MolNFT v1 · #119055 · protein
Crystal structure of mouse acetylcholinesterase in complex with C-547, an alkyl ammonium derivative of 6-methyl uracil
5FKJ: “Crystal structure of mouse acetylcholinesterase in complex with C-547, an alkyl ammonium derivative of…”. X-ray diffraction, 4 ligands (G0W, NAG, CL), 20 pockets (best druggability 0.83). MolNFT v1 #119055 on GenesisL1: 3D…
- PDB
- 5FKJ
- Type
- protein
- Length
- 2,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P21836
- Ligands
- G0W, NAG, CL, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 541 | 37% helix, 17% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 538 | 38% helix, 17% strand | P21836 |
| C, D | Acetylcholinesterase (EC 3.1.1.7) | protein | 536 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- G0W · 1,3-bis[5(diethyl-O-nitrobenzylammonium)pentyl]-6-methyluracil · ligand · 4 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 28 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.83 | 0.87 | 73 | G0W |
| 2 | 702 | 0.82 | 0.86 | 71 | G0W |
| 3 | 282 | 0.77 | 0.89 | 36 | G0W |
| 4 | 298 | 0.75 | 0.88 | 44 | G0W |
| 5 | 407 | 0.63 | 0.77 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–B · 951 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 938 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 619 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5FKJ · Crystal structure of mouse acetylcholinesterase in complex with C-547, an alkyl ammonium… · the same entry in another collection · chain D against D, TM-score 1.00
- P21836 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P21836) · 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 P21836
- Elsewhere: RCSB PDB 5FKJ · PDBe 5FKJ · UniProt P21836
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