Research workbench
Crystal structure of wild type aplysia californica achbp in complex with nicotine
Analyse Crystal structure of wild type aplysia californica achbp in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O87
- Type
- protein
- Length
- 2,065 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- NCT, NAG, PO4
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, I, J | Soluble acetylcholine receptor | protein | 206 | 9% helix, 53% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 212 | 8% helix, 51% strand | Q8WSF8 |
| H | Soluble acetylcholine receptor | protein | 205 | 9% helix, 53% strand | Q8WSF8 |
Ligands and binding sites
- NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- PO4 · Phosphate ion · ion · 20 copies · chains A, B, E, C, D, F, G, J, H, I
- EDO · 1,2-ethanediol · additive · 42 copies · chains A, B, E, C, D, F, G, J, H, I
- IPA · Isopropyl alcohol · additive · 10 copies · chains A, E, B, C, D, F, J, G, H, I
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 | 593 | 0.66 | 0.76 | 88 | EDO |
| 2 | 235 | 0.66 | 0.84 | 53 | NCT, PO4 |
| 3 | 134 | 0.64 | 0.87 | 29 | NCT |
| 4 | 226 | 0.64 | 0.82 | 41 | NCT, PO4 |
| 5 | 142 | 0.63 | 0.86 | 30 | NCT |
Interfaces
16 interfaces between chains.
- I–J · 1430 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1414 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1408 Ų buried · 19 hydrogen bonds · protein-protein
- F–J · 1400 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1391 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5O87 · Crystal structure of wild type Aplysia californica AChBP in complex with nicotine · 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 5O87 · PDBe 5O87 · UniProt Q8WSF8
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