MolNFT v1 · #119590 · protein
Methyl-coenzyme M reductase I from methanothermobacter marburgensis exposed to 3-nitrooxypropanol
5G0R · Methyl-coenzyme M reductase I subunit alpha: “Methyl-coenzyme M reductase I from methanothermobacter marburgensis exposed to 3-nitrooxypropanol”. X-ray diffraction, 6 ligands (F43, TP7, MG), 15 pockets (best druggability 0.89).…
- PDB
- 5G0R
- 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 I subunit alpha; Methyl-coenzyme M reductase I subunit beta…
- EC
- 2.8.4.1
- UniProt
- P11558, P11560, P11562
- Ligands
- F43, TP7, MG, NA, K, CL
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% 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 | 57% 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, F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 248 | 34% 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
- MG · Magnesium ion · metal · 18 copies · chains A, D, B, C, E, F
- NA · Sodium ion · metal · 3 copies · chains A, D
- K · Potassium ion · metal · chains A, D
- CL · Chloride ion · ion · 3 copies · chains A, D, B, C, E, F
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 | 1096 | 0.89 | 0.90 | 116 | TP7, MG, F43 |
| 2 | 1105 | 0.89 | 0.90 | 120 | F43, TP7, MG |
| 3 | 132 | 0.49 | 0.79 | 18 | empty |
| 4 | 223 | 0.48 | 0.74 | 27 | empty |
| 5 | 99 | 0.46 | 0.80 | 19 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4908 Ų buried · 92 hydrogen bonds · protein-protein
- B–C · 2577 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 2537 Ų buried · 56 hydrogen bonds · protein-protein
- D–F · 2487 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2464 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, nonstandard).
Compared structures
- 5G0R · Methyl-coenzyme M reductase I from methanothermobacter marburgensis exposed to… · the same entry in another collection · chain A against A, 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 5G0R · PDBe 5G0R · UniProt P11558 · UniProt P11560 · UniProt P11562
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