MolNFT v1 · #127633 · protein
Methyl-coenzyme M reductase III from methanotorris formicicus trigonal form
5N2A · Methyl-coenzyme M reductase subunit alpha: “Methyl-coenzyme M reductase III from methanotorris formicicus trigonal form”. X-ray diffraction, 5 ligands (COM, TP7, F43), 7 pockets (best druggability 0.77). MolNFT v1 #127633 on…
- PDB
- 5N2A
- Type
- protein
- Length
- 1,249 residues
- Chains
- 3
- 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, BR
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% 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 | Methyl-coenzyme M reductase, beta subunit (EC 2.8.4.1) | protein | 443 | 55% helix, 9% strand | H1KXL9 |
| C | Methyl-coenzyme M reductase, gamma subunit (EC 2.8.4.1) | protein | 258 | 31% helix, 17% strand | H1KXL6 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · chains A, B, C
- TP7 · Coenzyme B · ligand · chains A, B
- F43 · Factor 430 · ligand · chains A, B, C
- K · Potassium ion · metal · chains A
- BR · Bromide ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.77 | 0.79 | 74 | COM, TP7, F43 |
| 2 | 309 | 0.55 | 0.76 | 29 | empty |
| 3 | 141 | 0.40 | 0.74 | 27 | empty |
| 4 | 80 | 0.34 | 0.75 | 21 | empty |
| 5 | 55 | 0.33 | 0.77 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2837 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 2598 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard, methylation).
Compared structures
- 5N2A · Methyl-coenzyme M reductase III from methanotorris formicicus trigonal 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 5N2A · PDBe 5N2A · UniProt H1KXL5 · UniProt H1KXL9 · UniProt H1KXL6
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