Research workbench
Cryo-EM structure of torpedo acetylcholine receptor in complex with D- tubocurarine and carbachol
Analyse Cryo-EM structure of torpedo acetylcholine receptor in complex with D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SMT
- Type
- protein
- Length
- 2,022 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine receptor subunit alpha; Acetylcholine receptor subunit delta; Acetylcholine…
- UniProt
- P02710, P02718, P02712, P02714
- Ligands
- POV, CLR, CCE, TC9, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine receptor subunit alpha | protein | 387 | 41% helix, 25% strand | P02710 |
| B | Acetylcholine receptor subunit delta | protein | 425 | 38% helix, 23% strand | P02718 |
| C | Acetylcholine receptor subunit beta | protein | 406 | 40% helix, 25% strand | P02712 |
| D | Acetylcholine receptor subunit alpha | protein | 395 | 43% helix, 25% strand | P02710 |
| E | Acetylcholine receptor subunit gamma | protein | 409 | 38% helix, 26% strand | P02714 |
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
- CLR · Cholesterol · ligand · 3 copies · chains A, C, D
- CCE · 2-[(aminocarbonyl)oxy]-N,N,N-trimethylethanaminium · ligand · chains A, B
- TC9 · D-tubocurarine · ligand · chains D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, C, D
- DD9 · nonane · 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 | 1005 | 0.83 | 0.84 | 83 | empty |
| 2 | 719 | 0.74 | 0.79 | 57 | DD9 |
| 3 | 521 | 0.72 | 0.81 | 89 | empty |
| 4 | 424 | 0.71 | 0.81 | 37 | TC9 |
| 5 | 152 | 0.68 | 0.88 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3436 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3323 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 3175 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 3164 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 3159 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7SMT · Cryo-EM structure of Torpedo acetylcholine receptor in complex with d-tubocurarine and… · the same entry in another collection · chain E against E, TM-score 1.00
- 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
- 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
- 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 0.97
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
- Elsewhere: RCSB PDB 7SMT · PDBe 7SMT · UniProt P02710 · UniProt P02718 · UniProt P02712 · UniProt P02714
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