Structure of PDB 1yrq Chain B

Receptor sequence
>1yrqB (length=262) Species: 878 (Solidesulfovibrio fructosivorans) [Search protein sequence]
AKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAA
GEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAA
AKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPI
NFVGAVVHVLTKGIPDLDSNGRPKLFYGELVHDNCPRLPHFEASEFAPSF
DSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPD
FWDTMTPFYEQG
3D structure
PDB1yrq Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
ChainB
Resolution2.1 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 C114 C147 H184 C187 C212 C218 C227 P238 C245 C248
Catalytic site (residue number reindexed from 1) C15 C18 C112 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 B H184 C187 R189 L190 C212 L213 Y214 C218 P221 V239 H182 C185 R187 L188 C210 L211 Y212 C216 P219 V237
BS02 F3S B C227 F232 W237 P238 C245 L246 C248 C225 F230 W235 P236 C243 L244 C246
BS03 SF4 B E16 C17 G19 C20 G112 T113 C114 C147 P148 E14 C15 G17 C18 G110 T111 C112 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:1yrq, PDBe:1yrq, PDBj:1yrq
PDBsum1yrq
PubMed15803334
UniProtP18187|PHNS_SOLFR Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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