Research workbench
Crystal structure of recombinant human acetylcholinesterase inhibited by gd
Analyse Crystal structure of recombinant human acetylcholinesterase inhibited by gd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVC
- Type
- protein
- Length
- 1,073 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
- UCY, NAG, FUC
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 537 | 37% helix, 18% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 536 | 37% helix, 17% strand | P22303 |
Ligands and binding sites
- UCY · (1S)-2,2-dimethylcyclopentyl (R)-methylphosphinate · 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
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.76 | 0.89 | 34 | UCY |
| 2 | 254 | 0.73 | 0.87 | 34 | UCY |
| 3 | 462 | 0.63 | 0.76 | 44 | empty |
| 4 | 340 | 0.59 | 0.77 | 36 | empty |
| 5 | 116 | 0.48 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 363 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6WVC · Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by GD · 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 6WVC · PDBe 6WVC · UniProt P22303
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