S, T, M, N;   COAGULATION, PLASMA,                                               PLATELET, FIBRINOGEN, FIBRIN       426   1fzg   C   129   286   1e−38   0.22   1.00       FIBRINOGEN; CHAIN: A, B, C, D,   BLOOD COAGULATION BLOOD                                           E, F, S, T, M, N;   COAGULATION, PLASMA,                                               PLATELET, FIBRINOGEN, FIBRIN               432   2dnj   A   21   251   3.4e−100   0.93   1.00       ENDONUCLEASE                                           DEOXYRIBONUCLEASE I (DNASE                                           I) (E.C.3.1.21.1) COMPLEXED                                           WITH 2DNJ 3 DNA (5′-                                           D(*GP*CP*GP*AP*TP*CP*GP*CP)-                                           3′) 2DNJ 4       432   2dnj   A   21   252   3.4e−100           202.60   ENDONUCLEASE                                           DEOXYRIBONUCLEASE I (DNASE                                           I) (F.C.3.1.21.1) COMPLEXED                                           WITH 2DNJ 3 DNA (5′-                                           D(*GP*CP*GP*AP*TP*CP*GP*CP)-                                           3′) 2DNJ 4               433   1b50   A   25   92   1.1e−28           90.96   MIP-1A; CHAIN: A, B;   CHEMOKINE CHEMOKINE,                                               CYTOKINE, CHEMOTAXIS       433   1b50   A   26   92   1.1e−28   0.01   1.00       MIP-1A; CHAIN: A, B;   CHEMOKINE CHEMOKINE,                                               CYTOKINE, CHEMOTAXIS       433   1b50   A   27   92   5.1e−25   0.29   1.00       MIP-1A; CHAIN: A, B;   CHEMOKINE CHEMOKINE,                                               CYTOKINE, CHEMOTAXIS       433   1hum   A   24   92   6.8e−25           114.82   CYTOKINE(CHEMOTACTIC)                                           HUMAN MACROPHAGE                                           INFLAMMATORY PROTEIN 1                                           BETA (HMIP-1B) 1HUM 3 (NMR,                                           MINIMIZED AVERAGE                                           STRUCTURE) 1HUM 4       433   1hum   A   25   92   6.8e−25   0.28   1.00       CYTOKINE(CHEMOTACTIC)                                           HUMAN MACROPHAGE                                           INFLAMMATORY PROTEIN 1                                           BETA (HMIP-1B) 1HUM 3 (NMR,                                           MINIMIZED AVERAGE                                           STRUCTURE) 1HUM 4       433   1ncv   A   24   92   1.7e−25           61.57   MONOCYTE   CYTOKINE NMR, STRUCTURE, MCP-                                           CHEMOATTRACTANT PROTEIN 3;   3, BETA-CHEMOKINE, CYTOKINE,                                           CHAIN: A, B;   CHEMOTAXIS, 2 HEPARIN-BINDING,                                               GLYCOPROTEIN       433   1ncv   A   25   91   1.7e−25   −0.04   0.98       MONOCYTE   CYTOKINE NMR, STRUCTURE, MCP-                                           CHEMOATTRACTANT PROTEIN 3;   3, BETA-CHEMOKINE, CYTOKINE,                                           CHAIN: A, B;   CHEMOTAXIS, 2 HEPARIN-BINDING,                                               GLYCOPROTEIN               449   1awc   B   114   270   1.7e−39           61.04   GA BINDING PROTEIN ALPHA;   COMPLEX (TRANSCRIPTION                                           CHAIN: A; GA BINDING PROTEIN   REGULATION/DNA) GABPALPHA;                                           BETA 1; CHAIN: B; DNA; CHAIN:   GABPBETA1; COMPLEX                                           D, E;   (TRANSCRIPTION                                               REGULATION/DNA), DNA-BINDING, 2                                               NUCLEAR PROTEIN, ETS DOMAIN,                                               ANKYRIN REPEATS,                                               TRANSCRIPTION 3 FACTOR       449   1bd8       116   273   8.4e−33           57.66   P191NK4D CDK4/6 INHIBITOR;   TUMOR SUPPRESSOR TUMOR                                           CHAIN: NULL;   SUPPRESSOR, CDK4/6 INHIBITOR,                                               ANKYRIN MOTIF       449   1blx   B   115   276   1.4e−32           53.46   CYCLIN-DEPENDENT KINASE 6;   COMPLEX (INHIBITOR                                           CHAIN: A; P191NK4D; CHAIN: B;   PROTEIN/KINASE) INHIBITOR                                               PROTEIN, CYCLIN-DEPENDENT                                               KINASE, CELL CYCLE 2 CONTROL,                                               ALPHA/BETA, COMPLEX (INHIBITOR                                               PROTEIN/KINASE)       449   1bu9   A   113   280   3.4e−33           51.20   CYCLIN-DEPENDENT KINASE 6   HORMONE/GROWTH FACTOR P18-                                           INHIBITOR; CHAIN: A;   1NK4C; CELL CYCLE INHIBITOR,                                               P181NK4C, TUMOR, SUPPRESSOR,                                               CYCLIN-2 DEPENDENT KINASE,                                               HORMONE/GROWTH FACTOR       449   1ibb   A   122   273   1.5e−32           53.58   CYCLIN-DEPENDENT KINASE 6   CELL CYCLE INHIBITOR P18-                                           INHIBITOR; CHAIN: A, B;   1NK4C(1NK6); CELL CYCLE                                               INHIBITOR, P18-1NK4C(1NK6),                                               ANKYRIN REPEAT, 2 CDK 4/6                                               INHIBITOR       449   1ikn   D   81   293   2.8e−44           62.44   NF-KAPPA-B P65 SUBUNIT;   TRANSCRIPTION FACTOR P65; P50D;                                           CHAIN: A; NF-KAPPA-B P50D   TRANSCRIPTION FACTOR, IKB/NFKB                                           SUBUNIT; CHAIN: C; I-KAPPA-B-   COMPLEX                                           ALPHA; CHAIN: D;       449   1myo       48   166   9.8e−27           54.85   MYOTROPHIN; CHAIN: NULL   ANK-REPEAT MYOTROPHIN,                                               ACETYLATION, NMR, ANK-REPEAT       449   1nfl   E   78   282   2.8e−44           63.92   NF-KAPPA-B P65; CHAIN: A, C;   COMPLEX (TRANSCRIPTION                                           NF-KAPPA-B P50; CHAIN: B, D; I-   REG/ANK REPEAT) COMPLEX                                           KAPPA-B-ALPHA; CHAIN: E, F;   (TRANSCRIPTION REGULATION/AN K                                               REPEAT), ANKYRIN 2 REPEAT HELIX               451   1ndh       36   305   5.1e−79           366.08   ELECTRON TRANSPORT (FLAVO                                           PROTEIN) CYTOCHROME B = 5 =                                           REDUCTASE (E.C.1.6.2.2) 1NDH 3               456   1tub   A   2   440   0           308.77   TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX       456   1tub   B   2   440   0           353.89   TUBULIN; CHAIN: A, B;   MICROTUBULES MICROTUBULES,                                               ALPHA-TUBULIN, BETA-TUBULIN,                                               GTPASE HELIX               457   1klo       82   239   2.8e−34           138.52   LAMININ; CHAIN: NULL;   GLYCOPROTEIN GLYCOPROTEIN               458   1bih   A   1   327   6.8e−47           77.74   HEMOLIN; CHAIN: A, B;   INSECT IMMUNITY INSECT                                               IMMUNITY, LPS-BINDING,                                               HOMOPHILIC ADHESION       458   1fig   H   54   276   0.00034           61.84   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN GI (KAPPA                                           LIGHT CHAIN) FAB&#39; FRAGMENT                                           1FIG 3       458   1for   H   64   278   0.0019           60.01   IMMUNOGLOBULIN IGG2A FAB                                           FRAGMENT (FAB17-1A)                                           (ORTHORHOMBIC CRYSTAL                                           FORM) 1FOR 3       458   1igc   H   58   279   0.00017           61.96   COMPLEX (ANTIBODY/BINDING                                           PROTEIN) IGG1 FAB FRAGMENT                                           COMPLEXED WITH PROTEIN G                                           (DOMAIN III) HGC 5 PROTEIN G.                                           STREPTOCOCCUS HGC 15       458   1itb   B   1   279   4.2e−25           62.51   INTERLEUKIN-I BETA; CHAIN: A;   COMPLEX                                           TYPE 1 INTERLEUKIN-1   (IMMUNOGLOBULIN/RECEPTOR)                                           RECEPTOR; CHAIN: B;   IMMUNOGLOBULIN FOLD,                                               TRANSMEMBRANE, GLYCOPROTEIN,                                               RECEPTOR, 2 SIGNAL, COMPLEX                                               (IMMUNOGLOBULIN/RECEPTOR)       458   1kb5   H   54   278   0.0024           63.34   KB5-C20 T-CELL ANTIGEN   COMPLEX                                           RECEPTOR; CHAIN: A, B;   (IMMUNOGLOBULIN/RECEPTOR)                                           ANTIBODY DESIRE-I; CHAIN: L,   TCR VAPLHA VBETA DOMAIN; T-                                           H;   CELL RECEPTOR, STRAND SWITCH,                                               FAB, ANTICLONOTYPIC, 2                                               (IMMUNOGLOBULIN/RECEPTOR)       458   2gfb   B   58   279   0.00034           67.09   IMMUNOGLOBULIN IGG2A FAB                                           FRAGMENT (CNJ206) 2GFB 3       458   7fab   L   65   260   1.5e−11           58.17   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB&#39; NEW                                           (LAMBDA LIGHT CHAIN) 7FAB 3               462   1au7   A   143   289   3.4e−33           105.92   PIT-1; CHAIN: A, B; DNA; CHAIN:   COMPLEX (DNA-BINDING                                           C, D;   PROTEIN/DNA) GHF-I; COMPLEX                                               (DNA-BINDING PROTEIN/DNA),                                               PITUITARY, CPHD, 2 POU DOMAIN.                                               TRANSCRIPTION FACTOR       462   1ocp       223   289   2.8e−22           84.91   OCT-3; 1OCP 5 CHAIN: NULL;   DNA-BINDING PROTEIN                                           1OCP 6       462   1oct   C   143   290   1.3e−40           120.80   DNA-BINDING PROTEIN OCT-I                                           (POU DOMAIN) 1OCT 3       462   1pou       143   212   5.6e−32           79.90   DNA-BINDING PROTEIN OCT-I                                           (POU-SPECIFIC DOMAIN) (NMR,                                           20 STRUCTURES) 1POU 3               473   1fht       30   143   2.8e−16           53.05   U1 SMALL NUCLEAR   RIBONUCLEOPROTEIN U1A117;                                           RIBONUCLEOPROTEIN A; CHAIN:   RIBONUCLEOPROTEIN, RNP                                           NULL;   DOMAIN, SPLICEOSOME               476   1c96   A   82   963   0           253.82   MITOCHONDRIAL ACONITASE;   LYASE CITRATE HYDRO-LYASE;                                           CHAIN: A;   LYASE, TRICARBOXYLIC ACID                                               CYCLE, IRON-SULFUR,                                               MITOCHONDRION, 2 TRANSIT                                               PEPTIDE, 4FE-4S, 3D-STRUCTURE               477   1bab   B   2   140   6.8e−55           179.81   OXYGEN TRANSPORT                                           HEMOGLOBIN THIONVILLE                                           ALPHA CHAIN MUTANT WITH                                           VAL 1 1BAB 3 REPLACED BY GLU                                           AND AN ACETYLATED MET                                           BOUND TO THE 1BAB 4 AMINO                                           TERMINUS 1BAB 5       477   1ch4   A   2   140   1.7e−55           168.27   MODULE-SUBSTITUTED   OXYGEN TRANSPORT OXYGEN                                           CHIMERA HEMOGLOBIN BETA-   TRANSPORT, CHIMERA PROTEIN,                                           ALPHA; CHAIN: A, B, C, D;   RESPIRATORY PROTEIN, HEME       477   1fdh   G   3   140   1e−55           150.09   OXYGEN TRANSPORT                                           HEMOGLOBIN (DEOXY, HUMAN                                           FETAL F═/11$═) 1FDHG 1 1FDHH 2       477   1hda   B   3   140   8.5e−51           154.60   OXYGEN TRANSPORT                                           HEMOGLOBIN (DEOXY) 1HDA 3       477   1ibe   B   2   140   1e−52           154.97   HEMOGLOBIN (DEOXY); CHAIN:   OXYGEN TRANSPORT HEME,                                           A, B;   OXYGEN TRANSPORT,                                               RESPIRATORY PROTEIN,                                               ERYTHROCYTE       477   1qpw   B   2   140   1e−52           163.36   PORICINE HEMOGLOBIN (ALPHA   OXYGEN TRANSPORT X-RAY                                           SUBUNIT); CHAIN: A, C;   STUDY, PORCINE HEMOGLOBIN,                                           PORICINE HEMOGLOBIN (BETA   ARTIFICIAL HUMAN BLOOD, 2                                           SUBUNIT); CHAIN: B, D   OXYGEN TRANSPORT               480   1b6e       66   196   4.2e−29           81.88   CD94; CHAIN: NULL;   NK CELL NK CELL, RECEPTOR, C-                                               TYPE LECTIN, C-TYPE LECTIN-LIKE,                                               NKD       480   1bj3   A   67   193   3.4e−32           63.00   COAGULATION FACTOR IX-   COLLAGEN BINDING PROTEIN IX-BP;                                           BINDING PROTEIN A; CHAIN: A;   IX-BP; COAGULATION FACTOR IX-                                           COAGULATION FACTOR IX-   BINDING, HETERODIMER, VENOM,                                           BINDING PROTEIN B; CHAIN: B;   HABU 2 SNAKE, C-TYPE LECTIN                                               SUPERFAMILY, COLLAGEN BINDING                                               PROTEIN       480   1byf   A   77   194   5.1e−16           54.78   POLYANDROCARPA LECTIN;   SUGAR BINDING PROTEIN TC14; C-                                           CHAIN: A, B;   TYPE LECTIN, GALACTOSE-                                               SPECIFIC, SUGAR BINDING PROTEIN       480   1esl       78   197   8.5e−31           53.21   CELL ADHESION PROTEIN E-                                           SELECTIN (LECTIN AND EGF                                           DOMAINS, RESIDUES 1-157)                                           1ESL 3 (FORMERLY KNOWN AS                                           ELAM-1) 1ESL 4       480   1htn       46   196   1e−26           58.22   TETRANECTIN; CHAIN: NULL;   LECTIN TETRANECTIN,                                               PLASMINOGEN BINDING, KRINGLE                                               4, ALPHA-HELICAL 2 COILED COIL,                                               C-TYPE LECTIN, CARBOHYDRATE                                               RECOGNITION DOMAIN       480   1hup       46   194   1.7e−23           53.60   MANNOSE-BINDING PROTEIN;   C-TYPE LECTIN ALPHA-HELICAL                                           1HUP 4 CHAIN: NULL; 1HUP 5   COILED-COIL 1HUP 12       480   1ixx   A   67   193   5.1e−30           60.13   COAGULATION FACTORS IX/X-   COAGULATION FACTOR BINDING                                           BINDING PROTEIN; CHAIN: A, B,   IX/X-BP COAGULATION FACTOR                                           C, D, E, F;   BINDING, C-TYPE LECTIN, GLA-                                               DOMAIN 2 BINDING, C-TYPE CRD                                               MOTIF, LOOP EXCHANGED DIMER       480   1ixx   B   67   195   8.5e−32           69.01   COAGULATION FACTORS IX/X-   COAGULATION FACTOR BINDING                                           BINDING PROTEIN; CHAIN: A, B,   IX/X-BP COAGULATION FACTOR                                           C, D, E, F;   BINDING, C-TYPE LECTIN, GLA-                                               DOMAIN 2 BINDING, C-TYPE CRD                                               MOTIF, LOOP EXCHANGED DIMER       480   1lit       67   195   1.7e−33           77.94   LITHOSTATHINE; CHAIN: NULL   PANCREATIC STONE INHIBITOR                                               PANCREATIC STONE INHIBITOR,                                               LECTIN       480   1qdd   A   51   195   6.8e−35           84.76   LITHOSTATHINE; CHAIN: A;   METAL BINDING PROTEIN                                               PANCREATIC STONE PROTEIN, PSP:                                               PANCREATIC STONE INHIBITOR,                                               LITHOSTATHINE       480   1rtm   1   36   195   1e−22           50.50   LECTIN MANNOSE-BINDING                                           PROTEIN A (CLOSTRIPAIN                                           FRAGMENT) (CL-MBP-A) 1RTM 3                                           1RTM 96       480   1tn3       62   196   5.1e−25           59.09   TETRANECTIN; CHAIN: NULL;   LECTIN TETRANECTIN,                                               PLASMINOGEN BINDING, KRINGLE                                               4, C-TYPE LECTIN, 2                                               CARBOHYDRATE RECOGNITION                                               DOMAIN       480   2msh   A   77   193   1.2e−21           53.42   LECTIN MANNOSE-BINDING                                           PROTEIN A (LECTIN DOMAIN)                                           COMPLEX WITH 2MSB 3                                           CALCIUM AND GLYCOPEPTIDE                                           2MSB 4               489   1adq   L   21   235   3.4e−84           313.02   IGG4 REA; CHAIN: A; RF-AN   COMPLEX                                           IGM/LAMBDA; CHAIN: H, L;   (IMMUNOGLOBULIN/AUTOANTIGEN)                                               COMPLEX                                               (IMMUNOGLOBULIN/AUTOANTIGEN),                                               RHEUMATOID FACTOR 2 AUTO-                                               ANTIBODY COMPLEX       489   1aqk   L   22   235   5.1e−83           285.37   FAB B7-15A2; CHAIN: L, H;   IMMUNOGLOBULIN HUMAN FAB,                                               ANTI-TETANUS TOXOID, HIGH                                               AFFINITY, CRYSTAL 2 PACKING                                               MOTIF, PROGRAMMING                                               PROPENSITY TO CRYSTALLIZE, 3                                               IMMUNOGLOBULIN       489   1bjm   A   20   235   6.8e−79           287.81   LOC-LAMBDA I TYPE LIGHT-   IMMUNOGLOBULIN BENCE-JONES                                           CHAIN DIMER: 1BJM 6 CHAIN: A,   PROTEIN; 1BJM 8 BENCE JONES,                                           B: 1BJM 7   ANTIBODY, MULTIPLE                                               QUATERNARY STRUCTURES 1BJM 13       489   1lil   A   21   235   1.2e−80           311.90   LAMBDA III BENCE JONES   IMMUNOGLOBULIN                                           PROTEIN CLE: CHAIN: A, B   IMMUNOGLOBULIN, BENCE JONES                                               PROTEIN       489   1mew   W   20   235   8.5e−76           277.24   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN                                           HETEROLOGOUS LIGHT CHAIN                                           DIMER 1MCW 3 (/MCG$-/WEIR$                                           HYBRID) 1MCW 4       489   1mfb   L   22   232   1.4e−96           225.27   IMMUNOGLOBULIN FAB                                           FRAGMENT (MURINE SE155-4)                                           COMPLEX WITH                                           HEPTASACCHARIDE 1MFB 3 B:                                           GAL(1-2)MAN(1-4)RAM(1-                                           3)GAL(1-2)[ABE(1-3)]MAN(1-                                           4)RAM 1MFB 4       489   2fb4   L   22   235   8.5e−83           298.26   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB 2FB4 4       489   2mcg   1   20   235   8.5e−81           292.66   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN LAMBDA                                           LIGHT CHAIN DIMER (/MCG$)                                           2MCG 3 (TRIGONAL FORM) 2MCG 4       489   7fab   L   20   231   1.4e−89           252.72   IMMUNOGLOBULIN                                           IMMUNOGLOBULIN FAB′ NEW                                           (LAMBDA LIGHT CHAIN) 7FAB 3       489   8fab   A   22   231   1.7e−81           313.64   IMMUNOGLOBULIN FAB                                           FRAGMENT FROM HUMAN                                           IMMUNOGLOBULIN IGGI                                           (LAMBDA, HIL) 8FAB 3                    
     [0450]                           TABLE 6                           Position Of the Last                   Amino Acid Of Signal       SEQ ID NO:   Peptide   Maximum Score   Mean Score                                                246   23   0.948   0.886       247   20   0.954   0.900       249   19   0.992   0.946       252   35   0.906   0.594       255   20   0.943   0.601       256   18   0.895   0.587       257   26   0.966   0.902       258   20   0.974   0.942       262   44   0.967   0.702       273   20   0.954   0.900       291   19   0.992   0.946       296   26   0.965   0.852       309   16   0.885   0.571       328   18   0.939   0.693       338   18   0.988   0.897       340   13   0.887   0.839       355   21   0.895   0.558       356   18   0.906   0.614       357   19   0.966   0.927       362   26   0.994   0.899       376   35   0.906   0.594       379   23   0.989   0.919       405   20   0.943   0.601       418   18   0.895   0.587       426   26   0.966   0.902       428   22   0.970   0.910       430   14   0.941   0.861       432   20   0.974   0.942       433   23   0.994   0.967       451   26   0.978   0.885       457   27   0.980   0.853       482   27   0.989   0.918       484   18   0.996   0.953       489   19   0.981   0.914                    
     [0451]                   TABLE 7                       SEQ ID NO:   Chromosomal location                                        1   6q27       2   4p16.3       3   4p16.3       4   1p21       5   8q13-q22       6   17       7   X       8    5       10   16       11   10       12   10       13   8pter-p23.3       15   17       16   X       17   11q23.2       18   19p13.3-p13.2       19   3p21.1       20   10       21    1       22    8       23   16       24    8       25    1       26   22q13.1       27   22q13.1       28    1       29    3       30   X       31   Xq27.3       32   Xq27.3       33    4       34   7q35-q36       35   11q12-1q22.2       36   11q23.1-q23.2       37   12       38   2q11.1-q11.2       39   17       40   7q32       41   22q13.2       42   1q42.13-q42.2       43   19q13.3       44   19p12       45   1q23.1-24.3       46   22q11.1-q11.2       48   17       49   8p22       50   22       51   3q23-q24       52   7p22-p21       53   16       54   12       55   21q22.3       56   18q       57    6       60    1       61   19       62   14       63   6q15-q16.1       64   13q12.3-q13.1       65   17q21-q22       66   7q11.2       67   12       68   12p13       69   19q13.13-q13.2       70   12       71   19       72   18       73   1p36.13-q31.3       74   14       75   7q21       76   7q21-q22       78   11p11.2-p11.1       80   22q13.31-q13.33       81   3p26-p25       82    2       84   22q13.2-q13.31       86   19       87   22q11.1-q11.2       88   17       89   7q11.21-q11.23       91    9       92   1p35.1-36.12       93   3q13.1-q13.2       94   15       95   19q13.2       96    1       97   20p11.1-11.22       98   19       100   6p12       101    3       102    3       103   X       104   3q29-qter       105   15       107   12       108   20p11.21-12.3       110    5       111   10       112   10       113   6p21.2-p21.3       114   12q15       115   22       118   19       119   Xp11.2       121   15       122    3       123    3       124   20       125    9       126   11q13       127   13       128   Xq21.1-Xq21.3       129   Xq28       130   19p13.1-p12       131   8q22-q23       133   17       134   1p36.3-p36.12       136   11p15.5       137   11p15.5       138   11p15.5       139   10p15-p13       140   3q29       141   11       142   20p12.2-13       143   20q13.3       144   19q13.3-q13.4       146   17       147   12p13.3       148   8q22       149   8q22       150    5       151   9q34       152   7q21       153   7p13-p12       154   Xp22.33       155   15       156   14       158   19q13.3       159   19q13.3       160    6       161   14q24.3       162   11       164   16       165   22q13.2-q13.31       166   19       167   11       168    5       169   1p34       170   8q11       171   8q11       172   17       173   19       176   19       177   11       178   7q22-q32       179   16q22.1       181   4q28       182   16p13.3       183    5       184    1       187   3p21.1-p14.3       188   17q21       189   7q21-q22       190   3p13-q26.1       191   17q21.2       192   3q27       193   22q13.2-13.3       194   11q22.2-q22.3       195   12q24.31-q24.32       196   19q13.4       197   17       198   17       199   16       200   20       201   20       202    5       203   17       204   11       205   20q11.2-q12       206   1q24-q41       207   17       208   14       209   11q13       210    6       211   17q21       212   6q21       214   16       216   17       217   6p21.31       219   Xp22       220   20       221    3       222   22q13.31-13.32       223   11q12       224   11q13.3       225   11q13.3       226   12       227   17q24-q25       228   20       229    9       230   11       231   15q24-q25       233   19q13.4       234   22q11.2       235   12p13       236    9       237   3p25-p24       238   14q24.3       240   19q13.3       241   20       242    6       243   16q21-q23       244   22q11.1-q11.2                    
     [0452]                       TABLE 8                               SEQ ID NO: in USSN               09/654,935               (Numbers to the right of       SEQ ID NO:   SEQ ID NO:   the under score correlate to       of nucleotide   of polypeptide   sequence identifiers in       sequence   sequence   USSN 09/654,935)                                            1   246   793_3        2   247   793_4        3   248   793_5        4   249   793_6        5   250   793_7        6   251   793_9        7   252   793_15        8   253   793_16        9   254   793_17        10   255   793_18        11   256   793_19        12   257   793_20        13   258   793_21        14   259   793_22        15   260   793_25        16   261   793_28        17   262   793_29        18   263   793_30        19   264   793_31        20   265   793_32        21   266   793_33        22   267   793_34        23   268   793_35        24   269   793_36        25   270   793_37        26   271   793_38        27   272   793_39        28   273   793_40        29   274   793_41        30   275   793_42        31   276   793_43        32   277   793_44        33   278   793_47        34   279   793_48        35   280   793_49        36   281   793_50        37   282   793_51        38   283   793_52        39   284   793_55        40   285   793_56        41   286   793_57        42   287   793_58        43   288   793_60        44   289   793_61        45   290   793_62        46   291   793_63        47   292   793_64        48   293   793_65        49   294   793_66        50   295   793_67        51   296   793_68        52   297   793_69        53   298   793_70        54   299   793_71        55   300   793_72        56   301   793_74        57   302   793_75        58   303   793_76        59   304   793_77        60   305   793_78        61   306   793_79        62   307   793_80        63   308   793_81        64   309   793_82        65   310   793_83        66   311   793_85        67   312   793_86        68   313   793_87        69   314   793_88        70   315   793_89        71   316   793_90        72   317   793_91        73   318   793_92        74   319   793_93        75   320   793_94        76   321   793_95        77   322   793_96        78   323   793_97        79   324   793_98        80   325   793_99        81   326   793_101       82   327   793_102       83   328   793_103       84   329   793_104       85   330   793_106       86   331   793_107       87   332   793_108       88   333   793_109       89   334   793_110       90   335   793_111       91   336   793_112       92   337   793_113       93   338   793_114       94   339   793_115       95   340   793_116       96   341   793_117       97   342   793_118       98   343   793_119       99   344   793_120       100   345   793_121       101   346   793_122       102   347   793_123       103   348   793_124       104   349   793_125       105   350   793_126       106   351   793_127       107   352   793_128       108   353   793_129       109   354   793_130       110   355   793_131       111   356   793_132       112   357   793_133       113   358   793_134       114   359   793_135       115   360   793_136       116   361   793_137       117   362   793_138       118   363   793_139       119   364   793_140       120   365   793_141       121   366   793_142       122   367   793_143       123   368   793_144       124   369   793_145       125   370   793_146       126   371   793_147       127   372   793_148       128   373   793_149       129   374   793_150       130   375   793_151       131   376   793_152       132   377   793_153       133   378   793_154       134   379   793_155       135   380   793_156       136   381   793_157       137   382   793_158       138   383   793_159       139   384   793_160       140   385   793_161       141   386   793_162       142   387   793_163       143   388   793_164       144   389   793_165       145   390   793_166       146   391   793_167       147   392   793_168       148   393   793_169       149   394   793_170       150   395   793_171       151   396   793_172       152   397   793_173       153   398   793_174       154   399   793_175       155   400   793_176       156   401   793_177       157   402   793_178       158   403   793_179       159   404   793_180       160   405   793_181       161   406   793_182       162   407   793_183       163   408   793_184       164   409   793_185       165   410   793_186       166   411   793_187       167   412   793_188       168   413   793_189       169   414   793_190       170   415   793_191       171   416   793_192       172   417   793_193       173   418   793_194       174   419   793_195       175   420   793_196       176   421   793_197       177   422   793_198       178   423   793_200       179   424   793_201       180   425   793_202       181   426   793_203       182   427   793_204       183   428   793_205       184   429   793_206       185   430   793_207       186   431   793_209       187   432   793_210       188   433   793_211       189   434   793_212       190   435   793_213       191   436   793_214       192   437   793_215       193   438   793_216       194   439   793_217       195   440   793_218       196   441   793_219       197   442   793_220       198   443   793_221       199   444   793_222       200   445   793_223       201   446   793_224       202   447   793_225       203   448   793_226       204   449   793_227       205   450   793_229       206   451   793_230       207   452   793_231       208   453   793_232       209   454   793_233       210   455   793_234       211   456   793_235       212   457   793_236       213   458   793_237       214   459   793_238       215   460   793_239       216   461   793_240       217   462   793_241       218   463   793_242       219   464   793_244       220   465   793_245       221   466   793_247       222   467   793_248       223   468   793_249       224   469   793_250       225   470   793_251       226   471   793_252       227   472   793_253       228   473   793_254       229   474   793_255       230   475   793_256       231   476   793_257       232   477   793_258       233   478   793_259       234   479   793_260       235   480   793_261       236   481   793_262       237   482   793_263       238   483   793_264       239   484   793_265       240   485   793_266       241   486   793_267       242   487   793_268       243   488   793_269       244   489   793_270       245   490   793_271                    
     [0453] 
    
     
       
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                 SEQUENCE LISTING 
               
            
           
           
               
            
               
                 The patent application contains a lengthy “Sequence Listing” section. A copy of the “Sequence Listing” is available in electronic form from the USPTO 
               
               
                 web site (http://seqdata.uspto.gov/sequence.html?DocID=20040044181). An electronic copy of the “Sequence Listing” will also be available from the 
               
               
                 USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).