MolNFT v1 · #99333 · protein
Structure of human acetylcholinesterase in complex with dihydrotanshinone I
4M0E: “Structure of human acetylcholinesterase in complex with dihydrotanshinone I”. X-ray diffraction, 4 ligands (1YL, NAG, FUC), 12 pockets (best druggability 0.72). MolNFT v1 #99333 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4M0E
- 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
- P22303
- Ligands
- 1YL, NAG, FUC, NO3
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 38% helix, 18% strand | P22303 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 537 | 37% helix, 18% strand | P22303 |
Ligands and binding sites
- 1YL · Dihydrotanshinone I · 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
- NO3 · Nitrate ion · ion · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.72 | 0.87 | 38 | 1YL |
| 2 | 229 | 0.70 | 0.86 | 37 | 1YL |
| 3 | 338 | 0.60 | 0.77 | 35 | empty |
| 4 | 330 | 0.59 | 0.77 | 34 | empty |
| 5 | 163 | 0.55 | 0.81 | 21 | NO3 |
Interfaces
1 interface between chains.
- A–B · 996 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4M0E · Structure of human acetylcholinesterase in complex with dihydrotanshi I · 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 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 P22303
- Elsewhere: RCSB PDB 4M0E · PDBe 4M0E · UniProt P22303
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