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Fragment growing induces conformational changes in acetylcholine- binding protein: a structural and thermodynamic analysis - (compound 6)
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
- 2Y58
- 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
- V38, CL, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Soluble acetylcholine receptor | protein | 205 | 8% helix, 51% strand | Q8WSF8 |
Ligands and binding sites
- V38 · [(1R,5S)-8-[(2R)-2-hydroxy-2-phenyl-ethyl]-8-methyl-8-azoniabicyclo[3.2.1]octan-3-yl] benzoate · ligand · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.72 | 0.80 | 68 | SO4, V38 |
| 2 | 556 | 0.72 | 0.80 | 64 | SO4, V38 |
| 3 | 493 | 0.70 | 0.80 | 57 | V38 |
| 4 | 477 | 0.70 | 0.80 | 51 | V38, CL |
| 5 | 466 | 0.69 | 0.80 | 51 | V38 |
Interfaces
5 interfaces between chains.
- A–B · 1336 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1329 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1293 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1288 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1220 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2Y58 · 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 2Y58 · PDBe 2Y58 · UniProt Q8WSF8
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