2QVD
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
Summary for 2QVD
| Entry DOI | 10.2210/pdb2qvd/pdb |
| Related | 2OYF 2PYC |
| Descriptor | Phospholipase A2 VRV-PL-VIIIa, BERBERINE (3 entities in total) |
| Functional Keywords | phospholipids, membrane, hydrolysis, inhibitor, plant extraxt, lipid degradation, metal-binding, neurotoxin, presynaptic neurotoxin, secreted, toxin, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor |
| Biological source | Daboia russellii pulchella (Russell's viper) |
| Cellular location | Secreted: P59071 |
| Total number of polymer chains | 1 |
| Total formula weight | 13966.13 |
| Authors | Kumar, S.,Chandra, D.N.,Singh, N.,Jithesh, O.,Sharma, S.,Haridas, M.,Singh, T.P. (deposition date: 2007-08-08, release date: 2007-08-21, Last modification date: 2024-11-20) |
| Primary citation | Chandra, D.N.,Prasanth, G.K.,Singh, N.,Kumar, S.,Jithesh, O.,Sadasivan, C.,Sharma, S.,Singh, T.P.,Haridas, M. Identification of a novel and potent inhibitor of phospholipase A(2) in a medicinal plant: crystal structure at 1.93A and Surface Plasmon Resonance analysis of phospholipase A(2) complexed with berberine Biochim.Biophys.Acta, 1814:657-663, 2011 Cited by PubMed Abstract: Crystal of Russell Viper venom phospholipase A(2) complexed with an isoquinoline alkaloid, berberine from a herbaceous plant Cardiospermum halicacabum, was prepared and its structure was solved by X-ray crystallography. The crystal diffracted up to 1.93Å and the structure solution clearly located the position of berberine in the active site of the enzyme. Two hydrogen bonds, one direct and the other water mediated, were formed between berberine and the enzyme. Gly 30 and His 48 made these two hydrogen bonds. Additionally, the hydrophobic surface of berberine made a number of hydrophobic contacts with side chains of neighboring amino acids. Surface Plasmon Resonance studies revealed strong binding affinity between berberine and phospholipase A(2). Enzyme inhibition studies proved that berberine is a competitive inhibitor of phospholipase A(2). It was inferred that the isoquinoline alkaloid, berberine, is a potent natural inhibitor of phospholipaseA(2). PubMed: 21420512DOI: 10.1016/j.bbapap.2011.03.002 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.93 Å) |
Structure validation
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