Structure of PDB 4xyd Chain A Binding Site BS01

Receptor Information
>4xyd Chain A (length=445) Species: 375451 (Roseobacter denitrificans OCh 114) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVSPNFLSEILPFNIVR
MLHTNSLIVWLLLGFMGAAYFVIPEESEREIHSPLLAYLQLAIMVLGTLG
VVVTYLFNLFEGNWLLGKEGREFLEQPVWVKMGIVVAALIFMYNISMTVL
QGRKTAITNVLLLGLWGLTLLFLFAFYNPSNLALDKMYWWYVVHLWVEGT
WELVMASVLAFLMLKLTGVDREIIEKWLYLIVATALFSGILGTGHHYFWI
GTPGYWQWIGSIFSALEVVPFFGMMAFAFVMVWKGRKDHPNKAALLWSLG
CATLAFFGAGVWGFLHTLHGINYYTHGTQITAAHGHLAFFGAYVSLNLAI
FSYAFPILRKRDPYNQVLNMASFWLMAGGMTFMTFVLTFAGTVQTHAQRV
QGDYFMDVQDAITIFYWMRFGSGIAVVLGALLFIYAVAVPRKEII
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 chain4xyd 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

[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]
PDB4xyd Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		Q23 V24 G27 L28 L30 Y34 R50 H53 L57 H336 F339 M380 R419
Binding residue
(residue number reindexed from 1)		Q23 V24 G27 L28 L30 Y34 R50 H53 L57 H336 F339 M380 R419
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.5: nitric-oxide reductase (cytochrome c).
Gene Ontology
Molecular Function
GO:0004129 cytochrome-c oxidase activity
GO:0016491 oxidoreductase activity
GO:0016966 nitric oxide reductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0009060 aerobic respiration
GO:0015990 electron transport coupled proton transport
GO:0022904 respiratory electron transport chain
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xyd, PDBe:4xyd, PDBj:4xyd
PDBsum4xyd
PubMed27185533
UniProtQ16A04

[Back to BioLiP]