Research workbench
Fragment growing induces conformational changes in acetylcholine- binding protein: a structural and thermodynamic analysis - (compound 4)
Analyse Fragment growing induces conformational changes in acetylcholine- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y57
- Type
- protein
- Length
- 1,025 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- V37, SO4, CL
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Soluble acetylcholine receptor | protein | 205 | 8% helix, 56% strand | Q8WSF8 |
Ligands and binding sites
- V37 · [(1R,5S)-8-phenethyl-8-azabicyclo[3.2.1]octan-3-yl] benzoate · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 8 copies · chains A, E, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.71 | 0.83 | 64 | V37 |
| 2 | 354 | 0.71 | 0.84 | 60 | V37 |
| 3 | 308 | 0.71 | 0.84 | 49 | V37 |
| 4 | 291 | 0.69 | 0.84 | 44 | V37 |
| 5 | 276 | 0.68 | 0.84 | 46 | V37 |
Interfaces
5 interfaces between chains.
- A–B · 1341 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1335 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1334 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1312 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1295 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2Y57 · Fragment growing induces conformational changes in acetylcholine- binding protein: A… · 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 2Y57 · PDBe 2Y57 · UniProt Q8WSF8
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