Structure of PDB 5xlh Chain L

Receptor sequence

>5xlhL (length=533) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F')

SYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRD
PRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQ
YLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKA
VQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQ
VKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFV
DEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVV
FKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDR
YSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEA
LFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQA
EGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVE
ASLIGTPVADAKRPVEILRTVHSFDPCIACGVH

3D structure

• PDB: 5xlh Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
• Chain: L
• Resolution: 1.93 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E34 C81 C84 H88 R479 S502 C546 C549
• Catalytic site (residue number reindexed from 1): E15 C62 C65 H69 R460 S483 C527 C530
• 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	L	R79 H235	R60 H216
BS02	NFV	L	C81 C84 H88 A477 P478 R479 L482 V500 P501 S502 C546 C549	C62 C65 H69 A458 P459 R460 L463 V481 P482 S483 C527 C530
BS03	MG	L	E62 L498 H552	E43 L479 H533

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:5xlh, PDBe:5xlh, PDBj:5xlh
• PDBsum: 5xlh
• PubMed: 28967475
• UniProt: P21852|PHNL_NITV9 Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)