Research workbench
Crystal structure of wild type aplysia californica achbp in complex with strychnine
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
- 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
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