Research workbench
ALPHA7-achbp in complex with lobeline and fragment 4
Analyse ALPHA7-achbp in complex with lobeline and fragment 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFM
- 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, 9Z0, NAG
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 205 | 11% helix, 49% strand | — |
| B | Acetylcholine-binding protein, neuronal acetylcholine receptor subunit alpha-7 | protein | 207 | 9% helix, 47% strand | — |
Ligands and binding sites
- L0B · Alpha-Lobeline · ligand · 5 copies · chains A, B, C, D, E
- 9Z0 · 4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide · 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
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.72 | 0.79 | 64 | L0B |
| 2 | 598 | 0.71 | 0.79 | 64 | L0B, GOL |
| 3 | 445 | 0.70 | 0.80 | 39 | 9Z0 |
| 4 | 405 | 0.70 | 0.81 | 36 | 9Z0 |
| 5 | 486 | 0.69 | 0.79 | 39 | 9Z0 |
Interfaces
5 interfaces between chains.
- D–E · 1399 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1383 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1382 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1357 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5AFM · alpha7-AChBP in complex with lobeline and fragment 4 · 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 5AFM · PDBe 5AFM
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