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Identification of a potent anti-inflammatory agent from the natural extract of plant cardiospermun helicacabum: crystal structure of the complex of phospholipase A2 with BENZO(G)-1,3-BENZODIOXOLO(5,6-a) quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 a resolution
Analyse Identification of a potent anti-inflammatory agent from the natural extract of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QVD
- Type
- protein
- Length
- 121 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 vrv-pl-viiia
- EC
- 3.1.1.4
- UniProt
- P59071
- Ligands
- BER
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 45% helix, 8% strand | P59071 |
Ligands and binding sites
- BER · Berberine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.48 | 0.78 | 18 | BER |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2QVD · Identification of a potent anti-inflammatory agent from the natural extract of plant… · the same entry in another collection · 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 P59071
- Elsewhere: RCSB PDB 2QVD · PDBe 2QVD · UniProt P59071
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