MolNFT v1 · #113214 · protein
Methyl-coenzyme M reductase from methanothermobacter wolfeii at 1.4 a resolution
5A8K: “Methyl-coenzyme M reductase from methanothermobacter wolfeii at 1.4 a resolution”. X-ray diffraction, 7 ligands (ETX, COM, TP7), 12 pockets (best druggability 0.89). MolNFT v1 #113214 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5A8K
- Type
- protein
- Length
- 2,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M reductase
- EC
- 2.8.4.1
- Ligands
- ETX, COM, TP7, F43, CA, K, MG
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-coenzyme M reductase (EC 2.8.4.1) | protein | 548 | 57% helix, 6% strand | — |
| B, E | Methyl-coenzyme M reductase (EC 2.8.4.1) | protein | 442 | 56% helix, 9% strand | — |
| C, F | Methyl-coenzyme M reductase (EC 2.8.4.1) | protein | 248 | 33% helix, 18% strand | — |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · 26 copies · chains A, B, E, C, D, F
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
- F43 · Factor 430 · ligand · 2 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 12 copies · chains A, D, E, F
- K · Potassium ion · metal · 5 copies · chains A, D, C, E
- MG · Magnesium ion · metal · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.89 | 0.90 | 115 | COM, TP7, F43 |
| 2 | 1085 | 0.89 | 0.90 | 125 | TP7, COM, F43 |
| 3 | 95 | 0.55 | 0.85 | 14 | ETX |
| 4 | 267 | 0.51 | 0.75 | 32 | empty |
| 5 | 202 | 0.47 | 0.75 | 23 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4891 Ų buried · 92 hydrogen bonds · protein-protein
- B–C · 2640 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 2585 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 2459 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 2451 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard).
Compared structures
- 5A8K · Methyl-coenzyme M reductase from methanothermobacter wolfeii at 1.4 a resolution · the same entry in another collection · chain A against A, 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 5A8K · PDBe 5A8K
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