MolNFT v1 · #83798 · protein
Crystal structure of lymnaea stagnalis acetylcholine binding protein complexed with desnitro-imidacloprid
3WTN · Acetylcholine-binding protein: “Crystal structure of lymnaea stagnalis acetylcholine binding protein complexed with desnitro-imidacloprid”. X-ray diffraction, 3 ligands (N2Y, CD, NA), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3WTN
- Type
- protein
- Length
- 2,080 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- N2Y, CD, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Acetylcholine-binding protein | protein | 208 | 8% helix, 48% strand | P58154 |
Ligands and binding sites
- N2Y · (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CD · Cadmium ion · metal · 54 copies · chains A, G, F, B, C, J, D, I, E, H
- NA · Sodium ion · metal · 2 copies · chains B, C
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 | 532 | 0.81 | 0.88 | 77 | empty |
| 2 | 219 | 0.79 | 0.93 | 45 | empty |
| 3 | 192 | 0.72 | 0.89 | 37 | empty |
| 4 | 129 | 0.72 | 0.92 | 33 | empty |
| 5 | 119 | 0.71 | 0.92 | 27 | N2Y |
Interfaces
20 interfaces between chains.
- F–J · 1433 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1407 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1394 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1389 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3WTN · Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with… · 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 I against A, TM-score 0.99
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 3WTN · PDBe 3WTN · UniProt P58154
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