Research workbench
Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by tabun
Analyse Crystal structure of human plasma platelet activating factor acetylhydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F98
- Type
- protein
- Length
- 1,131 residues
- Chains
- 3
- 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
- NTJ
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 377 | 37% helix, 20% strand | Q13093 |
Ligands and binding sites
- NTJ · R-ethyl N,N-dimethylphosphonamidate · ligand · 3 copies · chains A, C, B
- FMT · Formic acid · additive · 86 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.82 | 0.83 | 100 | FMT |
| 2 | 1080 | 0.77 | 0.79 | 99 | NTJ, FMT |
| 3 | 228 | 0.61 | 0.80 | 27 | NTJ |
| 4 | 215 | 0.57 | 0.78 | 28 | NTJ |
| 5 | 52 | 0.31 | 0.77 | 15 | FMT |
Interfaces
3 interfaces between chains.
- A–C · 920 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 573 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3F98 · 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 0.98
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 3F98 · PDBe 3F98 · UniProt Q13093
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