Research workbench
Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Analyse Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KOQ
- Type
- protein
- Length
- 1,955 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal acetylcholine receptor subunit alpha-7,SOLUBLE cytochrome B562 fusion
- UniProt
- P36544
- Ligands
- EPJ, NAG, CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Neuronal acetylcholine receptor subunit alpha-7,SOLUBLE cytochrome B562 fusion | protein | 391 | 39% helix, 22% strand | P36544 |
Ligands and binding sites
- EPJ · Epibatidine · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.81 | 0.82 | 94 | empty |
| 2 | 463 | 0.79 | 0.87 | 59 | CA |
| 3 | 435 | 0.79 | 0.87 | 55 | CA |
| 4 | 580 | 0.77 | 0.83 | 66 | CA |
| 5 | 418 | 0.77 | 0.85 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–E · 3213 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 3210 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3181 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 3180 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 3177 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KOQ · Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state · the same entry in another collection · chain E against E, TM-score 1.00
- P36544 · AlphaFold monomer V2.0 prediction for neuronal acetylcholine receptor subunit alpha-7… · a predicted model of the same protein · chain E against A, TM-score 0.96
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 P36544
- Elsewhere: RCSB PDB 7KOQ · PDBe 7KOQ · UniProt P36544
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