Structure of PDB 5odr Chain K Binding Site BS01

Receptor Information

>5odr Chain K (length=297) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095)

VKIATTWLGGCSGCHISLLDLHEELLNLLENVELVHCPVLMDVKEIPDEV
EVALIEGGIRNEENLEIAKEMRERAKIVIAFGTCAAFGGVPGLGNLYSND
ELLDKAYKTTITTKNDDGIIPNEEVPELVSRVKPLSEVIEVDYFIPGCPP
NPEMIAEVVKALLEGKEPELPKKNLCEECARKKSEEGVAIETIKRNYEGN
PDPEKCLLEQGYICLGIATREGCGAPCPSSGVPCSGCSGPTDAVVDQGAK
MISALCSDFGIDNDRDVDPMILPKSIKDKIGSFYKFTLPSAFVPIRL

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 5odr Chain K Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5odr Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): C12 G14 C15 E57 T84 C85 C149 P150
• Binding residue (residue number reindexed from 1): C11 G13 C14 E56 T83 C84 C148 P149
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.12.1.2: hydrogen dehydrogenase.
  1.12.99.6: hydrogenase (acceptor).

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0033748 hydrogenase (acceptor) activity
• GO:0046872 metal ion binding
• GO:0047985 hydrogen dehydrogenase activity
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:5odr, PDBe:5odr, PDBj:5odr
• PDBsum: 5odr
• PubMed: 28818947
• UniProt: A0A2D0TC99