Research workbench
Aplysia californica achbp bound to in silico compound 31
Analyse Aplysia californica achbp bound to in silico compound 31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W8F
- Type
- protein
- Length
- 2,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- BS1
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Soluble acetylcholine receptor | protein | 205 | 8% helix, 54% strand | Q8WSF8 |
Ligands and binding sites
- BS1 · (3-exo)-3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-yloxy)-8,8-dimethyl-8-azoniabicyclo[3.2.1]octane · ligand · 2 copies · chains A, B, F, G
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 | 776 | 0.74 | 0.79 | 78 | BS1 |
| 2 | 749 | 0.73 | 0.79 | 74 | BS1 |
| 3 | 505 | 0.70 | 0.80 | 61 | empty |
| 4 | 643 | 0.68 | 0.77 | 71 | empty |
| 5 | 531 | 0.67 | 0.77 | 54 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1355 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 1301 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1296 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1292 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1278 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2W8F · Aplysia californica AChBP bound to in silico compound 31 · 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 2W8F · PDBe 2W8F · UniProt Q8WSF8
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