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BioLiP

Structure of PDB 8w6x Chain L Binding Site BS01

Receptor Information
>8w6x Chain L (length=533) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRD
PRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQ
YLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKA
VQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQ
VKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFV
DEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVV
FKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDR
YSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEA
LFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQA
EGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVE
ASLIGTPVADAKRPVEILRTVHSFDPCIACGVH
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 chain8w6x Chain L Residue 601 [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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PDB8w6x New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.
Resolution1.04 Å
Binding residue
(original residue number in PDB)		C81 C84 H88 P478 R479 L482 V500 P501 S502 C546 C549
Binding residue
(residue number reindexed from 1)		C62 C65 H69 P459 R460 L463 V481 P482 S483 C527 C530
Annotation score1
Enzymatic activity
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Cellular Component
External links
PDB RCSB:8w6x, PDBe:8w6x, PDBj:8w6x
PDBsum8w6x
PubMed37712026
UniProtP21852|PHNL_NITV9 Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)

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