MolNFT v1 · #63420 · protein
Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by soman
3F97 · Platelet-activating factor acetylhydrolase: “Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by soman”. X-ray diffraction, 2 ligands (GD7, SO4), 8 pockets (best druggability 0.60).…
- PDB
- 3F97
- Type
- protein
- Length
- 744 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
- GD7, SO4
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 372 | 37% helix, 20% strand | Q13093 |
Ligands and binding sites
- GD7 · (1R)-1,2,2-trimethylpropyl (R)-methylphosphinate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- ACT · Acetate ion · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.60 | 0.78 | 34 | GD7, ACT |
| 2 | 260 | 0.60 | 0.78 | 31 | GD7 |
| 3 | 357 | 0.55 | 0.75 | 47 | empty |
| 4 | 66 | 0.42 | 0.81 | 14 | empty |
| 5 | 73 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 732 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3F97 · 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 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 Q13093
- Elsewhere: RCSB PDB 3F97 · PDBe 3F97 · UniProt Q13093
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