Research workbench
ALPHA7-achbp in complex with lobeline and fragment 3
Analyse ALPHA7-achbp in complex with lobeline and fragment 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFL
- Type
- protein
- Length
- 1,025 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7
- Ligands
- L0B, FHV, NAG, BMA
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 205 | 8% helix, 47% strand | — |
Ligands and binding sites
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, B, C, D, E
- FHV · N-(3-methylphenyl)pyrrolidine-1-carboxamide · ligand · chains D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 5 copies · chains A, B, D, E
- TLA · L(+)-tartaric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.72 | 0.78 | 68 | L0B |
| 2 | 688 | 0.72 | 0.79 | 71 | L0B |
| 3 | 677 | 0.71 | 0.78 | 65 | L0B |
| 4 | 115 | 0.68 | 0.90 | 18 | FHV |
| 5 | 424 | 0.67 | 0.79 | 38 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1332 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1324 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1304 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5AFL · PDBe 5AFL
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