Structure of PDB 4xyd Chain A Binding Site BS02

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 504 [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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PDB4xyd Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		E122 W190 V197 E198 H245 H246 E267 F271 A309 G313 F314 H316 T317 N322 H326 T331 H334 A338 F339 Y343
Binding residue
(residue number reindexed from 1)		E122 W190 V197 E198 H245 H246 E267 F271 A309 G313 F314 H316 T317 N322 H326 T331 H334 A338 F339 Y343
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

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

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