MolNFT v1 · #149581 · protein
Non-aged form of torpedo californica acetylcholinesterase inhibited by tabun analog nedpa bound to uncharged reactivator 1
6G4O: “Non-aged form of torpedo californica acetylcholinesterase inhibited by tabun analog nedpa bound to uncharged…”. X-ray diffraction, 5 ligands (ELT, DQ5, NAG), 9 pockets (best druggability 0.80). MolNFT v1 #149581 on GenesisL1: 3D…
- PDB
- 6G4O
- Type
- protein
- Length
- 1,060 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
- ELT, DQ5, NAG, NA, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 528 | 38% helix, 17% strand | P04058 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 39% helix, 17% strand | P04058 |
Ligands and binding sites
- ELT · ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid · ligand · 2 copies · chains A, B
- DQ5 · 2-[(~{E})-hydroxyiminomethyl]-6-[4-(1,2,3,4-tetrahydroacridin-9-ylamino)butyl]pyridin-3-ol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 8 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.80 | 0.89 | 47 | ELT, DQ5, PG4 |
| 2 | 326 | 0.77 | 0.88 | 37 | ELT, P6G |
| 3 | 357 | 0.59 | 0.76 | 33 | empty |
| 4 | 321 | 0.58 | 0.76 | 32 | empty |
| 5 | 241 | 0.53 | 0.76 | 27 | CL |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6G4O · Non-aged form of Torpedo californica acetylcholinesterase inhibited by tabun analog NEDPA… · 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 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 P04058
- Elsewhere: RCSB PDB 6G4O · PDBe 6G4O · UniProt P04058
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