MolNFT v1 · #38453 · protein
Crystal structure of mus musculus acetylcholinesterase in complex with hi-6
2GYU: “Crystal structure of mus musculus acetylcholinesterase in complex with hi-6”. X-ray diffraction, 4 ligands (HI6, P4G, NAG), 13 pockets (best druggability 0.83). MolNFT v1 #38453 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2GYU
- 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
- HI6, P4G, NAG, FUC
- Pockets
- 13 · best druggability 0.83
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 | 535 | 38% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 533 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- HI6 · 4-(aminocarbonyl)-1-[({2-[(E)-(hydroxyimino)methyl]pyridinium-1-yl}methoxy)methyl]pyridinium · ligand · 2 copies · chains A, B
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- P6G · Hexaethylene 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 | 245 | 0.83 | 0.95 | 34 | HI6 |
| 2 | 250 | 0.80 | 0.93 | 43 | HI6 |
| 3 | 221 | 0.62 | 0.82 | 28 | P4G, P6G |
| 4 | 353 | 0.62 | 0.78 | 39 | empty |
| 5 | 331 | 0.61 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1001 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2GYU · Crystal structure of Mus musculus Acetylcholinesterase in complex with HI-6 · 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 2GYU · PDBe 2GYU · UniProt P21836
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