MolNFT v1 · #113440 · protein
ALPHA7-achbp in complex with lobeline and fragment 1
5AFJ · Acetylcholine-binding protein, neuronal acetylcholine…: “ALPHA7-achbp in complex with lobeline and fragment 1”. X-ray diffraction, 5 ligands (42R, L0B, NAG), 20 pockets (best druggability 0.70). MolNFT v1 #113440 on GenesisL1: 3D…
- PDB
- 5AFJ
- 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
- 42R, L0B, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 204 | 8% helix, 48% strand | — |
| B, C, D, E | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 205 | 7% helix, 50% strand | — |
Ligands and binding sites
- 42R · (3S)-6-(4-bromophenyl)-3-hydroxy-1,3-dimethyl-2,3-dihydropyridin-4(1H)-one · ligand · 10 copies · chains A, B, C, D, E
- 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
- GOL · Glycerol · additive · 3 copies · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.70 | 0.80 | 50 | 42R, L0B |
| 2 | 455 | 0.69 | 0.80 | 48 | 42R, L0B |
| 3 | 498 | 0.68 | 0.79 | 51 | 42R, L0B |
| 4 | 530 | 0.68 | 0.78 | 55 | 42R, L0B |
| 5 | 423 | 0.67 | 0.79 | 38 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 1412 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1346 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1331 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1309 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5AFJ · alpha7-AChBP in complex with lobeline and fragment 1 · 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 5AFJ · PDBe 5AFJ
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