4YU7

Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for the Inhibition of a Phospholipase A2-Like Toxin by Caffeic and Aristolochic Acids.

Fernandes, C.A.Cardoso, F.F.Cavalcante, W.G.Soares, A.M.Dal-Pai, M.Gallacci, M.Fontes, M.R.

(2015) PLoS One 10: e0133370-e0133370

  • DOI: 10.1371/journal.pone.0133370
  • Primary Citation of Related Structures:  
    4YU7, 4YZ7

  • PubMed Abstract: 
  • One of the main challenges in toxicology today is to develop therapeutic alternatives for the treatment of snake venom injuries that are not efficiently neutralized by conventional serum therapy. Venom phospholipases A2 (PLA2s) and PLA2-like proteins ...

    One of the main challenges in toxicology today is to develop therapeutic alternatives for the treatment of snake venom injuries that are not efficiently neutralized by conventional serum therapy. Venom phospholipases A2 (PLA2s) and PLA2-like proteins play a fundamental role in skeletal muscle necrosis, which can result in permanent sequelae and disability. This leads to economic and social problems, especially in developing countries. In this work, we performed structural and functional studies with Piratoxin-I, a Lys49-PLA2 from Bothropspirajai venom, complexed with two compounds present in several plants used in folk medicine against snakebites. These ligands partially neutralized the myotoxic activity of PrTX-I towards binding on the two independent sites of interaction between Lys49-PLA2 and muscle membrane. Our results corroborate the previously proposed mechanism of action of PLA2s-like and provide insights for the design of structure-based inhibitors that could prevent the permanent injuries caused by these proteins in snakebite victims.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of a Lys49-phospholipase A2 complexed with caffeic acid, a molecule with inhibitory properties against snake venoms.
      Shimabuku, P.S., Fernandes, C.A., Magro, A.J., Costa, T.R., Soares, A.M., Fontes, M.R.
      (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 249

    Organizational Affiliation

    Dep. de Física e Biofísica, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, São Paulo, Brazil; Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq, São Paulo, São Paulo, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog piratoxin-1AB121Bothrops pirajaiMutation(s): 0 
Find proteins for P58399 (Bothrops pirajai)
Explore P58399 
Go to UniProtKB:  P58399
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download CCD File 
A, B
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
DHC
Query on DHC

Download CCD File 
A, B
CAFFEIC ACID
C9 H8 O4
QAIPRVGONGVQAS-DUXPYHPUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.233α = 90
b = 72.082β = 102.08
c = 44.644γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2009/10905-5
Sao Paulo Research Foundation (FAPESP)Brazil2014/17864-8

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence