Structure of PDB 5odh Chain H Binding Site BS04

Receptor Information

>5odh Chain H (length=291) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095)

MKYAFFLGCIMPNRYAGVEAATRTVMEKLGVELVDMTGASCCPAPGVFGS
FDQKTWLTLAARNLCIAEEMGVDIVTVCNGCYGSLFEAAHLLHDNKEALN
FVNEKLDKVGKEYKGNVKVRHFAELIYNDIGVDKIAEKVERPLNINVGVH
YGCHFLKPTDVKHLGSAERPVMLDEIVEATGAKSVPYADKMMCCGAGGGV
RARELELSLDMTNEKIENMIKAGADCTVNVCPFCHLQFDRGQIEIKEKFG
KEYNFPVLHLSQLLGLAMGMDPKDLALSVHQISVDPLLKKI

Ligand information

• Ligand ID: TP7
• InChI: InChI=1S/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)/t8-,10+/m1/s1
• InChIKey: JBJSVEVEEGOEBZ-SCZZXKLOSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C[C@H]([C@@H](C(=O)O)NC(=O)CCCCCCS)OP(=O)(O)O
  OpenEye OEToolkits 1.7.6: CC(C(C(=O)O)NC(=O)CCCCCCS)OP(=O)(O)O
  CACTVS 3.385: C[C@@H](O[P](O)(O)=O)[C@H](NC(=O)CCCCCCS)C(O)=O
  CACTVS 3.385: C[CH](O[P](O)(O)=O)[CH](NC(=O)CCCCCCS)C(O)=O
• Formula: C11 H22 N O7 P S
• Name: Coenzyme B;
  7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE
• ZINC: ZINC000003869535
• PDB chain: 5odh Chain H Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5odh Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): R201 F233 R240
• Binding residue (residue number reindexed from 1): R201 F233 R240
• Annotation score: 3

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0051912 CoB--CoM heterodisulfide reductase activity

Biological Process

• GO:0015948 methanogenesis

External links

• PDB: RCSB:5odh, PDBe:5odh, PDBj:5odh
• PDBsum: 5odh
• PubMed: 28818947
• UniProt: A0A2D0TCB4