Research workbench
Crystal structure of lymnaea stagnalis acetylcholine-binding protein Q55R mutant complexed with nitromethylene analogue of imidacloprid
Analyse Crystal structure of lymnaea stagnalis acetylcholine-binding protein Q55R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WTM
- Type
- protein
- Length
- 1,038 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- N1Y
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Acetylcholine-binding protein | protein | 207 | 8% helix, 48% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 209 | 7% helix, 47% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 208 | 7% helix, 46% strand | P58154 |
Ligands and binding sites
- N1Y · 2-chloro-5-{[(2E)-2-(nitromethylidene)imidazolidin-1-yl]methyl}pyridine · ligand · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.74 | 0.97 | 15 | N1Y |
| 2 | 210 | 0.73 | 0.88 | 36 | N1Y |
| 3 | 248 | 0.71 | 0.86 | 30 | N1Y |
| 4 | 254 | 0.69 | 0.85 | 31 | N1Y |
| 5 | 123 | 0.69 | 0.90 | 27 | N1Y |
Interfaces
5 interfaces between chains.
- B–C · 1379 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1369 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1342 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3WTM · 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 C 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 3WTM · PDBe 3WTM · UniProt P58154
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