Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).

Ligands and binding sites

• F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
• TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
• COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
• TXZ · O-phosphono-N-(6-sulfanylhexanoyl)-L-threonine · ligand · 2 copies · chains A, B, D, E
• MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, F, E
• ZN · Zinc ion · metal · chains A, D
• EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, D, F
• ACT · Acetate ion · additive · 2 copies · chains A, C
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

14 interfaces between chains.

• A–D · 4927 Ų buried · 91 hydrogen bonds · protein-protein
• D–F · 2492 Ų buried · 40 hydrogen bonds · protein-protein
• E–F · 2484 Ų buried · 57 hydrogen bonds · protein-protein
• B–C · 2478 Ų buried · 50 hydrogen bonds · protein-protein
• A–C · 2466 Ų buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (methylation, nonstandard).

Compared structures

• 3M2U · Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues · the same entry in another collection · chain F against F, TM-score 1.00
• P11558 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase I subunit alpha (P11558) · a predicted model of the same protein · chain A against A, TM-score 1.00
• P11560 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase I subunit beta (P11560) · a predicted model of the same protein · chain E against A, TM-score 1.00
• P11562 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase I subunit gamma (P11562) · a predicted model of the same protein · chain F against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P11558
• Every structure of UniProt P11560
• Every structure of UniProt P11562
• Elsewhere: RCSB PDB 3M2U · PDBe 3M2U · UniProt P11558 · UniProt P11560 · UniProt P11562