Research workbench
Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-bungarotoxin
Analyse Cryo-EM structure of Torpedo acetylcholine receptor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UWZ
- Type
- protein
- Length
- 2,178 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.69
- Source
- Tetronarce californica; SYNTHETIC CONSTRUCT
- Molecule
- Acetylcholine receptor subunit alpha; Acetylcholine receptor subunit delta; Acetylcholine…
- UniProt
- P02710, P02718, P02712, P02714, P60615
- Ligands
- POV, MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · resolution 2.69 · 5 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acetylcholine receptor subunit alpha | protein | 395 | 38% helix, 24% strand | P02710 |
| B | Acetylcholine receptor subunit delta | protein | 426 | 36% helix, 22% strand | P02718 |
| C | Acetylcholine receptor subunit beta | protein | 406 | 40% helix, 26% strand | P02712 |
| E | Acetylcholine receptor subunit gamma | protein | 410 | 38% helix, 25% strand | P02714 |
| F, G | Alpha-bungarotoxin | protein | 73 | 0% helix, 36% strand | P60615 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 5 copies · chains A, E, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, F, D, G, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, D
- OCT · N-octane · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.76 | 0.95 | 18 | empty |
| 2 | 627 | 0.75 | 0.81 | 72 | MAN |
| 3 | 542 | 0.74 | 0.81 | 48 | OCT |
| 4 | 289 | 0.74 | 0.87 | 52 | empty |
| 5 | 790 | 0.72 | 0.78 | 95 | empty |
Interfaces
10 interfaces between chains.
- B–C · 3445 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 3360 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3349 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3312 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 3180 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan, 1 covalent, 1 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 6UWZ · Cryo-EM structure of torpedo acetylcholine receptor in complex with alpha-bungarotoxin · the same entry in another collection · chain G against G, TM-score 1.00
- P02714 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit gamma (P02714) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P02712 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit beta (P02712) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P02718 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit delta (P02718) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P02710 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit alpha (P02710) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P02710
- Every structure of UniProt P02718
- Every structure of UniProt P02712
- Every structure of UniProt P02714
- Every structure of UniProt P60615
- Elsewhere: RCSB PDB 6UWZ · PDBe 6UWZ · UniProt P02710 · UniProt P02718 · UniProt P02712 · UniProt P02714 · UniProt P60615
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