Research workbench
Crystal structure of Lp-PLA2 in complex with a novel covalent inhibitor
Analyse Crystal structure of Lp-PLA2 in complex with a novel covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M07
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.64
- Source
- Homo sapiens
- Molecule
- Platelet-activating factor acetylhydrolase
- EC
- 3.1.1.47
- UniProt
- Q13093
- Ligands
- BWO
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.64 · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 369 | 36% helix, 22% strand | Q13093 |
Ligands and binding sites
- BWO · (2S)-2-[(E)-3-[2-(diethylamino)ethyl-[[4-[4-(trifluoromethyl)-2-[2,2,2-tris(fluoranyl) ethoxy]phenyl]phenyl]methyl]amino]-1-oxidanyl-3-oxidanylidene-prop-1-enyl]pyrrolidine-1-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.63 | 0.76 | 59 | empty |
| 2 | 218 | 0.55 | 0.77 | 29 | BWO |
| 3 | 213 | 0.54 | 0.77 | 29 | BWO |
| 4 | 50 | 0.33 | 0.78 | 15 | empty |
| 5 | 83 | 0.31 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6M07 · Crystal structure of lp-PLA2 in complex with a novel covalent inhibitor · 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 6M07 · PDBe 6M07 · UniProt Q13093
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