Structure of PDB 4gd3 Chain A Binding Site BS01

Receptor Information
>4gd3 Chain A (length=179) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVSHYVFEAPVRIWHWLTVLCMAVLMVTGYFIGKPLPSVSGEATYLFYMG
YIRLIHFSAGMVFTVVLLMRIYWAFVGNRYSRQGVWYEIRWYLFLPIAQA
AMFGYFLMSVFMIITGFALYSEHSQYAIFAPFRYVVEFFYWTGGNSMDIH
SWHRLGMWLIGAFVIGHVYMALREDIMSD
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 chain4gd3 Chain A Residue 301 [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]
PDB4gd3 Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L32 M33 G36 I39 G40 R60 H63 F64 M143 G147 F148 Y151 H181 H184 R185 M188
Binding residue
(residue number reindexed from 1)		L25 M26 G29 I32 G33 R53 H56 F57 M112 G116 F117 Y120 H150 H153 R154 M157
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0020037 heme binding
GO:0033748 hydrogenase (acceptor) activity
GO:0046872 metal ion binding
Biological Process
GO:0006113 fermentation
GO:0009061 anaerobic respiration
GO:0009267 cellular response to starvation
GO:0019645 anaerobic electron transport chain
GO:0022904 respiratory electron transport chain
GO:1902421 hydrogen metabolic process
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0044569 [Ni-Fe] hydrogenase complex
GO:0098567 periplasmic side of plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4gd3, PDBe:4gd3, PDBj:4gd3
PDBsum4gd3
PubMed23260654
UniProtP0AAM1|CYBH_ECOLI Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit (Gene Name=hyaC)

[Back to BioLiP]