MolNFT v1 · #8801 · protein
Methyl-coenzyme M reductase enzyme product complex
1HBM · Methyl-coenzyme M reductase I alpha subunit: “Methyl-coenzyme M reductase enzyme product complex”. X-ray diffraction, 6 ligands (F43, SHT, NA), 15 pockets (best druggability 0.89). MolNFT v1 #8801 on GenesisL1: 3D structure, binding…
- PDB
- 1HBM
- Type
- protein
- Length
- 2,474 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-coenzyme M reductase I alpha subunit; Methyl-coenzyme M reductase I beta subunit…
- UniProt
- P11558, P11560, P11562
- Ligands
- F43, SHT, NA, MG, ZN, 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 alpha subunit | protein | 548 | 56% helix, 6% strand | P11558 |
| B, E | Methyl-coenzyme M reductase I beta subunit | protein | 442 | 54% helix, 9% strand | P11560 |
| C, F | Methyl-coenzyme M reductase I gamma subunit | protein | 247 | 34% helix, 17% strand | P11562 |
Ligands and binding sites
- F43 · Factor 430 · ligand · 2 copies · chains A, B, C, D, E, F
- SHT · O-phosphono-N-{(2E)-7-[(2-sulfoethyl)dithio]hept-2-enoyl}-L-threonine · ligand · 2 copies · chains A, B, D, E
- NA · Sodium ion · metal · 9 copies · chains A, D, B
- MG · Magnesium ion · metal · 5 copies · chains C, F, E, A
- ZN · Zinc ion · metal · chains A, D
- CL · Chloride ion · ion · 2 copies · chains B, E, F
- GOL · Glycerol · additive · 11 copies · chains A, D, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.89 | 0.90 | 124 | F43, SHT, NA, GOL |
| 2 | 1150 | 0.89 | 0.90 | 120 | GOL, F43, SHT, NA |
| 3 | 91 | 0.53 | 0.84 | 17 | empty |
| 4 | 208 | 0.48 | 0.75 | 23 | empty |
| 5 | 225 | 0.47 | 0.74 | 32 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4941 Ų buried · 87 hydrogen bonds · protein-protein
- B–C · 2653 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2626 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 2468 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2466 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard).
Compared structures
- 1HBM · Methyl-coenzyme M reductase enzyme product complex · the same entry in another collection · chain F against F, 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 0.99
- 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 1HBM · PDBe 1HBM · UniProt P11558 · UniProt P11560 · UniProt P11562
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.