Structure of PDB 5gnm Chain A Binding Site BS01

Receptor Information
>5gnm Chain A (length=399) Species: 2074 (Pseudonocardia autotrophica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYA
DVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLV
GRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICE
LLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEP
DDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLAL
LTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTI
PAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCMGAQL
ARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPR
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 chain5gnm Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5gnm Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site
Resolution2.7 Å
Binding residue
(original residue number in PDB)		K65 M87 R99 A236 G237 T240 V283 P287 R289 F339 F340 H345 C347 M348 G349 A353
Binding residue
(residue number reindexed from 1)		K63 M85 R97 A234 G235 T238 V281 P285 R287 F337 F338 H343 C345 M346 G347 A351
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D173 A236 E239 T240 T241 V283 C347 M348 G349 E356 V388
Catalytic site (residue number reindexed from 1) D171 A234 E237 T238 T239 V281 C345 M346 G347 E354 V386
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:5gnm, PDBe:5gnm, PDBj:5gnm
PDBsum5gnm
PubMed28471358
UniProtC4B644|CPVDH_PSEAH Vitamin D(3) 25-hydroxylase (Gene Name=vdh)

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