Structure of PDB 5dyp Chain A Binding Site BS01

Receptor Information
>5dyp Chain A (length=440) Species: 1404 (Priestia megaterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRY
LSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHN
ILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLD
TIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLNKRQFQEDIKVMN
DLVDKIIADRKASQSDDLLTHMLNGKDPETGEPLDGENIRYQIITFLIAG
HETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKHVKQLKYVG
MVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKT
IWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLG
MMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL
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 chain5dyp 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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PDB5dyp Subtle structural changes in the Asp251Gly/Gln307His P450 BM3 mutant responsible for new activity toward diclofenac, tolbutamide and ibuprofen.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		K69 L86 F87 W96 G265 T268 A328 F331 P392 F393 R398 C400 I401 G402 A406
Binding residue
(residue number reindexed from 1)		K68 L85 F86 W95 G250 T253 A313 F316 P377 F378 R383 C385 I386 G387 A391
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T268 F393 C400
Catalytic site (residue number reindexed from 1) T253 F378 C385
Enzyme Commision number 1.14.14.1: unspecific monooxygenase.
1.6.2.4: NADPH--hemoprotein reductase.
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

View graph for
Molecular Function
External links
PDB RCSB:5dyp, PDBe:5dyp, PDBj:5dyp
PDBsum5dyp
PubMed26718083
UniProtP14779|CPXB_PRIM2 Bifunctional cytochrome P450/NADPH--P450 reductase (Gene Name=cyp102A1)

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