Research workbench
Xfel serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase
Analyse Xfel serial crystallography reveals the room temperature structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SUC
- Type
- protein
- Length
- 2,472 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
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Methyl-coenzyme M reductase I subunit alpha (EC 2.8.4.1) | protein | 548 | 57% helix, 6% strand | P11558 |
| B, b | Methyl-coenzyme M reductase I subunit beta (EC 2.8.4.1) | protein | 442 | 56% helix, 9% strand | P11560 |
| C, c | Methyl-coenzyme M reductase I subunit gamma (EC 2.8.4.1) | protein | 246 | 34% helix, 18% strand | P11562 |
Ligands and binding sites
- F43 · Factor 430 · ligand · 2 copies · chains A, a, b, c, B, C
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, a, b
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, a, b, c
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, a, c, b
- ACT · Acetate ion · 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
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.89 | 0.90 | 114 | TP7, COM, F43 |
| 2 | 1107 | 0.89 | 0.90 | 120 | F43, TP7, COM |
| 3 | 57 | 0.56 | 0.90 | 14 | empty |
| 4 | 229 | 0.49 | 0.75 | 30 | empty |
| 5 | 208 | 0.47 | 0.74 | 23 | empty |
Interfaces
14 interfaces between chains.
- A–a · 4907 Ų buried · 81 hydrogen bonds · protein-protein
- b–c · 2580 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 2544 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 2492 Ų buried · 40 hydrogen bonds · protein-protein
- a–c · 2458 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, nonstandard).
Compared structures
- 7SUC · XFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M… · the same entry in another collection · chain c against c, 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 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 7SUC · PDBe 7SUC · UniProt P11558 · UniProt P11560 · UniProt P11562
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