Research workbench
Crystal structure of recombinant human acetylcholinesterase in complex with empa and hi-6
Analyse Crystal structure of recombinant human acetylcholinesterase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CQY
- Type
- protein
- Length
- 1,061 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P22303
- Ligands
- HI6, VX, NAG, FUC
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 38% helix, 17% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 529 | 38% helix, 17% strand | P22303 |
Ligands and binding sites
- HI6 · 4-(aminocarbonyl)-1-[({2-[(E)-(hydroxyimino)methyl]pyridinium-1-yl}methoxy)methyl]pyridinium · ligand · 2 copies · chains A, B
- VX · O-ethylmethylphosphonic acid ester group · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.75 | 0.88 | 40 | HI6, VX |
| 2 | 253 | 0.75 | 0.88 | 37 | HI6, VX |
| 3 | 703 | 0.68 | 0.76 | 80 | empty |
| 4 | 401 | 0.64 | 0.78 | 38 | empty |
| 5 | 393 | 0.63 | 0.78 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 337 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQY · Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with EMPA and HI-6 · the same entry in another collection · chain A against A, TM-score 1.00
- P22303 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P22303) · a predicted model of the same protein · chain A 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 P22303
- Elsewhere: RCSB PDB 6CQY · PDBe 6CQY · UniProt P22303
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