Research workbench
Crystal structure of human acetylcholinesterase in complex with C35.
Analyse Crystal structure of human acetylcholinesterase in complex with C35. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F25
- Type
- protein
- Length
- 1,068 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
- CVZ, NAG, FUC, CL, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 533 | 36% helix, 18% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 535 | 37% helix, 19% strand | P22303 |
Ligands and binding sites
- CVZ · 3-[(~{E})-5-[ethyl-[(2-nitrophenyl)methyl]amino]pent-1-enyl]-1-[5-[ethyl-[(2-nitrophenyl) methyl]amino]pentyl]-6-methyl-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 29 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.75 | 0.87 | 38 | CVZ |
| 2 | 258 | 0.75 | 0.88 | 39 | CVZ |
| 3 | 331 | 0.61 | 0.78 | 34 | empty |
| 4 | 350 | 0.60 | 0.77 | 35 | CL |
| 5 | 217 | 0.58 | 0.80 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1037 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6F25 · Crystal structure of human acetylcholinesterase in complex with C35. · 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 6F25 · PDBe 6F25 · UniProt P22303
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