Structure of PDB 1ubt Chain L Binding Site BS03

Receptor Information
>1ubt 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
AVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRL
QVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAF
VDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGV
VFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDD
RYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPE
ALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQ
AEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPV
EASLIGTPVADAKRPVEILRTVHSFDPCIACGVH
Ligand information
Ligand IDFNE
InChIInChI=1S/3CO.Fe.Ni.S/c3*1-2;;;
InChIKeyRSNJUOPWNIKDNA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(#O)[Fe]1(S[Ni]1)(C#O)C#O
CACTVS 3.385[Fe]S[Ni].[C-]#[O+].[C-]#[O+].[C-]#[O+]
FormulaC3 Fe Ni O3 S
Name(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
ChEMBL
DrugBank
ZINC
PDB chain1ubt Chain L Residue 1004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1ubt Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen
Resolution1.34 Å
Binding residue
(original residue number in PDB)		C81 C84 H88 A477 P478 R479 V500 P501 S502 C546 C549
Binding residue
(residue number reindexed from 1)		C63 C66 H70 A459 P460 R461 V482 P483 S484 C528 C531
Annotation score1
Enzymatic activity
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:1ubt, PDBe:1ubt, PDBj:1ubt
PDBsum1ubt
PubMed12296727
UniProtP21852|PHNL_NITV9 Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)

[Back to BioLiP]