Structure of PDB 5kyo Chain D Binding Site BS01

Receptor Information
>5kyo Chain D (length=384) Species: 13690 (Sphingobium yanoikuyae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERPDNVPADRVFDFDIYRDVPGLDFHQSWREIMRPHPLMWTPHNGGHWVA
LRSDLAETVMSDFERFSNHTVLVPKETAGEAYRLIPLSLDPPEHRPFRSL
LNENLGPKPLRPIEQVVTDLAVSLIEGFRPKGRCNFTHEFAEQLPVRIFM
RIVDLPVEDLPKLKHLADQYTRPDPLDDVTKQFREYLRPVIEARRIKPGE
DMISRMINLTDIEAENICIQVLVGGLDTVVNMLGFTFSHLAKDHALRRAI
AADPSLIDDALLEFFRRFPVVSSAREVLRDQEFEGVLLKAGDMVMAPTVV
VAMDDARNEDPLEFRLGRKARQHSTFGKGSHTCPGAHLARMEMKVVLREW
FARIPEFRIEDDAPLRYSNGIVGSVKPFVLEWPV
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 chain5kyo Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5kyo X-ray crystal structure of cytochrome P450 monooxygenase CYP101J2 from Sphingobium yanoikuyae strain B2.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L103 H110 L117 G250 G251 T254 S299 R301 T351 F352 H357 C359 P360 G361 L364
Binding residue
(residue number reindexed from 1)		L87 H94 L101 G224 G225 T228 S273 R275 T325 F326 H331 C333 P334 G335 L338
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R188 G250 D253 T254 V255 C359 P360 G361 E368 V398
Catalytic site (residue number reindexed from 1) R172 G224 D227 T228 V229 C333 P334 G335 E342 V372
Enzyme Commision number ?
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

View graph for
Molecular Function
External links
PDB RCSB:5kyo, PDBe:5kyo, PDBj:5kyo
PDBsum5kyo
PubMed27936485
UniProtA0A1C9CIU0

[Back to BioLiP]