Research workbench
Structure of xenon-derivatized methyl-coenzyme M reductase from methanothermobacter marburgensis
Analyse Structure of xenon-derivatized methyl-coenzyme M reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SXM
- 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
- F43, TP7, COM, MG, NA, XE
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 9% 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 | 54% helix, 5% strand | P11558 |
| B, E | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 442 | 55% helix, 9% strand | P11560 |
| C, F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 243 | 33% helix, 17% strand | P11562 |
Ligands and binding sites
- F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, D
- NA · Sodium ion · metal · chains A, D
- XE · Xenon · ion · 8 copies · chains A, B, D, E
- ACT · Acetate ion · additive · 4 copies · chains A, E, B, D
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 | 1084 | 0.89 | 0.90 | 118 | TP7, COM, F43, ACT |
| 2 | 1098 | 0.89 | 0.90 | 120 | F43, ACT, TP7, COM |
| 3 | 79 | 0.54 | 0.86 | 15 | empty |
| 4 | 223 | 0.47 | 0.74 | 23 | empty |
| 5 | 185 | 0.44 | 0.74 | 23 | empty |
Interfaces
14 interfaces between chains.
- A–D · 4944 Ų buried · 96 hydrogen bonds · protein-protein
- E–F · 2510 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2498 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 2470 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2450 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, nonstandard).
Compared structures
- 7SXM · Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter… · 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 C 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 7SXM · PDBe 7SXM · UniProt P11558 · UniProt P11560 · UniProt P11562
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