MolNFT v1 · #129048 · protein
Crystal structure of wild type aplysia californica achbp in complex with strychnine
5O8T · Soluble acetylcholine receptor: “Crystal structure of wild type aplysia californica achbp in complex with strychnine”. X-ray diffraction, 2 ligands (SY9, NAG), 11 pockets (best druggability 0.69). MolNFT v1 #129048 on GenesisL1: 3D…
- PDB
- 5O8T
- Type
- protein
- Length
- 1,027 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- SY9, NAG
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Soluble acetylcholine receptor | protein | 206 | 9% helix, 53% strand | Q8WSF8 |
| B, D, E | Soluble acetylcholine receptor | protein | 205 | 9% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- SY9 · Strychnine · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.79 | 50 | SY9 |
| 2 | 487 | 0.69 | 0.80 | 53 | SY9 |
| 3 | 501 | 0.69 | 0.79 | 57 | SY9 |
| 4 | 498 | 0.69 | 0.79 | 57 | SY9 |
| 5 | 557 | 0.68 | 0.78 | 53 | SY9 |
Interfaces
5 interfaces between chains.
- A–E · 1405 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1357 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1350 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1348 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1321 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5O8T · Crystal structure of wild type Aplysia californica AChBP in complex with strychnine · 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 5O8T · PDBe 5O8T · UniProt Q8WSF8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.