Research workbench
Aplysia californica achbp bound to in silico compound 35
Analyse Aplysia californica achbp bound to in silico compound 35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W8G
- Type
- protein
- Length
- 1,037 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- BS2
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Soluble acetylcholine receptor | protein | 205 | 11% helix, 47% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 217 | 8% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- BS2 · (3-endo,8-anti)-8-benzyl-3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-yloxy)-8-azoniabicyclo[3.2.1]octane · ligand · 3 copies · chains A, B, D, E
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 | 643 | 0.69 | 0.77 | 74 | empty |
| 2 | 620 | 0.69 | 0.78 | 64 | BS2 |
| 3 | 666 | 0.67 | 0.76 | 71 | BS2 |
| 4 | 594 | 0.67 | 0.77 | 63 | empty |
| 5 | 517 | 0.64 | 0.76 | 55 | BS2 |
Interfaces
5 interfaces between chains.
- D–E · 1284 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1273 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1272 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1270 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1270 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2W8G · Aplysia californica AChBP bound to in silico compound 35 · 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 2W8G · PDBe 2W8G · UniProt Q8WSF8
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