Research workbench
Crystal structure of the methyl-coenzyme M reductase from methanothermobacter marburgensis derivatized with xenon
Analyse Crystal structure of the methyl-coenzyme M reductase from methanothermobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B2H
- Type
- protein
- Length
- 2,464 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
- COM, TP7, F43, MG, K, XE, CL, SO4
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methyl-coenzyme M reductase I subunit alpha (EC 2.8.4.1) | protein | 547 | 57% helix, 6% strand | P11558 |
| B | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 442 | 56% helix, 9% strand | P11560 |
| C | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 248 | 33% helix, 17% strand | P11562 |
| E | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 441 | 56% helix, 9% strand | P11560 |
| F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 239 | 34% helix, 17% strand | P11562 |
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, B, D, E
- F43 · Factor 430 · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 15 copies · chains A, D, B, F, C, E
- K · Potassium ion · metal · 4 copies · chains A, D, B
- XE · Xenon · ion · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains B, E
- SO4 · Sulfate ion · ion · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, D, B, F, E
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.89 | 0.90 | 118 | COM, TP7, F43, MG |
| 2 | 1110 | 0.89 | 0.90 | 120 | F43, COM, TP7 |
| 3 | 57 | 0.53 | 0.88 | 14 | XE |
| 4 | 224 | 0.47 | 0.74 | 26 | PEG |
| 5 | 158 | 0.44 | 0.75 | 27 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4937 Ų buried · 97 hydrogen bonds · protein-protein
- B–C · 2552 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2504 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 2454 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 2415 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, nonstandard).
Compared structures
- 7B2H · Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter… · the same entry in another collection · chain B against B, 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 B 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 7B2H · PDBe 7B2H · UniProt P11558 · UniProt P11560 · UniProt P11562
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