Structure of PDB 1yq9 Chain A

Receptor sequence
>1yq9A (length=261) Species: 879 (Megalodesulfovibrio gigas) [Search protein sequence]
KKRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAG
HAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKA
KAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPM
NFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSF
GSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPN
FWDLYSPFYSA
3D structure
PDB1yq9 Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
ChainA
Resolution2.35 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SF4 A H185 C188 R190 L191 C213 L214 Y215 C219 H182 C185 R187 L188 C210 L211 Y212 C216
BS02 F3S A C228 F233 W238 P239 C246 I247 C249 C225 F230 W235 P236 C243 I244 C246
BS03 SF4 A E16 C17 G19 C20 G110 C112 C148 P149 E13 C14 G16 C17 G107 C109 C145 P146
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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