Research workbench
Crystal structure of anopheles gambiae acetylcholinesterase in complex with pmsf
Analyse Crystal structure of anopheles gambiae acetylcholinesterase in complex with pmsf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YDJ
- 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, CO, SO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 538 | 36% helix, 17% strand | Q869C3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 29 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.69 | 0.78 | 85 | SO4 |
| 2 | 248 | 0.63 | 0.81 | 27 | empty |
| 3 | 233 | 0.62 | 0.81 | 26 | SO4 |
| 4 | 133 | 0.61 | 0.86 | 29 | empty |
| 5 | 349 | 0.57 | 0.75 | 51 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 5YDJ · Crystal structure of anopheles gambiae acetylcholinesterase in complex with PMSF · the same entry in another collection · chain B against B, 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 5YDJ · PDBe 5YDJ · UniProt Q869C3
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