Structure of PDB 5dyz Chain A Binding Site BS01

Receptor Information
>5dyz Chain A (length=445) Species: 1404 (Priestia megaterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRY
LSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHN
ILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLD
TIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRENKRQFQEDIK
VMNDLVDKIIADRKASEQSDDLLTHMLNGKDPETGEPLDGENIRYQIITF
LIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKHVKQL
KYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLH
RDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEAT
LVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLG
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 chain5dyz 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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PDB5dyz Subtle structural changes in the Asp251Gly/Gln307His P450 BM3 mutant responsible for new activity toward diclofenac, tolbutamide and ibuprofen.
Resolution1.967 Å
Binding residue
(original residue number in PDB)		K69 L86 F87 W96 F107 F261 A264 G265 T268 A328 F331 P392 F393 R398 C400 I401 A406
Binding residue
(residue number reindexed from 1)		K68 L85 F86 W95 F106 F250 A253 G254 T257 A317 F320 P381 F382 R387 C389 I390 A395
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T268 F393 C400
Catalytic site (residue number reindexed from 1) T257 F382 C389
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:5dyz, PDBe:5dyz, PDBj:5dyz
PDBsum5dyz
PubMed26718083
UniProtP14779|CPXB_PRIM2 Bifunctional cytochrome P450/NADPH--P450 reductase (Gene Name=cyp102A1)

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