Structure of PDB 8gf5 Chain C Binding Site BS03

Receptor Information

>8gf5 Chain C (length=429) Species: 188937 (Methanosarcina acetivorans C2A)

DTVDIYDDRGKLLESNVDIMSLAPTRNAAIKKIILDTKRSVAVSLAGIQG
ALASGKMGGKGRQILGRGLNYDLVGNADAIAENVKNLVQVDEGDDTSVKV
IKGGKSLLIQAPSSRIAAGADYMSATTVGAAAVTQTIIDMFGTDMYDAPI
AKSAVWGSYPQTMDLMGGNVQGVLSIPQNNEGLGFSLRNIMANHIAAITS
RGAMNAAALSSIYEQSGIFEMGGAVGMFERHQLLGLACQGLNANNVVYDI
VKENGKDGTIGTVIESIVGRAVEDGVISVDKTAPSGYKFYKANDVPMWNA
YAAAGTLAATFVNCGAGRAAQNVSSTLLYFNDILEKETGLPGCDYGKVQG
VAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAVALDAGTQ
MFTIESTSGLIGDVFGSIEEFRQPIKAVA

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: 8gf5 Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gf5 McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): F359 F360 Y365 G366 H377
• Binding residue (residue number reindexed from 1): F357 F358 Y363 G364 H375
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 2.8.4.1: coenzyme-B sulfoethylthiotransferase.

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0050524 coenzyme-B sulfoethylthiotransferase activity

Biological Process

• GO:0015948 methanogenesis

External links

• PDB: RCSB:8gf5, PDBe:8gf5, PDBj:8gf5
• PDBsum: 8gf5
• PubMed: 37307484
• UniProt: Q8THG7