Research workbench
ALPHA7-achbp in complex with lobeline and fragment 5
Analyse ALPHA7-achbp in complex with lobeline and fragment 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFN
- Type
- protein
- Length
- 1,027 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, OJD, NAG, BMA, MAN
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 205 | 10% helix, 48% strand | — |
| B | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 207 | 6% helix, 51% strand | — |
Ligands and binding sites
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, B, C, D, E
- OJD · (4R)-4-(2-phenylethyl)pyrrolidin-2-one · 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 · 4 copies · chains D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.71 | 0.78 | 72 | L0B |
| 2 | 429 | 0.68 | 0.79 | 36 | OJD |
| 3 | 431 | 0.67 | 0.79 | 36 | OJD |
| 4 | 430 | 0.67 | 0.79 | 38 | OJD |
| 5 | 488 | 0.67 | 0.78 | 50 | L0B |
Interfaces
5 interfaces between chains.
- B–C · 1347 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1340 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1334 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1312 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1283 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5AFN · alpha7-AChBP in complex with lobeline and fragment 5 · 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 5AFN · PDBe 5AFN
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