Research workbench
Crystal structure of a chimeric acetylcholine binding protein from aplysia californica (ac-achbp) containing loop C from the human alpha 6 nicotinic acetylcholine receptor in complex with 2-((5-(3,7- DIAZABICYCLO[3.3.1]NONAN-3-YL)PYRIDIN-3-YL)OXY)- N,N- dimethylethanamine (bpc)
Analyse Crystal structure of a chimeric acetylcholine binding protein from aplysia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KE4
- Type
- protein
- Length
- 1,036 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- 6S7
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 207 | 12% helix, 53% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 212 | 12% helix, 49% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 211 | 12% helix, 48% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 204 | 10% helix, 51% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 202 | 10% helix, 53% strand | Q8WSF8 |
Ligands and binding sites
- 6S7 · 2-((5-(3,7-diazabicyclo[3.3.1]nonan-3-yl)pyridin-3-yl) oxy)-N,N-dimethylethanamine · ligand · 4 copies · chains A, E, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.71 | 0.86 | 41 | 6S7 |
| 2 | 394 | 0.68 | 0.81 | 60 | 6S7 |
| 3 | 217 | 0.66 | 0.84 | 41 | 6S7 |
| 4 | 249 | 0.66 | 0.83 | 40 | 6S7 |
| 5 | 441 | 0.64 | 0.77 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1495 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1476 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1350 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1339 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1256 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5KE4 · Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8WSF8
- Elsewhere: RCSB PDB 5KE4 · PDBe 5KE4 · UniProt Q8WSF8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.