Structure of PDB 5y4n Chain L Binding Site BS03

Receptor Information
>5y4n Chain L (length=534) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGR
DPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGA
QYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLK
AVQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRL
QVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAF
VDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGV
VFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDD
RYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPE
ALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQ
AEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPV
EASLIGTPVADAKRPVEILRTVHSFDPCIACGVH
Ligand information
Ligand IDNFU
InChIInChI=1S/2CN.CHO.Fe.Ni/c3*1-2;;/h;;1H;;
InChIKeyQCZROEOIPZWDEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370[Ni]|[Fe](C=O)(C#N)C#N
ACDLabs 12.01N#C[Fe]([Ni])(C#N)C=O
OpenEye OEToolkits 1.7.0C(=O)[Fe](C#N)(C#N)[Ni]
FormulaC3 H Fe N2 Ni O
Nameformyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni);
NI-FE REDUCED ACTIVE CENTER
ChEMBL
DrugBank
ZINC
PDB chain5y4n Chain L Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5y4n Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		C81 C84 H88 A477 P478 R479 L482 V500 P501 S502 C546 C549
Binding residue
(residue number reindexed from 1)		C63 C66 H70 A459 P460 R461 L464 V482 P483 S484 C528 C531
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E34 C81 C84 H88 R479 S502 C546 C549
Catalytic site (residue number reindexed from 1) E16 C63 C66 H70 R461 S484 C528 C531
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:5y4n, PDBe:5y4n, PDBj:5y4n
PDBsum5y4n
PubMed28967475
UniProtP21852|PHNL_NITV9 Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)

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