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
- 3M2V
- Type
- protein
- Length
- 2,475 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, XP8, MG, ZN
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% 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 | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 248 | 34% helix, 17% strand | P11562 |
| F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 247 | 33% helix, 18% 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
- XP8 · O-phosphono-N-(8-sulfanyloctanoyl)-L-threonine · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, F
- ZN · Zinc ion · metal · chains A, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, F
- ACT · Acetate ion · additive · chains A
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 | 1057 | 0.89 | 0.90 | 119 | TP7, COM, XP8, F43 |
| 2 | 1082 | 0.89 | 0.90 | 123 | F43, TP7, COM, XP8 |
| 3 | 216 | 0.49 | 0.75 | 22 | empty |
| 4 | 230 | 0.48 | 0.74 | 26 | empty |
| 5 | 118 | 0.41 | 0.76 | 31 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4907 Ų buried · 93 hydrogen bonds · protein-protein
- E–F · 2607 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 2547 Ų buried · 55 hydrogen bonds · protein-protein
- D–F · 2481 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2457 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard).
Compared structures
- 3M2V · Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues · the same entry in another collection · chain E against E, 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 3M2V · PDBe 3M2V · UniProt P11558 · UniProt P11560 · UniProt P11562
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.