MolNFT v2 · #130478 · protein
X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor
5P2P: “X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor”. X-ray diffraction at 2.4, 2 ligands (DHG, CA), 4 pockets (best druggability 0.59). MolNFT v2 #130478 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5P2P
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Sus scrofa
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P00592
- Ligands
- DHG, CA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.4 · 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 | 119 | 48% helix, 8% strand | P00592 |
Ligands and binding sites
- DHG · Phosphonic acid 2-dodecanoylamino-hexyl ester propyl ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.59 | 0.79 | 29 | DHG |
| 2 | 212 | 0.58 | 0.80 | 22 | DHG |
| 3 | 51 | 0.26 | 0.74 | 15 | empty |
| 4 | 61 | 0.26 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 399 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5P2P · X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P00592 · AlphaFold monomer V2.0 prediction for phospholipase A2, major isoenzyme (P00592) · a predicted model of the same protein · chain B 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 P00592
- Elsewhere: RCSB PDB 5P2P · PDBe 5P2P · UniProt P00592
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