Structure of PDB 1yqw Chain C Binding Site BS01

Receptor Information
>1yqw Chain C (length=260) Species: 878 (Solidesulfovibrio fructosivorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGE
AAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAK
AKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINF
VGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDS
EEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFW
DTMTPFYEQG
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 chain1yqw Chain C Residue 265 [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]
PDB1yqw Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		H184 C187 R189 L190 C212 L213 Y214 C218 P221
Binding residue
(residue number reindexed from 1)		H180 C183 R185 L186 C208 L209 Y210 C214 P217
Annotation score1
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) C13 C16 C110 C143 H180 C183 C208 C214 C223 P234 C241 C244
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:1yqw, PDBe:1yqw, PDBj:1yqw
PDBsum1yqw
PubMed15803334
UniProtP18187|PHNS_SOLFR Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

[Back to BioLiP]