Research workbench
Fragment growing induces conformational changes in acetylcholine- binding protein: a structural and thermodynamic analysis - (fragment 1)
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
- 2Y54
- 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
- V63, CL, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Soluble acetylcholine receptor | protein | 205 | 9% helix, 49% strand | Q8WSF8 |
Ligands and binding sites
- V63 · [(1R,5S)-8-azabicyclo[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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.70 | 0.79 | 54 | V63 |
| 2 | 493 | 0.69 | 0.79 | 59 | V63, CL |
| 3 | 554 | 0.69 | 0.78 | 60 | V63 |
| 4 | 499 | 0.69 | 0.79 | 53 | V63 |
| 5 | 501 | 0.68 | 0.79 | 53 | V63 |
Interfaces
5 interfaces between chains.
- D–E · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1307 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1274 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1268 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1243 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2Y54 · 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 2Y54 · PDBe 2Y54 · UniProt Q8WSF8
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