MolNFT v1 · #34424 · protein
X-ray structure of aged di-isopropyl-phosphoro-fluoridate (dfp) bound to acetylcholinesterase
2DFP · Protein (acetylcholinesterase): “X-ray structure of aged di-isopropyl-phosphoro-fluoridate (dfp) bound to acetylcholinesterase”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.79). MolNFT v1 #34424 on GenesisL1…
- PDB
- 2DFP
- Type
- protein
- Length
- 534 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (acetylcholinesterase)
- EC
- 3.1.1.7
- UniProt
- P04058
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (acetylcholinesterase) (EC 3.1.1.7) | protein | 534 | 39% helix, 17% strand | P04058 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.79 | 0.89 | 35 | empty |
| 2 | 377 | 0.64 | 0.78 | 37 | empty |
| 3 | 104 | 0.41 | 0.76 | 19 | empty |
| 4 | 63 | 0.35 | 0.77 | 14 | MES |
| 5 | 62 | 0.34 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 2DFP · X-ray structure of aged di-isopropyl-phosphoro-fluoridate (dfp) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · 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 P04058
- Elsewhere: RCSB PDB 2DFP · PDBe 2DFP · UniProt P04058
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