Structure of PDB 3vrm Chain A Binding Site BS01

Receptor Information
>3vrm Chain A (length=402) Species: 2074 (Pseudonocardia autotrophica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRY
ADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKL
VGRSFAVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVIC
ELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTE
PDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLA
LLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVT
IPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCLGAQ
LARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPR
SA
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain3vrm Chain A Residue 501 [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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PDB3vrm A single mutation at the ferredoxin binding site of p450 vdh enables efficient biocatalytic production of 25-hydroxyvitamin d3.
Resolution2.57 Å
Binding residue
(original residue number in PDB)		I88 H95 R99 L232 L233 A236 T240 T241 V283 R289 F339 F340 G341 H345 C347 G349 A353
Binding residue
(residue number reindexed from 1)		I87 H94 R98 L231 L232 A235 T239 T240 V282 R288 F338 F339 G340 H344 C346 G348 A352
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D173 A236 E239 T240 T241 V283 C347 L348 G349 E356 V388
Catalytic site (residue number reindexed from 1) D172 A235 E238 T239 T240 V282 C346 L347 G348 E355 V387
Enzyme Commision number 1.14.15.15: cholestanetriol 26-monooxygenase.
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0047748 cholestanetetraol 26-dehydrogenase activity
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3vrm, PDBe:3vrm, PDBj:3vrm
PDBsum3vrm
PubMed24115473
UniProtC4B644|CPVDH_PSEAH Vitamin D(3) 25-hydroxylase (Gene Name=vdh)

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