MolNFT v1 · #88982 · protein
Aplysia californica-achbp in complex with triazole 18
4DBM · Soluble acetylcholine receptor: “Aplysia californica-achbp in complex with triazole 18”. X-ray diffraction, 4 ligands (0J0, NAG, MAN), 20 pockets (best druggability 0.71). MolNFT v1 #88982 on GenesisL1: 3D structure, binding sites…
- PDB
- 4DBM
- Type
- protein
- Length
- 1,048 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- 0J0, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 211 | 9% helix, 49% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 209 | 13% helix, 46% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 206 | 11% helix, 53% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 213 | 13% helix, 51% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 209 | 13% helix, 49% strand | Q8WSF8 |
Ligands and binding sites
- 0J0 · (3-exo)-8,8-dimethyl-3-(4-{[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]methyl}-1H-1,2,3-triazol-1-yl)-8-azoniabicyclo[3.2.1]octane · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.71 | 0.83 | 48 | 0J0 |
| 2 | 415 | 0.70 | 0.81 | 52 | 0J0 |
| 3 | 413 | 0.70 | 0.81 | 57 | 0J0 |
| 4 | 477 | 0.69 | 0.80 | 57 | 0J0 |
| 5 | 529 | 0.67 | 0.78 | 47 | 0J0 |
Interfaces
5 interfaces between chains.
- D–E · 1443 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1428 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1369 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1336 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4DBM · Aplysia californica-AChBP in complex with triazole 18 · 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 4DBM · PDBe 4DBM · UniProt Q8WSF8
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