Structure of PDB 5odi Chain A Binding Site BS05

Receptor Information
>5odi Chain A (length=651) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPRIGVYVCHCGVNIGGTVDCPDVTEFAKTLKNVVVARDYKYMCADPGQE
MIKKDIKEHNLNRVVVAACSPRLHEPTFRRCVAEAGLNPFLFEFANIREH
CSWVHMHEKEKATEKAKDLVRMAVAKARLLEPLEFIKVGVTQRALVIGGG
VAGIQTALDLGDMGFETILVEKTPSVGGRMAQLDKTFPTNDCSICILAPK
MVDVAKHPNVKLYAYSEVVDVQGYVGNFKVKIMKKARYIDETKCTGCGQC
SEVCPIDVPNEFDMGIGMRKAIYKPFPQAVPAKYTIDKEHCIECGLCAKV
CGPNAIDFDQEPEIIEAEVGTIICAIGYDAFDPTVREEYGYGVYDNVVTA
LELERMINASGPTGGKVIRLSDGQKPKRIAFIQCVGSRDAKVGNKYCSNV
CCMYAMKNSQLIKEKSPDTEIDIYYMDIRAFSKGYEEFYERSAKQYGIKF
MRGRPSQVIEDPETGNLVVRAEDTLLGEILEKEYDLVVLSVGMVPTKSAD
EVQKILGISRTPDQFFMEAHPKLRPVDTATDGVYLAGACQGPKDIPASVA
QGSAAASRAAIPLAKGEVEVEPIIASVDAEICGGCGVCVKQCPYGAPRLV
EKDGKVVAEVISALCKGCGTCPAGCPSGALEQDHFKTIQLFKQIEGMFRD
T
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain5odi Chain A Residue 706 [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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PDB5odi Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		C584 C587 G588 V589 C590 A610 C627 S629 L632
Binding residue
(residue number reindexed from 1)		C582 C585 G586 V587 C588 A608 C625 S627 L630
Annotation score4
Enzymatic activity
Enzyme Commision number 1.8.-.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:5odi, PDBe:5odi, PDBj:5odi
PDBsum5odi
PubMed28818947
UniProtA0A2D0TCB9

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