MolNFT v1 · #79002 · protein
Crystal structure of a methyl-coenzyme M reductase purified from black sea mats
3SQG · Methyl coenzyme M reductase, alpha subunit: “Crystal structure of a methyl-coenzyme M reductase purified from black sea mats”. X-ray diffraction, 6 ligands (TP7, COM, M43), 20 pockets (best druggability 0.90). MolNFT v1 #79002 on…
- PDB
- 3SQG
- Type
- protein
- Length
- 3,861 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl coenzyme M reductase, alpha subunit; Methyl-coenzyme M reductase, beta subunit…
- EC
- 2.8.4.1
- UniProt
- D1JBK4, D1JBK2, D1JBK3
- Ligands
- TP7, COM, M43, CA, SO4, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Methyl coenzyme M reductase, alpha subunit (EC 2.8.4.1) | protein | 578 | 54% helix, 5% strand | D1JBK4 |
| B, E, H | Methyl-coenzyme M reductase, beta subunit (EC 2.8.4.1) | protein | 431 | 54% helix, 9% strand | D1JBK2 |
| C, F, I | Methyl-coenzyme M reductase, gamma subunit (EC 2.8.4.1) | protein | 278 | 32% helix, 13% strand | D1JBK3 |
Ligands and binding sites
- TP7 · Coenzyme B · ligand · 3 copies · chains A, B, D, E, G, H
- COM · 1-thioethanesulfonic acid · ligand · 3 copies · chains A, B, C, D, E, F, G, H, I
- M43 · (17[2]S)-17[2]-methylthio-coenzyme F43 · ligand · 3 copies · chains A, D, E, F, B, C, G, H, I
- CA · Calcium ion · metal · 2 copies · chains A, D, G
- SO4 · Sulfate ion · ion · 9 copies · chains A, F, B, C, D, H, I
- CL · Chloride ion · ion · chains A
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, D, F, G, E, I, H
- PGE · Triethylene glycol · additive · 6 copies · chains A, D, G
- GOL · Glycerol · additive · 2 copies · chains C, B, E
- P6G · Hexaethylene glycol · additive · chains B, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.90 | 0.91 | 125 | M43, TP7, COM, 1PE |
| 2 | 1165 | 0.89 | 0.90 | 124 | TP7, COM, P6G, M43 |
| 3 | 1115 | 0.88 | 0.89 | 147 | PGE |
| 4 | 218 | 0.71 | 0.87 | 47 | M43, TP7, COM |
| 5 | 505 | 0.70 | 0.80 | 65 | 1PE, PGE |
Interfaces
21 interfaces between chains.
- A–D · 6124 Ų buried · 113 hydrogen bonds · protein-protein
- D–F · 3164 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 3148 Ų buried · 55 hydrogen bonds · protein-protein
- G–I · 3132 Ų buried · 52 hydrogen bonds · protein-protein
- H–I · 2788 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 3 disulfide (nonstandard, disulfide, methylation, oxidation).
Compared structures
- 3SQG · Crystal structure of a methyl-coenzyme M reductase purified from Black Sea mats · the same entry in another collection · chain G against G, 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 D1JBK4
- Every structure of UniProt D1JBK2
- Every structure of UniProt D1JBK3
- Elsewhere: RCSB PDB 3SQG · PDBe 3SQG · UniProt D1JBK4 · UniProt D1JBK2 · UniProt D1JBK3
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