Structure of PDB 1yqw Chain Q

Receptor sequence

>1yqwQ (length=544) Species: 878 (Solidesulfovibrio fructosivorans)

PTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEII
LKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNL
VMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGN
SAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAHY
LEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALS
KEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPSKH
LATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVT
DPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVD
MVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNT
LCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPATWNLGP
RGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH

3D structure

• PDB: 1yqw Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
• Chain: Q
• Resolution: 1.83 Å

Enzymatic activity

• 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	Q	R70 H228	R65 H223
BS02	FE2	Q	E53 L495 H549	E48 L490 H544
BS03	BCT	Q	S466 K467 R484	S461 K462 R479
BS04	FCO	Q	C75 V78 H79 A474 P475 R476 V497 P498 A499 C546	C70 V73 H74 A469 P470 R471 V492 P493 A494 C541
BS05	PER	Q	C75 R476 C543	C70 R471 C538

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

External links

• PDB: RCSB:1yqw, PDBe:1yqw, PDBj:1yqw
• PDBsum: 1yqw
• PubMed: 15803334
• UniProt: P18188|PHNL_SOLFR Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)