Research workbench
Varenicline interactions at the 5HT3 receptor ligand binding site are revealed by 5HTBP
Analyse Varenicline interactions at the 5HT3 receptor ligand binding site are revealed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AIN
- Type
- protein
- Length
- 1,030 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- QMR
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Soluble acetylcholine receptor | protein | 206 | 8% helix, 50% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 207 | 9% helix, 53% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 205 | 10% helix, 48% strand | Q8WSF8 |
Ligands and binding sites
- QMR · Varenicline · ligand · 5 copies · chains A, B, C, D, E
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 | 325 | 0.69 | 0.83 | 48 | QMR |
| 2 | 80 | 0.68 | 0.93 | 15 | QMR |
| 3 | 260 | 0.68 | 0.84 | 50 | QMR |
| 4 | 177 | 0.68 | 0.87 | 33 | QMR |
| 5 | 293 | 0.66 | 0.82 | 47 | QMR |
Interfaces
5 interfaces between chains.
- C–D · 1476 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1409 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1407 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1367 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1362 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5AIN · Varenicline Interactions at the 5HT3 Receptor Ligand Binding Site are Revealed by 5HTBP · 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 5AIN · PDBe 5AIN · UniProt Q8WSF8
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