Structure of PDB 3gyi Chain A Binding Site BS01

Receptor Information
>3gyi Chain A (length=498) Species: 74576 (Streptomyces sp. SA-COO) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GYVPAVVIGTGYGAAVSALRLGEAGVQTLMLEMGQLWNQPGPDGNIFCGM
LNPDKRSSWFKNRTEAPLGSFLWLDVVNRNIDPYAGVLDRVNYDQMSVYV
GRGVGGGSLVNGGMAVEPKRSYFEEILPRVDSSEMYDRYFPRANSMLRVN
HIDTKWFEDTEWYKFARVSREQAGKAGLGTVFVPNVYDFGYMQREAAGEV
PKSALATEVIYGNNHGKQSLDKTYLAAALGTGKVTIQTLHQVKTIRQTKD
GGYALTVEQKDTDGKLLATKEISCRYLFLGAGSLGSTELLVRARDTGTLP
NLNSEVGAGWGPNGNIMTARANHMWNPTGAHQSSIPALGIDAWDNSDSSV
FAEIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAP
AVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYHPLGGCVLGKAT
DDYGRVAGYKNLYVTDGSLIPGSVGVDPFVTITALAERNVERIIKQDV
Ligand information
Ligand IDFAD
InChIInChI=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
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(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
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain3gyi Chain A Residue 510 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gyi A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase.
Resolution1.0 Å
Binding residue
(original residue number in PDB)		I16 G17 G19 Y20 L39 E40 M41 Y107 R110 G114 G115 N119 G120 M122 I218 Q249 V250 A289 G290 Y446 H447 G475 D485 P486 F487
Binding residue
(residue number reindexed from 1)		I8 G9 G11 Y12 L31 E32 M33 Y99 R102 G106 G107 N111 G112 M114 I210 Q241 V242 A281 G282 Y438 H439 G467 D477 P478 F479
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E361 H447 D485
Catalytic site (residue number reindexed from 1) E353 H439 D477
Enzyme Commision number 1.1.3.6: cholesterol oxidase.
5.3.3.1: steroid Delta-isomerase.
Gene Ontology
Molecular Function
GO:0004769 steroid delta-isomerase activity
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016853 isomerase activity
GO:0016995 cholesterol oxidase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006707 cholesterol catabolic process
GO:0008203 cholesterol metabolic process
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gyi, PDBe:3gyi, PDBj:3gyi
PDBsum3gyi
PubMed19923719
UniProtP12676|CHOD_STRS0 Cholesterol oxidase (Gene Name=choA)

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