MolNFT v1 · #140527 · protein
Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, new crystal packing
5YDI: “Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, new…”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.76). MolNFT v1 #140527 on GenesisL1: 3D…
- PDB
- 5YDI
- Type
- protein
- Length
- 1,611 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- Q869C3
- Ligands
- NAG, BMA, MAN, NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acetylcholinesterase (EC 3.1.1.7) | protein | 537 | 36% helix, 16% strand | Q869C3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.76 | 0.85 | 34 | GOL, NA |
| 2 | 383 | 0.76 | 0.86 | 37 | GOL, NA |
| 3 | 737 | 0.75 | 0.80 | 82 | empty |
| 4 | 331 | 0.73 | 0.85 | 34 | GOL, NA |
| 5 | 53 | 0.63 | 0.94 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1207 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5YDI · 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 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 Q869C3
- Elsewhere: RCSB PDB 5YDI · PDBe 5YDI · UniProt Q869C3
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