Structure of PDB 5odq Chain I Binding Site BS01

Receptor Information

>5odq Chain I (length=183) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095)

MIYSSDLNKNLASQIIEAGTPIPGDDVVSSLKACYQCGTCTGSCPSGRRT
SYRTRKVIRKALLGMDDVLDSDDIWKCTTCYTCYERCPRDVKVTEIIKTI
RNLAAQKGNMAKAHKMTAMYVLKYGHAVPANKNTAELRKSIGLSEKAPIA
QFSEKDLNEMNTLIKELGFDELIGFDWEKGALK

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: 5odq Chain I Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5odq Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): C34 Y35 Q36 C37 G38 C40 C87 V91
• Binding residue (residue number reindexed from 1): C34 Y35 Q36 C37 G38 C40 C87 V91
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.8.98.1: dihydromethanophenazine:CoB--CoM heterodisulfide reductase.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0051912 CoB--CoM heterodisulfide reductase activity

Biological Process

• GO:0015948 methanogenesis

External links

• PDB: RCSB:5odq, PDBe:5odq, PDBj:5odq
• PDBsum: 5odq
• PubMed: 28818947
• UniProt: A0A2D0TC97