MolNFT v1 · #88980 · protein
Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine
4DBK · Phospholipase A2, major isoenzyme: “Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine”. X-ray diffraction, 2 ligands (BER, CA), 1 pocket (best druggability 0.55). MolNFT v1 #88980 on GenesisL1: 3D…
- PDB
- 4DBK
- Type
- protein
- Length
- 124 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2, major isoenzyme
- EC
- 3.1.1.4
- UniProt
- P00592
- Ligands
- BER, CA
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2, major isoenzyme (EC 3.1.1.4) | protein | 124 | 51% helix, 9% strand | P00592 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.55 | 0.80 | 25 | BER |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4DBK · Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine · 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 A against A, TM-score 0.96
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 4DBK · PDBe 4DBK · UniProt P00592
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