Research workbench
Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6
Analyse Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HF9
- Type
- protein
- Length
- 1,063 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
- DEP, HI6, NAG, FUC, NO3
- Pockets
- 15 · best druggability 0.76
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 | 530 | 38% helix, 17% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 533 | 38% helix, 18% strand | P22303 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · 2 copies · chains A, B
- HI6 · 4-(aminocarbonyl)-1-[({2-[(E)-(hydroxyimino)methyl]pyridinium-1-yl}methoxy)methyl]pyridinium · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.76 | 0.88 | 39 | DEP, HI6 |
| 2 | 272 | 0.75 | 0.88 | 38 | DEP, HI6 |
| 3 | 388 | 0.62 | 0.77 | 35 | empty |
| 4 | 352 | 0.61 | 0.77 | 35 | empty |
| 5 | 159 | 0.56 | 0.81 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5HF9 · Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6 · 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 B 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 5HF9 · PDBe 5HF9 · UniProt P22303
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