MolNFT v1 · #140526 · protein
Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, 3.2 a
5YDH: “Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, 3.2 a”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.74). MolNFT v1 #140526 on GenesisL1: 3D…
- PDB
- 5YDH
- Type
- protein
- Length
- 1,076 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- Q869C3
- Ligands
- NAG, MAN, BMA, CO, SO4
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 538 | 35% helix, 17% strand | Q869C3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 26 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.74 | 0.86 | 34 | EPE, GOL |
| 2 | 301 | 0.72 | 0.85 | 36 | SO4, EPE, GOL |
| 3 | 229 | 0.64 | 0.82 | 35 | empty |
| 4 | 122 | 0.60 | 0.86 | 26 | empty |
| 5 | 301 | 0.60 | 0.78 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1303 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5YDH · Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector… · the same entry in another collection · chain A against A, TM-score 1.00
- Q869C3 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (Q869C3) · 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 Q869C3
- Elsewhere: RCSB PDB 5YDH · PDBe 5YDH · UniProt Q869C3
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