Research workbench
Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues
Analyse Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M2R
- Type
- protein
- Length
- 2,472 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M reductase I subunit alpha; Methyl-coenzyme M reductase I subunit beta…
- EC
- 2.8.4.1
- UniProt
- P11558, P11560, P11562
- Ligands
- F43, TP7, COM, TPZ, MG, ZN
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-coenzyme M reductase I subunit alpha (EC 2.8.4.1) | protein | 548 | 56% helix, 6% strand | P11558 |
| B, E | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 442 | 55% helix, 9% strand | P11560 |
| C, F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 246 | 34% helix, 17% strand | P11562 |
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
- TPZ · O-phosphono-N-(5-sulfanylpentanoyl)-L-threonine · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, F, E
- ZN · Zinc ion · metal · chains A, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.89 | 0.90 | 118 | TP7, COM, TPZ, F43 |
| 2 | 1077 | 0.89 | 0.90 | 120 | F43, TP7, COM, TPZ |
| 3 | 104 | 0.47 | 0.80 | 17 | empty |
| 4 | 202 | 0.47 | 0.75 | 23 | empty |
| 5 | 72 | 0.45 | 0.82 | 16 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4913 Ų buried · 94 hydrogen bonds · protein-protein
- D–F · 2472 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2470 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2444 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2423 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard).
Compared structures
- 3M2R · 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 3M2R · PDBe 3M2R · UniProt P11558 · UniProt P11560 · UniProt P11562
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