Structure of PDB 4gd3 Chain S Binding Site BS01

Receptor Information
>4gd3 Chain S (length=304) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAG
TQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAA
AGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIP
DVMSAIITYMVTFDRLPDVDRMGRPLMFYGQRIHDKCYRRAHFDAGEFVQ
SWDDDAARKGYCLYKMGCKGPTTYNACSSTRWNDGVSFCIQSGHGCLGCA
ENGFWDRGSFYSRVVDIPQMGTHSTADTVGLTALGVVAAAVGVHAVASAV
DQRR
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain4gd3 Chain S Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		H187 C190 R192 R193 F196 C215 L216 Y217 C221 P224 I243
Binding residue
(residue number reindexed from 1)		H184 C187 R189 R190 F193 C212 L213 Y214 C218 P221 I240
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C149 C249 C252
Catalytic site (residue number reindexed from 1) C146 C246 C249
Enzyme Commision number 1.12.99.6: hydrogenase (acceptor).
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008901 ferredoxin hydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0033748 hydrogenase (acceptor) activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051538 3 iron, 4 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006113 fermentation
GO:0009061 anaerobic respiration
GO:0009267 cellular response to starvation
GO:0019645 anaerobic electron transport chain
GO:1902421 hydrogen metabolic process
Cellular Component
GO:0005886 plasma membrane
GO:0009375 ferredoxin hydrogenase complex
GO:0016020 membrane
GO:0044569 [Ni-Fe] hydrogenase complex
GO:0098567 periplasmic side of plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4gd3, PDBe:4gd3, PDBj:4gd3
PDBsum4gd3
PubMed23260654
UniProtP69739|MBHS_ECOLI Hydrogenase-1 small chain (Gene Name=hyaA)

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