MolNFT v1 · #116948 · protein
Crystal structure of dfp-inhibited mouse acetylcholinesterase in complex with the reactivator sp-134
5DTJ: “Crystal structure of dfp-inhibited mouse acetylcholinesterase in complex with the reactivator sp-134”. X-ray diffraction, 1 ligand (5G8), 13 pockets (best druggability 0.82). MolNFT v1 #116948 on GenesisL1: 3D structure, binding…
- PDB
- 5DTJ
- Type
- protein
- Length
- 1,069 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P21836
- Ligands
- 5G8
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 537 | 38% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 39% helix, 18% strand | P21836 |
Ligands and binding sites
- 5G8 · 1-[5-(2,4-dichlorophenoxy)pentyl]-1H-imidazole · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.82 | 0.92 | 45 | 5G8 |
| 2 | 357 | 0.80 | 0.90 | 45 | 5G8 |
| 3 | 252 | 0.66 | 0.83 | 37 | empty |
| 4 | 176 | 0.60 | 0.82 | 18 | empty |
| 5 | 193 | 0.59 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 919 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5DTJ · Crystal Structure of dfp-inhibited mouse acetylcholinesterase in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P21836 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P21836) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P21836
- Elsewhere: RCSB PDB 5DTJ · PDBe 5DTJ · UniProt P21836
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