MolNFT v1 · #49676 · protein

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

2QVD · Phospholipase A2 vrv-pl-viiia: “Identification of a potent anti-inflammatory agent from the natural extract of plant cardiospermun…”. X-ray diffraction, 1 ligand (BER), 1 pocket (best druggability 0.48). MolNFT v1 #49676 on…

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.

Pocket	Volume (Å³)	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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