Research workbench
Crystal structure of an acetylcholine binding protein from aplysia californica (ac-achbp) in complex with click chemistry compound 9- [[1-[8-methyl-8-(2-phenylethyl)-8-AZONIABICYCLO[3.2.1]OCTAN-3- YL]TRIAZOL-4-YL]METHYL]CARBAZOLE
Analyse Crystal structure of an acetylcholine binding protein from aplysia californica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZU
- 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
- 74S, SO4
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 207 | 11% helix, 50% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 212 | 13% helix, 49% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 205 | 11% helix, 50% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 206 | 11% helix, 49% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 206 | 12% helix, 49% strand | Q8WSF8 |
Ligands and binding sites
- 74S · 9-[[1-[8-methyl-8-(2-phenylethyl)-8-azoniabicyclo[3.2.1]octan-3-yl]triazol-4-yl]methyl]carbazole · ligand · chains C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.71 | 0.80 | 53 | 74S |
| 2 | 557 | 0.67 | 0.77 | 57 | PG4 |
| 3 | 514 | 0.64 | 0.76 | 47 | empty |
| 4 | 568 | 0.64 | 0.76 | 59 | empty |
| 5 | 472 | 0.64 | 0.77 | 54 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1411 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1377 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1298 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1216 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5KZU · Crystal structure of an acetylcholine binding protein from Aplysia californica (Ac-AChBP)… · 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 5KZU · PDBe 5KZU · UniProt Q8WSF8
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