satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 1.63 Angstrom data (PDB entry 7V0G)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.11
Sequence length: 350 residues
Sequence: GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1163
R free: 0.1625
Average B factor: 30.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT
Matthews coefficient: 2.72
Solvent content (%): 54.75
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-12-07
Human Sirt6 in complex with ADP-ribose and the activator cyanidin (PDB entry 6QCH)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.16328
R free: 0.19964
Average B factor: 50.493
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.63
Solvent content (%): 53.2
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-12-25
Crystal Structure of Human Complement C3b in Complex with MCP (CCP1-4) (PDB entry 5FO8)
Macromolecule: COMPLEMENT C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 645 residues
Sequence: SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYGKKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1879
R free: 0.2188
Average B factor: 67
Crystal growth procedure: 100MM AMMONIUM CITRATE 7% PEG 3350 5MM GLUTATHIONE 50MM BIS-TRIS PROPANE, PH 6.5
Matthews coefficient: 3.4
Solvent content (%): 63.9
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2016-04-06
Notum PPOH complex (PDB entry 7BMB)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1908
R free: 0.2375
Average B factor: 32.2222
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.93
Solvent content (%): 36.33
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2022-03-02
Crystal structure of the G262S mutant of human apoptosis inducing factor (PDB entry 5FS7)
Macromolecule: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 515 residues
Sequence: GLTPEQKQKKAALSASEGEEVPQDKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGSTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESEASEITIPPSTPAVPQAPVQGEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHEDLVPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.17885
R free: 0.21691
Average B factor: 20.89
Crystallization pH: 8.5
Crystal growth procedure: 0.2 M LITHIUM SULFATE, 0.1M TRIS, PH 8.5, AND 25% POLY-ETHYLENE GLYCOL 3350
Matthews coefficient: 2.82
Solvent content (%): 56.5
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2016-05-11
Structural basis for the regulation of inducible nitric oxide synthase (iNOS) by the SPRY domain-containing SOCS box protein 2 (SPSB2) (PDB entry 6KEY)
Macromolecule: SPRY domain-containing SOCS box protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 209 residues
Sequence: MGDLSCPEGLEELLSAPPPDLGAQRRHGWNPKDCSENIEVKEGGLYFERRPVAQSTDGARGKRGYSRGLHAWEISWPLEQRGTHAVVGVATALAPLQTDHYAALLGSNSESWGWDIGRGKLYHQSKGPGAPQYPAGTQGEQLEVPERLLVVLDMEEGTLGYAIGGTYLGPAFRGLKGRTLYPAVSAVWGQCQVRIRYLGERGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.1843
R free: 0.2043
Average B factor: 9.098
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Sodium chloride, 0.1M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 2.01
Solvent content (%): 38.66
Release date: 2020-07-01
Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor (PDB entry 6E2Q)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 483 residues
Sequence: GSDPVLQVYLYHSLGKSEADYLTFPSGEYVAEEICIAASKACGITPVYHNMFALMSETERIWYPPNHVFHIDESTRHNVLYRIRFYFPRWYCSGSNRAYRHGISRGAEAPLLDDFVMSYLFAQWRHDFVHGWIKVPVTHETQEECLGMAVLDMMRIAKENDQTPLAIYNSISYKTFLPKCIRAKIQDYHILTRKRIRYRFRRFIQQFSQCKATARNLKLKYLINLETLQSAFYTEKFEVKEPGSGPSGEEIFATIIITGNGGIQWSRGKHKESETLTEQDLQLYCDFPNIIDVSIKQANQEGSNESRVVTIHKQDGKNLEIELSSLREALSFVSLIDGYYRLTADAHHYLCKEVAPPAVLENIQSNCHGPISMDFAISKLKKAGNQTGLYVLRCSPKDFNKYFLTFAVERENVIEYKHCLITKNENEEYNLSGTKKNFSSLKDLLNCYQMETVRSDNIIFQFTKCCPPKPKDKSNLLVFRTGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2253
R free: 0.2625
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM Tris, pH 7.6, 2-4% PEG8000
Matthews coefficient: 3.55
Solvent content (%): 65.39
Release date: 2018-08-08
Human DNA polymerase eta-DNA-dT primer dCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion (PDB entry 8V7A)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1711
R free: 0.2182
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.08
Solvent content (%): 40.85
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2024-05-15
HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A SULFONAMIDE INHIBITOR (PDB entry 6SDS)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1462
R free: 0.1741
Average B factor: 11.079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M SODIUM CITRATE, 60 mM TRIS-HCL
Matthews coefficient: 2.07
Solvent content (%): 40.7
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-06-10
Crystal structure of compound 3-bound human Dynamin-1-like protein GTPase-BSE fusion (PDB entry 8SKN)
Macromolecule: Dynamin-1-like protein GTPase-BSE fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3
Sequence length: 382 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMEALIPVINKLQDVFNTVGADIIQLPQIVVVGTQSSGKSSVLESLVGRDLLPRGTGIVTRRPLILQLVHVSQEDKRKTTGEENGVEAEEWGKFLHTKNKLYTDFDEIRQEIENETERISGNNKGVSPEPIHLKIFSPNVVNLTLVDLPGMTKVPVGDQPKDIELQIRELILRFISNPNSIILAVTAANTDMATSEALKISREVDPDGRRTLAVITKLDLMDAGTDAMDVLMGRVIPVKLGIIGVVNRSQLDINNKKSVTDSIRDEYAFLQKKYPSLANRNGTKYLARTLNRLLMHHIRDCLPELKTRINVLAAQYQSLLNSYGEPVDDKHGTDSRRKEAADMLKALQGASQIIAEIRETHLW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.20563
R free: 0.25555
Average B factor: 43.259
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.05 M potassium chloride, 0.01 M magnesium chloride, 15% w/v PEG6000
Matthews coefficient: 2.16
Solvent content (%): 43.14
Ligand: N-[4-(azetidin-1-yl)-2-(4-methylphenyl)quinolin-6-yl]-2-methylpropanamide (6I9)
Ligand formula: C23 H25 N3 O
Ligand molecular weight: 359.464
Ligand SMILES: Cc1ccc(cc1)c2cc(c3cc(ccc3n2)NC(=O)C(C)C)N4CCC4
Ligand InChI: InChI=1S/C23H25N3O/c1-15(2)23(27)24-18-9-10-20-19(13-18)22(26-11-4-12-26)14-21(25-20)17-7-5-16(3)6-8-17/h5-10,13-15H,4,11-12H2,1-3H3,(H,24,27)
Release date: 2023-08-30
PWWP1 domain of NSD2 in complex with MR837 (PDB entry 6UE6)
Macromolecule: Histone-lysine N-methyltransferase NSD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 141 residues
Sequence: GGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQAEEAASMSVEERKAKFTFLYVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.235
R free: 0.252
Average B factor: 60.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 0.2 M potassium thiocyanate
Matthews coefficient: 2.17
Solvent content (%): 43.22
Ligand: 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide (Q5D)
Ligand formula: C16 H14 N2 O S
Ligand molecular weight: 282.36
Ligand SMILES: c1cc(sc1)CN(C2CC2)C(=O)c3ccc(cc3)C#N
Ligand InChI: InChI=1S/C16H14N2OS/c17-10-12-3-5-13(6-4-12)16(19)18(14-7-8-14)11-15-2-1-9-20-15/h1-6,9,14H,7-8,11H2
Release date: 2019-11-13
Crystal structure of monomeric FICD mutant L258D (PDB entry 6I7J)
Macromolecule: Adenosine monophosphate-protein transferase FICD
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 343 residues
Sequence: SLEARAALNQALEMKRQGKREKAQKLFMHALKMDPDFVDALTEFGIFSEEDKDIIQADYLYTRALTISPYHEKALVNRDRTLPLVEEIDQRYFSIIDSKVKKVMSIPKGNSALRRVMEETYYHHIYHTVAIEGNTLTLSEIRHILETRYAVPGKSDEEQNEVIGMHAAMKYINTTLVSRIGSVTISDVLEIHRRVLGYVDPVEAGRFRTTQVLVGHHIPPHPQDVEKQMQEFVQWLNSEEAMNLHPVEFAALAHYKLVYIHPFIDGNGRTSRLLMNLILMQAGYPPITIRKEQRSDYYHVLEAANEGDVRPFIRFIAKCTETTLDTLLFATTEYSVALPEAQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.22812
R free: 0.28281
Average B factor: 50.929
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 8.5; 2.0 M Ammonium Sulphate
Matthews coefficient: 4.07
Solvent content (%): 69.77
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2019-09-25
ATPase family AAA domain containing 2 with crystallization epitope mutations V1022R:Q1027E (PDB entry 8RU5)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.2109
R free: 0.2214
Average B factor: 29.255
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG6000
10% ethylene glycol
0.1M tris pH 7.5
0.1M calcium chloride
Matthews coefficient: 2.37
Solvent content (%): 48.17
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2024-03-06
Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine (PDB entry 5BWN)
Macromolecule: myristoyl H3K9 peptide
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: QTARXSTGGW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.942
R work: 0.2261
R free: 0.2745
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Ammonium tartrate dibasic (pH 7.0), 20% w/v PEG 3350, 0.01M Urea
Matthews coefficient: 1.98
Solvent content (%): 37.89
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-07-13
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13707a (PDB entry 5R5G)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1867
R free: 0.2298
Average B factor: 28.153
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.01
Solvent content (%): 38.72
Ligand: methyl 2-[(2~{S})-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanoate (S1M)
Ligand formula: C9 H14 N2 O4
Ligand molecular weight: 214.218
Ligand SMILES: CC(=O)N1CCNC(=O)C1CC(=O)OC
Ligand InChI: InChI=1S/C9H14N2O4/c1-6(12)11-4-3-10-9(14)7(11)5-8(13)15-2/h7H,3-5H2,1-2H3,(H,10,14)/t7-/m0/s1
Release date: 2020-07-01
Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4) (PDB entry 6F4S)
Macromolecule: JmjC domain-containing protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.47
Sequence length: 255 residues
Sequence: HHHHHHSSGVDLGTENLYFQSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPAMQKWSLEYIQEIAGARTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITICAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.461
R work: 0.1367
R free: 0.152
Average B factor: 23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M Bis-Tris pH 6.5, 29 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Matthews coefficient: 2.27
Solvent content (%): 45.88
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2018-04-04
Crystal structure of human MAT2a with S-Adenosylmethionine and a fragment bound in a novel pocket (PDB entry 8OOG)
Macromolecule: S-adenosylmethionine synthase isoform type-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.6
Sequence length: 397 residues
Sequence: QSMNGQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSRAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.384
R work: 0.19
R free: 0.2001
Average B factor: 19.35
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 8 % PEG8000, 12 % ethylene glycol, 0.1 M Hepes pH 8.0
Matthews coefficient: 2.13
Solvent content (%): 42.2
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2023-07-12
LSD1-CoREST in complex with AW2 and SNAG peptide (PDB entry 8F59)
Macromolecule: REST corepressor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 144 residues
Sequence: GPLGSPEFRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2206
R free: 0.2344
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Matthews coefficient: 5.65
Solvent content (%): 78.22
Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) (XB6)
Ligand formula: C42 H47 N9 O16 P2
Ligand molecular weight: 995.821
Ligand SMILES: Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7ccc(cc7)c8ccccc8
Ligand InChI: InChI=1S/C42H47N9O16P2/c1-21-14-26-27(15-22(21)2)51(31(54)13-10-23-8-11-25(12-9-23)24-6-4-3-5-7-24)33-39(47-42(59)48-40(33)58)49(26)16-28(52)34(55)29(53)17-64-68(60,61)67-69(62,63)65-18-30-35(56)36(57)41(66-30)50-20-46-32-37(43)44-19-45-38(32)50/h3-9,11-12,14-15,19-20,28-30,34-36,41,52-53,55-57H,10,13,16-18H2,1-2H3,(H,60,61)(H,62,63)(H2,43,44,45)(H2,47,48,58,59)/t28-,29+,30+,34-,35+,36+,41+/m0/s1
Release date: 2024-06-12
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000421a (PDB entry 7GSF)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1951
R free: 0.2275
Average B factor: 40.438
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.1
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24