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Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3531 (1-(pyridin-3-yl)-1,4- diazepane)
Analyse Crystal structure of the acetylcholine binding protein (achbp) from lymnaea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U8J
- Type
- protein
- Length
- 2,022 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 09O, NAG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Acetylcholine-binding protein | protein | 210 | 8% helix, 47% strand | P58154 |
| A | Acetylcholine-binding protein | protein | 206 | 8% helix, 47% strand | P58154 |
| C, D | Acetylcholine-binding protein | protein | 204 | 8% helix, 48% strand | P58154 |
| E, F | Acetylcholine-binding protein | protein | 198 | 8% helix, 50% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 203 | 8% helix, 48% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 199 | 9% helix, 50% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 200 | 8% helix, 49% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 200 | 10% helix, 49% strand | P58154 |
Ligands and binding sites
- 09O · 1-(pyridin-3-yl)-1,4-diazepane · ligand · 10 copies · chains B, C, A, D, E, F, J, G, I, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G
- SO4 · Sulfate ion · ion · 6 copies · chains B, A, E, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.82 | 0.84 | 94 | 09O |
| 2 | 388 | 0.67 | 0.80 | 43 | empty |
| 3 | 426 | 0.67 | 0.79 | 47 | empty |
| 4 | 413 | 0.67 | 0.79 | 46 | empty |
| 5 | 424 | 0.66 | 0.79 | 47 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1472 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1471 Ų buried · 20 hydrogen bonds · protein-protein
- F–J · 1459 Ų buried · 22 hydrogen bonds · protein-protein
- B–A · 1442 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1436 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3U8J · Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in… · the same entry in another collection · chain H against H, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain E 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
- Every structure of UniProt P58154
- Elsewhere: RCSB PDB 3U8J · PDBe 3U8J · UniProt P58154
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