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
- 6M06
- Type
- protein
- Length
- 742 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
- BWF
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Platelet-activating factor acetylhydrolase (EC 3.1.1.47) | protein | 371 | 36% helix, 20% strand | Q13093 |
Ligands and binding sites
- BWF · (2S)-2-[(Z)-1,3-bis(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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.57 | 0.78 | 30 | BWF |
| 2 | 194 | 0.56 | 0.79 | 24 | BWF |
| 3 | 188 | 0.46 | 0.75 | 31 | empty |
| 4 | 61 | 0.41 | 0.81 | 14 | empty |
| 5 | 90 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6M06 · 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 6M06 · PDBe 6M06 · UniProt Q13093
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