MolNFT v1 · #127613 · protein
Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus at 1.9 a resolution
5N1Q · Methyl-coenzyme M reductase III from methanothermococcus…: “Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus at 1.9 a resolution”. X-ray diffraction, 5 ligands (TP7, F43, COM), 20 pockets (best…
- PDB
- 5N1Q
- Type
- protein
- Length
- 2,502 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus subunit…
- EC
- 2.8.4.1
- Ligands
- TP7, F43, COM, K, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus subunit alpha (EC 2.8.4.1) | protein | 549 | 56% helix, 6% strand | — |
| B, E | Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus subunit beta (EC 2.8.4.1) | protein | 442 | 55% helix, 9% strand | — |
| C, F | Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus subunit gamma (EC 2.8.4.1) | protein | 260 | 33% helix, 17% strand | — |
Ligands and binding sites
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
- F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains D, E, F, A, B, C
- K · Potassium ion · metal · chains A, D
- MG · Magnesium ion · metal · chains E, F
- GOL · Glycerol · additive · 3 copies · chains B, E, A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.90 | 0.92 | 136 | TP7, COM, F43 |
| 2 | 586 | 0.89 | 0.94 | 70 | F43, COM, TP7 |
| 3 | 132 | 0.61 | 0.86 | 26 | empty |
| 4 | 175 | 0.60 | 0.82 | 16 | GOL |
| 5 | 195 | 0.53 | 0.78 | 19 | empty |
Interfaces
14 interfaces between chains.
- A–D · 5318 Ų buried · 91 hydrogen bonds · protein-protein
- B–C · 2917 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 2912 Ų buried · 48 hydrogen bonds · protein-protein
- D–F · 2628 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2582 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation, nonstandard).
Compared structures
- 5N1Q · Methyl-coenzyme M reductase III from methanothermococcus thermolithotrophicus at 1.9 a… · 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 5N1Q · PDBe 5N1Q
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.