MolNFT v1 · #113439 · protein
ALPHA7-achbp in complex with lobeline
5AFH · Acetylcholine-binding protein, neuronal acetylcholine…: “ALPHA7-achbp in complex with lobeline”. X-ray diffraction, 4 ligands (L0B, NAG, BMA), 13 pockets (best druggability 0.72). MolNFT v1 #113439 on GenesisL1: 3D structure…
- PDB
- 5AFH
- Type
- protein
- Length
- 1,024 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, NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 205 | 8% helix, 48% strand | — |
| C | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 204 | 8% helix, 43% strand | — |
Ligands and binding sites
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.72 | 0.79 | 62 | L0B |
| 2 | 687 | 0.70 | 0.77 | 69 | L0B |
| 3 | 424 | 0.68 | 0.79 | 47 | L0B |
| 4 | 418 | 0.67 | 0.79 | 37 | empty |
| 5 | 444 | 0.66 | 0.78 | 45 | L0B |
Interfaces
5 interfaces between chains.
- C–D · 1392 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1344 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1296 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1282 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5AFH · alpha7-AChBP in complex with lobeline · 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
- Elsewhere: RCSB PDB 5AFH · PDBe 5AFH
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