MolNFT v1 · #5072 · protein
Methyl-coenzyme M reductase from methanosarcina barkeri
1E6Y · Methyl-coenzyme M reductase subunit alpha: “Methyl-coenzyme M reductase from methanosarcina barkeri”. X-ray diffraction, 3 ligands (F43, TP7, COM), 16 pockets (best druggability 0.90). MolNFT v1 #5072 on GenesisL1: 3D structure…
- PDB
- 1E6Y
- Type
- protein
- Length
- 2,495 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M reductase subunit alpha; Methyl-coenzyme M reductase I beta subunit…
- EC
- 2.8.4.1
- UniProt
- P07962, P07955, P07964
- Ligands
- F43, TP7, COM
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-coenzyme M reductase subunit alpha (EC 2.8.4.1) | protein | 568 | 55% helix, 5% strand | P07962 |
| B | Methyl-coenzyme M reductase I beta subunit (EC 2.8.4.1) | protein | 432 | 55% helix, 9% strand | P07955 |
| C, F | Methyl-coenzyme M reductase subunit gamma (EC 2.8.4.1) | protein | 247 | 35% helix, 17% strand | P07964 |
| E | Methyl-coenzyme M reductase I beta subunit (EC 2.8.4.1) | protein | 433 | 54% helix, 9% strand | P07955 |
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
- GOL · Glycerol · additive · 3 copies · chains A, E, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.90 | 0.91 | 116 | F43, GOL, TP7, COM |
| 2 | 1174 | 0.88 | 0.89 | 117 | TP7, COM, F43 |
| 3 | 135 | 0.39 | 0.73 | 23 | empty |
| 4 | 55 | 0.39 | 0.80 | 16 | empty |
| 5 | 113 | 0.39 | 0.74 | 20 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4982 Ų buried · 101 hydrogen bonds · protein-protein
- B–C · 2762 Ų buried · 61 hydrogen bonds · protein-protein
- E–F · 2729 Ų buried · 60 hydrogen bonds · protein-protein
- D–F · 2545 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2540 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard, oxidation).
Compared structures
- 1E6Y · Methyl-coenzyme M reductase from Methanosarcina barkeri · the same entry in another collection · chain D against D, TM-score 1.00
- P07962 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase subunit alpha (P07962) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P07955 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase subunit beta (P07955) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P07964 · AlphaFold monomer V2.0 prediction for methyl-coenzyme M reductase subunit gamma (P07964) · a predicted model of the same protein · chain C 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 P07962
- Every structure of UniProt P07955
- Every structure of UniProt P07964
- Elsewhere: RCSB PDB 1E6Y · PDBe 1E6Y · UniProt P07962 · UniProt P07955 · UniProt P07964
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