Research workbench
Crystal structure of aplysia californica achbp in complex with the neonicotinoid imidacloprid
Analyse Crystal structure of aplysia californica achbp in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C79
- Type
- protein
- Length
- 1,054 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- IM4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 211 | 12% helix, 45% strand | Q8WSF8 |
| B, D | Soluble acetylcholine receptor | protein | 212 | 11% helix, 52% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 208 | 13% helix, 46% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 211 | 11% helix, 52% strand | Q8WSF8 |
Ligands and binding sites
- IM4 · (2E)-1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine · ligand · 4 copies · chains A, E, B, C, D
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, 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 | 282 | 0.73 | 0.86 | 60 | IM4, IPA |
| 2 | 591 | 0.70 | 0.79 | 64 | IPA |
| 3 | 391 | 0.68 | 0.80 | 56 | IM4 |
| 4 | 221 | 0.67 | 0.85 | 42 | IM4 |
| 5 | 363 | 0.67 | 0.80 | 55 | IM4 |
Interfaces
5 interfaces between chains.
- A–E · 1472 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1467 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1430 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1422 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1302 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3C79 · Crystal structure of Aplysia californica AChBP in complex with the neonicotinoid… · the same entry in another collection · chain C against C, 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 Q8WSF8
- Elsewhere: RCSB PDB 3C79 · PDBe 3C79 · UniProt Q8WSF8
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