Structure of PDB 3b6d Chain A Binding Site BS01

Receptor Information
>3b6d 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
FAQIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAP
AVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYQPLGGCVLGKAT
DDYGRVAGYKNLYVTDGSLIPGSVGVNPFVTITALAERNVERIIKQDV
Ligand information
Ligand IDFAE
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)/p+1/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-O
SMILES
SoftwareSMILES
CACTVS 3.370Cc1cc2N=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)n5c[nH+]c6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.7.0Cc1cc2c(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)n5c[nH+]c6c5ncnc6N)O)O)O)O)O
CACTVS 3.370Cc1cc2N=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)n5c[nH+]c6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.7.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5c[nH+]c6c5ncnc6N)O)O)O)O)O
ACDLabs 12.01O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5c[nH+]c4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H34 N9 O15 P2
NameFLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE
ChEMBL
DrugBankDB02332
ZINC
PDB chain3b6d Chain A Residue 510 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3b6d Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase
Resolution1.2 Å
Binding residue
(original residue number in PDB)		I16 G19 Y20 E40 M41 Y107 R110 G114 G115 N119 G120 M122 I218 Q249 V250 A289 G290 Y446 G475 N485 P486 F487
Binding residue
(residue number reindexed from 1)		I8 G11 Y12 E32 M33 Y99 R102 G106 G107 N111 G112 M114 I210 Q241 V242 A281 G282 Y438 G467 N477 P478 F479
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q361 Q447 N485
Catalytic site (residue number reindexed from 1) Q353 Q439 N477
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:3b6d, PDBe:3b6d, PDBj:3b6d
PDBsum3b6d
PubMed18029419
UniProtP12676|CHOD_STRS0 Cholesterol oxidase (Gene Name=choA)

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