MolNFT v1 · #113226 · protein
Methyl-coenzyme M reductase II from methanothermobacter wolfeii at 1. 8 a resolution
5A8W · Methyl-coenzyme M II reductase: “Methyl-coenzyme M reductase II from methanothermobacter wolfeii at 1. 8 a resolution”. X-ray diffraction, 4 ligands (COM, TP7, F43), 20 pockets (best druggability 0.90). MolNFT v1 #113226 on…
- PDB
- 5A8W
- Type
- protein
- Length
- 5,013 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M II reductase; Methyl-coenzyme M reductase II
- EC
- 2.8.4.1
- Ligands
- COM, TP7, F43, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Methyl-coenzyme M II reductase (EC 2.8.4.1) | protein | 548 | 56% helix, 5% strand | — |
| B, E, H, K | Methyl-coenzyme M reductase II (EC 2.8.4.1) | protein | 442 | 54% helix, 9% strand | — |
| C, F, I, L | Methyl-coenzyme M reductase II (EC 2.8.4.1) | protein | 263 | 34% helix, 16% strand | — |
| D | Methyl-coenzyme M II reductase (EC 2.8.4.1) | protein | 549 | 56% helix, 5% strand | — |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- TP7 · Coenzyme B · ligand · 4 copies · chains A, B, D, E, G, J, K, H
- F43 · Factor 430 · ligand · 4 copies · chains A, D, E, F, B, C, G, H, I, J, K, L
- NA · Sodium ion · metal · chains F
- ACT · Acetate ion · additive · 11 copies · chains A, D, B, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.90 | 0.91 | 126 | COM, F43, TP7 |
| 2 | 1172 | 0.88 | 0.89 | 124 | TP7, F43, COM, ACT |
| 3 | 1110 | 0.88 | 0.89 | 123 | TP7, F43, COM, ACT |
| 4 | 1173 | 0.88 | 0.89 | 128 | COM, TP7, F43 |
| 5 | 1081 | 0.81 | 0.82 | 90 | empty |
Interfaces
29 interfaces between chains.
- A–D · 5195 Ų buried · 76 hydrogen bonds · protein-protein
- G–J · 5189 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 3066 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 3049 Ų buried · 49 hydrogen bonds · protein-protein
- K–L · 3038 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (methylation, nonstandard).
Compared structures
- 5A8W · Methyl-coenzyme M reductase II from methanothermobacter wolfeii at 1. 8 a resolution · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5A8W · PDBe 5A8W
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