MolNFT v1 · #12721 · protein
First structural evidence of a specific inhibition of phospholipase A2 by vitamin E and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and vitamin E at 1.8 a resolution.
1KPM: “First structural evidence of a specific inhibition of phospholipase A2 by vitamin E and its implications in…”. X-ray diffraction, 1 ligand (VIT), 4 pockets (best druggability 0.74). MolNFT v1 #12721 on GenesisL1: 3D structure…
- PDB
- 1KPM
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P59071
- Ligands
- VIT
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 121 | 48% helix, 8% strand | P59071 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.74 | 0.89 | 31 | VIT |
| 2 | 231 | 0.71 | 0.87 | 35 | empty |
| 3 | 162 | 0.57 | 0.81 | 22 | empty |
| 4 | 52 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 676 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1KPM · First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and… · the same entry in another collection · chain A against A, TM-score 1.00
- P59071 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 vrv-pl- viiia (P59071) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P59071
- Elsewhere: RCSB PDB 1KPM · PDBe 1KPM · UniProt P59071
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