Structure of PDB 1yq9 Chain B Binding Site BS01

Receptor Information
>1yq9 Chain B (length=260) Species: 879 (Megalodesulfovibrio gigas) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGH
AVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAK
AVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMN
FVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFG
SPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNF
WDLYSPFYSA
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 chain1yq9 Chain B Residue 265 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yq9 Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		H185 C188 R190 L191 C213 L214 Y215 C219 P222
Binding residue
(residue number reindexed from 1)		H181 C184 R186 L187 C209 L210 Y211 C215 P218
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) C13 C16 C108 C144 H181 C184 C209 C215 C224 P235 C242 C245
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yq9, PDBe:1yq9, PDBj:1yq9
PDBsum1yq9
PubMed15803334
UniProtP12943|PHNS_MEGGA Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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