Structure of PDB 5odq Chain F Binding Site BS01

Receptor Information
>5odq Chain F (length=447) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKLSVEPVTRVEGHGKISVSFDDSGNLDKVRFHVVEVRGFEKFLEGRYVE
DAPIYTPRICGICQVAHHLASAKAVDNVFGVKIPETAELLRNLMHQGATV
HSHALHFYMLAAPDLMFPTTDDVLKRNLMGIAKEHPEIIKDAIELRKAGQ
NVVRVVGGRAIHPVTAVVGGQSKSLKEEERDELLKLSERTIELSEKSIEV
GKKLLENIKDEDLLDIGYFESAHMGMVNNGVHDLYDGKLRVVNSEGKVEY
EFDPSEYMNYIAEGVKPYSYLKFPYLKDKGEEDGIYRVNTLSRLNVSDKM
ATPLAQKYYDEFVKEFGKPCHHPMLFHYARLIELLSSAEMVKELLENDKI
VGEDIRAEPEEVVGDGVGCVEAPRGTLIHHFKTDDDGIITDTNLVVATVQ
NNPAMDIGVRKVAEKYIKAPEDATPQVLNYMEMLIRAYDPCLSCATH
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 chain5odq Chain F Residue 501 [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]
PDB5odq Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		C61 C64 H68 A373 P374 R375 L378 V397 A398 T399 C442 C445
Binding residue
(residue number reindexed from 1)		C60 C63 H67 A372 P373 R374 L377 V396 A397 T398 C441 C444
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R375 T399 C442 C445
Catalytic site (residue number reindexed from 1) R374 T398 C441 C444
Enzyme Commision number 1.12.1.2: hydrogen dehydrogenase.
1.12.99.6: hydrogenase (acceptor).
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0033748 hydrogenase (acceptor) activity
GO:0046872 metal ion binding
GO:0047985 hydrogen dehydrogenase activity

View graph for
Molecular Function
External links
PDB RCSB:5odq, PDBe:5odq, PDBj:5odq
PDBsum5odq
PubMed28818947
UniProtA0A2D0TCA6

[Back to BioLiP]