Structure of PDB 6vwy Chain B Binding Site BS03

Receptor Information
>6vwy Chain B (length=625) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKTIRSRSIWDDAHAMLEKAKAEGISTVWDRAAEQTPACKFGELGTCCRN
CIMGPCRIANRKDGKMRLGVCGADADVIVARNFGRFIAGGAAGHSDHGRD
LIETLEAVAEGKAPGYTIRDVAKLRRIAAELGVADAATRPAHDVAADLVT
ICYNDFGSRRNALAFLARAPQVRRDLWQRLGMTPRGVDREIAEMMHRTHM
GCDNDHTSLLVHAARTALADGWGGSMIGTELSDILFGTPRPRQSTVNLGV
LRKDAVNILVHGHNPVVSEMILAATREPAVRQAAQDAGAADINVAGLCCT
GNELLMRQGIPMAGNHLMTELAIVTGAADAIVADYQCIMPSLVQIAACYH
TRFVTTSPKGRFTGATHVEVHPHNAQERCREIVMLAIDAYTRRDPARVDI
PSQPVSIMSGFSNEAILEALGGTPKPLIDAVVAGQIRGFVGIVGCNNPKI
RQDSANVTLTRELIRRDIMVLATGCVTTAAGKAGLLVPEAASKAGEGLAA
VCRSLGVPPVLHMGSCVDNSRILQLCALLATTLGVDISDLPVGASSPEWY
SEKAAAIAMYAVASGIPTHLGLPPNILGSENVTAMALHGLQDVVGAAFMV
EPDPVKAADMLEAHIVARRARLGLT
Ligand information
Ligand IDXCC
InChIInChI=1S/4Fe.Ni.4S
InChIKeyQGLWBXDZIHZONR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385[Fe]S[Fe]S[Fe]S[Fe]S[Ni]
OpenEye OEToolkits 2.0.7S1[Fe]2[S]([Fe]3[S]2[Fe]1[S]3[Ni])[Fe]
OpenEye OEToolkits 2.0.7S1[Fe]2[S@@]([Fe]3[S@@]2[Fe]1[S@]3[Ni])[Fe]
FormulaFe4 Ni S4
NameFE(4)-NI(1)-S(4) CLUSTER;
C CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain6vwy Chain B Residue 702 [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]
PDB6vwy The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance inDesulfovibrio vulgarisNi-Fe Carbon Monoxide Dehydrogenase.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		H266 C301 C302 C340 G447 C448 C478 C519 Y553 S554 K556
Binding residue
(residue number reindexed from 1)		H263 C298 C299 C337 G444 C445 C475 C516 Y550 S551 K553
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.7.4: anaerobic carbon-monoxide dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004601 peroxidase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0043885 anaerobic carbon-monoxide dehydrogenase activity
GO:0046872 metal ion binding
GO:0050418 hydroxylamine reductase activity
GO:0051537 2 iron, 2 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006091 generation of precursor metabolites and energy
GO:0042542 response to hydrogen peroxide
GO:0098869 cellular oxidant detoxification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vwy, PDBe:6vwy, PDBj:6vwy
PDBsum6vwy
PubMed32655979
UniProtQ72A99

[Back to BioLiP]