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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Chandra, D.N.Prasanth, G.K.Singh, N.Kumar, S.Jithesh, O.Sadasivan, C.Sharma, S.Singh, T.P.Haridas, M.

(2011) Biochim.Biophys.Acta 1814: 657-663

  • DOI: 10.1016/j.bbapap.2011.03.002

  • 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 ...

    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).


    Organizational Affiliation

    Department of Biotechnology & Microbiology, Kannur University, Palayad, Kerala 670661, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2 VRV-PL-VIIIa
A
121Daboia russeliiMutation(s): 0 
EC: 3.1.1.4
Find proteins for P59071 (Daboia russelii)
Go to UniProtKB:  P59071
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BER
Query on BER

Download SDF File 
Download CCD File 
A
BERBERINE
C20 H18 N O4
YBHILYKTIRIUTE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BERKd: 1450 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.175 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 53.311α = 90.00
b = 53.311β = 90.00
c = 48.379γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-23
    Type: Database references, Structure summary