Structure of PDB 1yrq Chain H Binding Site BS04

Receptor Information
>1yrq Chain H (length=545) Species: 878 (Solidesulfovibrio fructosivorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEI
ILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRN
LVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPG
NSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAH
YLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLAL
SKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPSK
HLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGV
TDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVV
DMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDN
TLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLG
PRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH
Ligand information
Ligand IDFCO
InChIInChI=1S/2CN.CO.Fe/c3*1-2;
InChIKeyVBQUCMTXYFMTTE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(#N)[Fe](=C=O)C#N
ACDLabs 10.04N#C\[Fe](C#N)=C=O
CACTVS 3.341O=C=[Fe](C#N)C#N
FormulaC3 Fe N2 O
NameCARBONMONOXIDE-(DICYANO) IRON
ChEMBL
DrugBank
ZINC
PDB chain1yrq Chain H Residue 550 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1yrq Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		C75 V78 H79 A474 P475 R476 L479 V497 P498 S499 C546
Binding residue
(residue number reindexed from 1)		C71 V74 H75 A470 P471 R472 L475 V493 P494 S495 C542
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E25 C72 C75 H79 R476 S499 C543 C546
Catalytic site (residue number reindexed from 1) E21 C68 C71 H75 R472 S495 C539 C542
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1yrq, PDBe:1yrq, PDBj:1yrq
PDBsum1yrq
PubMed15803334
UniProtP18188|PHNL_SOLFR Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)

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