Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.2 of the entry. See complete history


Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) at 1.9 A resolution reveals unique features

Singh, R.K.Vikram, P.Makker, J.Jabeen, T.Sharma, S.Dey, S.Kaur, P.Srinivasan, A.Singh, T.P.

(2003) Biochemistry 42: 11701-11706

  • DOI: https://doi.org/10.1021/bi035076x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phospholipase A(2) (PLA(2)) (E. C. is a common enzyme in the two-way cascade mechanism leading to the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A(2) to the membrane surface and hydrolysis of phospholipids are thought to involve the formation of a hydrophobic channel into which a single substrate molecule diffuses before its cleavage. To regulate the production of proinflammatory compounds, a specific peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) for the group I PLA(2) enzymes has been designed and synthesized. PLA(2) was isolated from Indian cobra (Naja naja sagittifera) venom and purified to homogeneity. The binding studies indicated the K(i) value of 1.02 +/- 0.10 x 10(-8) M. The purified PLA(2) samples and the designed inhibitor VAFRS were cocrystallized. The crystal structure of the complex was determined and refined to 1.9 A resolution. The peptide binds to PLA(2) at the active site and fills the hydrophobic channel completely. However, its placement with respect to the channel is in the opposite direction as compared to those observed in group II PLA(2)'s. Furthermore, the predominant intermolecular interactions involve strong electrostatic interactions between the side chains of peptide Arg and Asp 49 of PLA(2) together with a number of van der Waals interactions with other residues. A good number of observed interactions between the peptide and the protein indicate the significance of a structure-based drug design approach. The novel factor in the present sequence of the peptide is related to the introduction of a positively charged residue at the C-terminal part of the peptide.

  • Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase A2119Naja sagittiferaMutation(s): 0 
Find proteins for P60045 (Naja sagittifera)
Explore P60045 
Go to UniProtKB:  P60045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60045
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VAL-ALA-PHE-ARG-SER5N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.779α = 90
b = 42.779β = 90
c = 65.866γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance