Research workbench
Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors
Analyse Acetylcholine binding protein (AChBP) as template for hierarchical in silico… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XNU
- Type
- protein
- Length
- 1,027 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- APLYSIA CALIFORNICA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- VU3
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.55 · 2 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Soluble acetylcholine receptor | protein | 205 | 9% helix, 54% strand | Q8WSF8 |
| D, E | Soluble acetylcholine receptor | protein | 206 | 9% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- VU3 · 2-(2-(4-phenylpiperidin-1-yl)ethyl)-1H-indole · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.71 | 0.81 | 58 | empty |
| 2 | 394 | 0.70 | 0.82 | 54 | empty |
| 3 | 591 | 0.66 | 0.76 | 54 | VU3 |
| 4 | 555 | 0.65 | 0.76 | 56 | empty |
| 5 | 492 | 0.64 | 0.77 | 48 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1419 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1305 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1288 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1279 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2XNU · Acetylcholine binding protein (achbp) as template for hierarchical in silico screening… · 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 2XNU · PDBe 2XNU · UniProt Q8WSF8
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