Structure of PDB 2frv Chain I Binding Site BS03

Receptor Information
>2frv Chain I (length=261) Species: 879 (Megalodesulfovibrio gigas) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAG
HAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKA
KAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPM
NFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSF
GSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPN
FWDLYSPFYSA
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 chain2frv Chain I Residue 267 [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]
PDB2frv Crystal Structure of the Nickel-Iron Hydrogenase from Desulfovibrio Gigas
Resolution2.54 Å
Binding residue
(original residue number in PDB)		E16 C17 G19 C20 G110 C112 C148 P149
Binding residue
(residue number reindexed from 1)		E13 C14 G16 C17 G107 C109 C145 P146
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C17 C20 C112 C148 H185 C188 C213 C219 C228 P239 C246 C249
Catalytic site (residue number reindexed from 1) C14 C17 C109 C145 H182 C185 C210 C216 C225 P236 C243 C246
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
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:0009061 anaerobic respiration
Cellular Component
GO:0009375 ferredoxin hydrogenase complex
GO:0016020 membrane
GO:0042597 periplasmic space
GO:0044569 [Ni-Fe] hydrogenase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2frv, PDBe:2frv, PDBj:2frv
PDBsum2frv
PubMed
UniProtP12943|PHNS_MEGGA Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

[Back to BioLiP]