satarupa22/MacromolecularLigandDB huggingface dataset:
E. coli Microcin-processing metalloprotease TldD/E with DRVY angiotensin fragment bound (PDB entry 5NJ9)
Macromolecule: Metalloprotease TldD
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.4
Sequence length: 495 residues
Sequence: MGSSHHHHHHSQDPMSLNLVSEQLLAANGLKHQDLFAILGQLAERRLDYGDLYFQSSYHESWVLEDRIIKDGSYNIDQGVGVRAISGEKTGFAYADQISLLALEQSAQAARTIVRDSGDGKVQTLGAVEHSPLYTSVDPLQSMSREEKLDILRRVDKVAREADKRVQEVTASLSGVYELILVAATDGTLAADVRPLVRLSVSVLVEEDGKRERGASGGGGRFGYEFFLADLDGEVRADAWAKEAVRMALVNLSAVAAPAGTMPVVLGAGWPGVLLHEAVGHGLEGDFNRRGTSVFSGQVGELVASELCTVVDDGTMVDRRGSVAIDDEGTPGQYNVLIENGILKGYMQDKLNARLMGMTPTGNGRRESYAHLPMPRMTNTYMLPGKSTPQEIIESVEYGIYAPNFGGGQVDITSDKFVFSTSEAYLIENGKVTKPVKGATLIGSGIETMQQISMVGNDLKLDNGVGVCGKEGQSLPVGVGQPTLKVDNLTVGGTA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1494
R free: 0.1822
Average B factor: 12.982
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Matthews coefficient: 2.28
Solvent content (%): 45.96
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: 2017-10-04
DYRK1a in Complex with a Bromo-Triazolo-Pyridine (PDB entry 7ZH8)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 382 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1988
R free: 0.2351
Average B factor: 58.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M TRIS (pH = 8.5), 0.1 M Li2SO4, 34 % (v/v) PEG300, 12 mg/ml Protein, Dropsize (resovoir + Protein) 2 + 4
Matthews coefficient: 3.22
Solvent content (%): 61.85
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2022-11-09
The ligand-free structure of human PPARgamma LBD C285Y mutant in the presence of the SRC-1 coactivator peptide (PDB entry 7CXF)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 283 residues
Sequence: AEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGYQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2292
R free: 0.2693
Average B factor: 38.006
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 295
Crystal growth procedure: 2.2 M sodium malonate (pH 7.0)
Matthews coefficient: 2.68
Solvent content (%): 54.16
Ligand: MALONIC ACID (MLA)
Ligand formula: C3 H4 O4
Ligand molecular weight: 104.061
Ligand SMILES: C(C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
Release date: 2021-09-01
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000605a (PDB entry 7GSD)
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): 1.8
R work: 0.1986
R free: 0.2305
Average B factor: 42.096
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: 3.37
Solvent content (%): 63.45
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
Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS022 (PDB entry 6H0Y)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 342 residues
Sequence: METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.212
R work: 0.1242
R free: 0.1584
Average B factor: 18.9037
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.53
Solvent content (%): 51.43
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: 2020-01-29
Structure of a lysozyme antibody complex (PDB entry 4TTD)
Macromolecule: Lysozyme C
Type: Protein, polypeptide(L)
Source organism: Gallus gallus
EC number: 3.2.1.17
Sequence length: 129 residues
Sequence: KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2549
R free: 0.2789
Average B factor: 53.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM PCTP pH 4.5, 25% w/v Peg3350, ethanol 5%
Matthews coefficient: 2.39
Solvent content (%): 48.55
Release date: 2015-07-08
LSD1-FCPA-MPE five-membered ring adduct model (PDB entry 6KGQ)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.1682
R free: 0.1969
Average B factor: 65.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES (pH 7.5), 5% MPD, 3.5-4.0% PEG MME 2000
Matthews coefficient: 3.73
Solvent content (%): 67.05
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: 2020-03-25
Crystal structure of Pol theta polymerase domain in complex with compound 22 (PDB entry 7ZX1)
Macromolecule: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: TTCCAATGACAGCCGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.829
R work: 0.2281
R free: 0.2602
Average B factor: 93.617
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 285
Crystal growth procedure: 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Matthews coefficient: 2.73
Solvent content (%): 59.8
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-10-12
DNA Polymerase Mu, 8-oxorGTP:At Reaction State Ternary Complex, 50 mM Mn2+ (30 min) (PDB entry 6VF4)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.168
R free: 0.1923
Average B factor: 31.8205
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.51
Solvent content (%): 50.93
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: 2021-09-01
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor KM-06-057 (PDB entry 8CJJ)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66415657298
R work: 0.175245155349
R free: 0.203226343466
Average B factor: 26.3932631618
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% PEG 5000 MME, 0.2 M lithium acetate
Matthews coefficient: 2.14
Solvent content (%): 42.65
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2024-01-10
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102660 (PDB entry 5QIW)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1839
R free: 0.2153
Average B factor: 18.957
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.36
Solvent content (%): 47.83
Ligand: N-[(E)-(4-methylphenyl)methylidene]acetamide (J5S)
Ligand formula: C10 H11 N O
Ligand molecular weight: 161.2
Ligand SMILES: Cc1ccc(cc1)C=NC(=O)C
Ligand InChI: InChI=1S/C10H11NO/c1-8-3-5-10(6-4-8)7-11-9(2)12/h3-7H,1-2H3/b11-7+
Release date: 2019-12-18
11-BETA DEHYDROGENASE ISOZYME 1 IN COMPLEX WITH COLLETOIC ACID (PDB entry 6NJ7)
Macromolecule: Corticosteroid 11-beta-dehydrogenase isozyme 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.146
Sequence length: 289 residues
Sequence: MKHQHQHQHQHQHQQPLQPLNEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVVSHCLELGAASAHYIAGTMEDMTFAEQFVAQAGKLMGGLDMLILNHITNTSLNLFHDDIHHVRKSMEVNFLSYVVLTVAALPMLKQSNGSIVVVSSLAGKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMKAVSGIVHMQAAPKEECALEIIKGGALRQEEVYYDSSLWTTLLIRNPSRKILEFLYSTSYNMDRFINK
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.213
R free: 0.264
Average B factor: 93.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: THE 4 UL DROP CONTAINED 2 UL PROTEIN
 (25 MM TRIS, PH 8.0, 250 MM NACL, 4 MM CHAPS, 10 MG/ML PROTEIN)
 AND 2 UL WELL SOLUTION (100 MM MES, PH 6.5, 20 PEG 4000), VAPOR
 DIFFUSION, HANGING DROP, TEMPERATURE 291K
Matthews coefficient: 2.52
Solvent content (%): 51.15
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-07-24
Histone deacetylases complex with peptide macrocycles (PDB entry 6WHZ)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 385 residues
Sequence: AAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.227
R free: 0.2813
Average B factor: 64.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40% (v/v) PEG600 and 100mM CHES pH 9.5
Matthews coefficient: 2.32
Solvent content (%): 47.07
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: 2021-04-21
Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex (PDB entry 6CVQ)
Macromolecule: Aprataxin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.7
Sequence length: 180 residues
Sequence: GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYQWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1178
R free: 0.1677
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM HEPES, 25% w/v polyethylene glycol 3350
Matthews coefficient: 2.54
Solvent content (%): 51.67
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-07-04
Crystal Structure of human phosphodiesterase 10 in complex with 6-chloro-2,3-dimethyl-8-pyrrolidin-1-ylimidazo[1,2-b]pyridazine (PDB entry 5SHL)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1753
R free: 0.2374
Average B factor: 55.619
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.61
Solvent content (%): 52.9
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: 2022-10-12
Crystal Structure Analysis of PIP4K2A (PDB entry 6OSP)
Macromolecule: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.149
Sequence length: 394 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVECEENDGEEEGESDGTHPVGTPPDSPGNTLNSSPPLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFLDFIGHIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1773
R free: 0.2253
Average B factor: 55.1703
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 200mM Malic acid
Matthews coefficient: 2.53
Solvent content (%): 51.35
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: 2020-04-29
Crystal Structure of human phosphodiesterase 10 in complex with 1-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethyl]-3-(2-phenylpyrazol-3-yl)urea (PDB entry 5SFZ)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1905
R free: 0.2349
Average B factor: 39.198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.05
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-10-12
Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT0911 from cocktail soak (PDB entry 6DHU)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1812
R free: 0.2109
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03 M sodium fluoride
0.03 M sodium bromide
0.03 M sodium iodide
Matthews coefficient: 2.45
Solvent content (%): 49.79
Ligand: benzene-1,2,4-tricarboxylic acid (GHM)
Ligand formula: C9 H6 O6
Ligand molecular weight: 210.14
Ligand SMILES: c1cc(c(cc1C(=O)O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C9H6O6/c10-7(11)4-1-2-5(8(12)13)6(3-4)9(14)15/h1-3H,(H,10,11)(H,12,13)(H,14,15)
Release date: 2019-05-29
Novel, potent, selective and brain penetrant phosphodiesterase 10A inhibitors (PDB entry 6MSC)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 332 residues
Sequence: GSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWIS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.206
R free: 0.242
Average B factor: 75.89
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 5% Tascimate pH7.0, 100mM HEPES pH7, 10% PMME5000
Matthews coefficient: 2.15
Solvent content (%): 42.71
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: 2019-01-09