MolNFT v1 · #60890 · protein
Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by paraoxon
3D5E · Platelet-activating factor acetylhydrolase: “Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by paraoxon”. X-ray diffraction, 1 ligand (DEP), 6 pockets (best druggability 0.58).…
- PDB
- 3D5E
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-activating factor acetylhydrolase
- EC
- 3.1.1.47
- UniProt
- Q13093
- Ligands
- DEP
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 373 | 36% helix, 20% strand | Q13093 |
| B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 370 | 38% helix, 21% strand | Q13093 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.58 | 0.79 | 29 | DEP |
| 2 | 220 | 0.57 | 0.79 | 29 | DEP |
| 3 | 287 | 0.54 | 0.76 | 42 | FMT |
| 4 | 287 | 0.53 | 0.75 | 38 | FMT |
| 5 | 71 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3D5E · Crystal structure of human plasma platelet activating factor acetylhydrolase covalently… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13093 · AlphaFold monomer V2.0 prediction for platelet-activating factor acetylhydrolase (Q13093) · 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 Q13093
- Elsewhere: RCSB PDB 3D5E · PDBe 3D5E · UniProt Q13093
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