Research workbench
Structural analysis of a NI(III)-methyl species in methyl-coenzyme M reductase from methanothermobacter marburgensis
Analyse Structural analysis of a NI(III)-methyl species in methyl-coenzyme M reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3POT
- Type
- protein
- Length
- 2,476 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, COM, 06C, MG, K
- Pockets
- 16 · best druggability 0.88
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 subunit alpha (EC 2.8.4.1) | protein | 550 | 57% helix, 6% strand | P11558 |
| B, E | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 442 | 54% helix, 9% strand | P11560 |
| C, F | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 246 | 34% helix, 17% strand | P11562 |
Ligands and binding sites
- F43 · Factor 430 · ligand · 2 copies · chains A, D, E, F, B, C
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- 06C · Iodomethane · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · chains A, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.88 | 0.96 | 54 | COM, 06C, F43 |
| 2 | 433 | 0.87 | 0.95 | 54 | F43, COM, 06C |
| 3 | 1007 | 0.78 | 0.80 | 80 | empty |
| 4 | 966 | 0.78 | 0.80 | 76 | empty |
| 5 | 211 | 0.48 | 0.74 | 22 | empty |
Interfaces
14 interfaces between chains.
- A–D · 5071 Ų buried · 120 hydrogen bonds · protein-protein
- D–F · 2483 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2479 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2455 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 2428 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (nonstandard, methylation).
Compared structures
- 3POT · Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from… · the same entry in another collection · chain F against F, 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
- 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
- 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 3POT · PDBe 3POT · UniProt P11558 · UniProt P11560 · UniProt P11562
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