Research workbench
Extended sensor paddles with bound lipids revealed in mechanosensitive channel ynai
Analyse Extended sensor paddles with bound lipids revealed in mechanosensitive channel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6URT
- Type
- protein
- Length
- 2,317 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low conductance mechanosensitive channel ynai
- UniProt
- P0AEB5
- Ligands
- QGD
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A, B, C, D, E, F | Low conductance mechanosensitive channel ynai | protein | 331 | 53% helix, 12% strand | P0AEB5 |
Ligands and binding sites
- QGD · O-{(R)-hydroxy[(2r)-3-(icosyloxy)-2-(tetradecanoyloxy) propoxy]phosphoryl}-L-serine · ligand · 7 copies · chains G, E, F, A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.74 | 0.78 | 62 | empty |
| 2 | 782 | 0.71 | 0.76 | 84 | empty |
| 3 | 846 | 0.69 | 0.74 | 95 | empty |
| 4 | 830 | 0.67 | 0.74 | 83 | empty |
| 5 | 116 | 0.57 | 0.83 | 21 | empty |
Interfaces
14 interfaces between chains.
- B–C · 3337 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3336 Ų buried · 25 hydrogen bonds · protein-protein
- G–F · 3334 Ų buried · 26 hydrogen bonds · protein-protein
- G–A · 3333 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3329 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6URT · Extended Sensor Paddles with Bound Lipids Revealed in Mechanosensitive Channel YnaI · the same entry in another collection · chain F against F, TM-score 1.00
- P0AEB5 · AlphaFold monomer V2.0 prediction for low conductance mechanosensitive channel ynai… · a predicted model of the same protein · chain G against A, TM-score 0.84
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 P0AEB5
- Elsewhere: RCSB PDB 6URT · PDBe 6URT · UniProt P0AEB5
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