Research workbench
Torpedo californica acetylcholinesterase bound to uncharged hybrid reactivator 1
Analyse Torpedo californica acetylcholinesterase bound to uncharged hybrid reactivator 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G4M
- Type
- protein
- Length
- 1,064 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P04058
- Ligands
- DQ5, NAG, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 39% helix, 17% strand | P04058 |
Ligands and binding sites
- DQ5 · 2-[(~{E})-hydroxyiminomethyl]-6-[4-(1,2,3,4-tetrahydroacridin-9-ylamino)butyl]pyridin-3-ol · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.76 | 0.87 | 40 | DQ5 |
| 2 | 346 | 0.76 | 0.86 | 37 | DQ5 |
| 3 | 352 | 0.58 | 0.75 | 33 | empty |
| 4 | 318 | 0.56 | 0.76 | 32 | empty |
| 5 | 154 | 0.47 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 962 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6G4M · Torpedo californica acetylcholinesterase bound to uncharged hybrid reactivator 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · 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 P04058
- Elsewhere: RCSB PDB 6G4M · PDBe 6G4M · UniProt P04058
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