MolNFT v1 · #127631 · protein
Methyl-coenzyme M reductase III from methanotorris formicicus monoclinic form
5N28 · Methyl-coenzyme M reductase subunit alpha: “Methyl-coenzyme M reductase III from methanotorris formicicus monoclinic form”. X-ray diffraction, 4 ligands (COM, TP7, F43), 20 pockets (best druggability 0.90). MolNFT v1 #127631 on…
- PDB
- 5N28
- Type
- protein
- Length
- 2,491 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, beta subunit…
- EC
- 2.8.4.1
- UniProt
- H1KXL5, H1KXL9, H1KXL6
- Ligands
- COM, TP7, F43, K
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-coenzyme M reductase subunit alpha (EC 2.8.4.1) | protein | 548 | 54% helix, 5% strand | H1KXL5 |
| B, E | Methyl-coenzyme M reductase, beta subunit (EC 2.8.4.1) | protein | 443 | 54% helix, 9% strand | H1KXL9 |
| C | Methyl-coenzyme M reductase, gamma subunit (EC 2.8.4.1) | protein | 258 | 32% helix, 17% strand | H1KXL6 |
| D | Methyl-coenzyme M reductase subunit alpha (EC 2.8.4.1) | protein | 547 | 53% helix, 5% strand | H1KXL5 |
| F | Methyl-coenzyme M reductase, gamma subunit (EC 2.8.4.1) | protein | 252 | 33% helix, 15% strand | H1KXL6 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- TP7 · Coenzyme B · ligand · 2 copies · chains A, D, E, B
- F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
- K · Potassium ion · metal · chains A, D
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 | 977 | 0.90 | 0.91 | 112 | COM, TP7, F43 |
| 2 | 1200 | 0.88 | 0.89 | 113 | TP7, F43, COM |
| 3 | 66 | 0.65 | 0.93 | 20 | empty |
| 4 | 120 | 0.62 | 0.87 | 18 | empty |
| 5 | 185 | 0.52 | 0.78 | 31 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4973 Ų buried · 86 hydrogen bonds · protein-protein
- E–F · 2849 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2826 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 2620 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 2598 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (nonstandard, methylation).
Compared structures
- 5N28 · Methyl-coenzyme M reductase III from methanotorris formicicus monoclinic form · 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
- Every structure of UniProt H1KXL5
- Every structure of UniProt H1KXL9
- Every structure of UniProt H1KXL6
- Elsewhere: RCSB PDB 5N28 · PDBe 5N28 · UniProt H1KXL5 · UniProt H1KXL9 · UniProt H1KXL6
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