Research workbench
Mscs D67R1 high resolution
Analyse Mscs D67R1 high resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AJI
- Type
- protein
- Length
- 1,809 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small-conductance mechanosensitive channel
- UniProt
- P0C0S2
- Ligands
- D10
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small-conductance mechanosensitive channel | protein | 264 | 53% helix, 23% strand | P0C0S2 |
| B, C | Small-conductance mechanosensitive channel | protein | 255 | 53% helix, 23% strand | P0C0S2 |
| D | Small-conductance mechanosensitive channel | protein | 263 | 53% helix, 22% strand | P0C0S2 |
| E | Small-conductance mechanosensitive channel | protein | 262 | 53% helix, 22% strand | P0C0S2 |
| F | Small-conductance mechanosensitive channel | protein | 256 | 53% helix, 23% strand | P0C0S2 |
| G | Small-conductance mechanosensitive channel | protein | 254 | 53% helix, 23% strand | P0C0S2 |
Ligands and binding sites
- D10 · Decane · ligand · 3 copies · chains C, D, G
- HEX · Hexane · additive · 10 copies · chains A, B, C, D, E, F, G
- OCT · N-octane · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.77 | 0.79 | 85 | HEX |
| 2 | 1149 | 0.76 | 0.78 | 78 | HEX |
| 3 | 1083 | 0.76 | 0.78 | 86 | HEX |
| 4 | 150 | 0.72 | 0.89 | 21 | empty |
| 5 | 358 | 0.70 | 0.82 | 52 | empty |
Interfaces
14 interfaces between chains.
- F–G · 2400 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2397 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2380 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2369 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2367 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (nonstandard).
Compared structures
- P0C0S2 · AlphaFold monomer V2.0 prediction for small-conductance mechanosensitive channel (P0C0S2) · a predicted model of the same protein · chain G against A, TM-score 0.90
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 P0C0S2
- Elsewhere: RCSB PDB 5AJI · PDBe 5AJI · UniProt P0C0S2
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