Research workbench
Crystal structure of the mouse acetylcholinesterase-decidium complex
Analyse Crystal structure of the mouse acetylcholinesterase-decidium complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J07
- Type
- protein
- Length
- 1,070 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
- DCU, NAG, FUC, CO3, CL
- Pockets
- 13 · best druggability 0.77
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 | 536 | 38% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 534 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- DCU · 3,8-diamino-5,10'-(trimethylammonium)decyl-6-phenyl phenanthridinium · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.77 | 0.90 | 34 | CO3 |
| 2 | 274 | 0.76 | 0.88 | 37 | CO3, CL |
| 3 | 269 | 0.64 | 0.82 | 42 | P6G, PG4 |
| 4 | 391 | 0.63 | 0.78 | 39 | empty |
| 5 | 351 | 0.60 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1010 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1J07 · Crystal structure of the mouse acetylcholinesterase-decidium complex · 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 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 P21836
- Elsewhere: RCSB PDB 1J07 · PDBe 1J07 · UniProt P21836
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.