Research workbench
Crystal structure of human acetylcholinesterase in complex with paraoxon in the aged state
Analyse Crystal structure of human acetylcholinesterase in complex with paraoxon in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HF6
- Type
- protein
- Length
- 1,066 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
- EFS, NAG, FUC
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 528 | 37% helix, 18% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 538 | 38% helix, 18% strand | P22303 |
Ligands and binding sites
- EFS · Ethyl dihydrogen phosphate · 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
- EDO · 1,2-ethanediol · additive · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.76 | 0.88 | 44 | EFS |
| 2 | 255 | 0.73 | 0.87 | 37 | EFS |
| 3 | 413 | 0.66 | 0.79 | 40 | empty |
| 4 | 432 | 0.66 | 0.78 | 40 | empty |
| 5 | 154 | 0.56 | 0.81 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5HF6 · Crystal structure of human acetylcholinesterase in complex with paraoxon in the aged state · 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 5HF6 · PDBe 5HF6 · UniProt P22303
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