MolNFT v1 · #80824 · protein
Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3570 (1-(5-phenylpyridin-3-yl)-1, 4-diazepane)
3U8L · Acetylcholine-binding protein: “Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3570…”. X-ray diffraction, 2 ligands (09Q, SO4), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3U8L
- Type
- protein
- Length
- 2,019 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 09Q, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Acetylcholine-binding protein | protein | 202 | 8% helix, 48% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 205 | 10% helix, 47% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 201 | 8% helix, 47% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 199 | 9% helix, 49% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 206 | 8% helix, 47% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 200 | 9% helix, 49% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 200 | 9% helix, 50% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 204 | 8% helix, 48% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 200 | 8% helix, 50% strand | P58154 |
Ligands and binding sites
- 09Q · 1-(5-phenylpyridin-3-yl)-1,4-diazepane · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, 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 | 661 | 0.81 | 0.86 | 73 | empty |
| 2 | 634 | 0.78 | 0.84 | 59 | empty |
| 3 | 509 | 0.78 | 0.85 | 60 | empty |
| 4 | 394 | 0.78 | 0.87 | 43 | empty |
| 5 | 387 | 0.75 | 0.85 | 44 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1424 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1376 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1375 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1347 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1337 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3U8L · Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in… · the same entry in another collection · chain J against J, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain G 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 3U8L · PDBe 3U8L · UniProt P58154
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