Research workbench
Crystal structure of mus musculus acetylcholinesterase in complex with ortho-7
Analyse Crystal structure of mus musculus acetylcholinesterase in complex with ortho-7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GYV
- Type
- protein
- Length
- 1,068 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
- HBP, P3G, NAG, CO3
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 535 | 39% helix, 19% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 533 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- HBP · 1,7-heptylene-bis-N,N'-syn-2-pyridiniumaldoxime · ligand · 2 copies · chains A, B
- P3G · 3,6,9,12,15-pentaoxaheptadecane · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CO3 · Carbonate ion · ion · 2 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 | 242 | 0.78 | 0.91 | 40 | CO3, HBP |
| 2 | 227 | 0.77 | 0.90 | 33 | CO3, HBP |
| 3 | 179 | 0.61 | 0.83 | 35 | empty |
| 4 | 296 | 0.59 | 0.77 | 33 | empty |
| 5 | 144 | 0.57 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2GYV · Crystal structure of Mus musculus Acetylcholinesterase in complex with Ortho-7 · 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 2GYV · PDBe 2GYV · UniProt P21836
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