MolNFT v1 · #83792 · protein
Crystal structure of lymnaea stagnalis acetylcholine-binding protein Q55R mutant complexed with imidacloprid
3WTH: “Crystal structure of lymnaea stagnalis acetylcholine-binding protein Q55R mutant complexed with imidacloprid”. X-ray diffraction, 1 ligand (IM4), 20 pockets (best druggability 0.74). MolNFT v1 #83792 on GenesisL1: 3D structure…
- PDB
- 3WTH
- Type
- protein
- Length
- 1,041 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- IM4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Acetylcholine-binding protein | protein | 208 | 8% helix, 48% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 209 | 10% helix, 48% strand | P58154 |
Ligands and binding sites
- IM4 · (2E)-1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine · ligand · 5 copies · chains A, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.74 | 0.82 | 60 | IM4 |
| 2 | 315 | 0.73 | 0.85 | 41 | IM4 |
| 3 | 249 | 0.73 | 0.87 | 32 | IM4 |
| 4 | 306 | 0.72 | 0.85 | 42 | IM4 |
| 5 | 229 | 0.70 | 0.86 | 29 | IM4 |
Interfaces
5 interfaces between chains.
- C–D · 1357 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1355 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1339 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1337 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1321 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3WTH · Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant… · the same entry in another collection · chain E against E, 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 0.98
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 3WTH · PDBe 3WTH · UniProt P58154
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