4YU7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.647 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Basic phospholipase A2 homolog piratoxin-1
B, A
121Bothrops pirajaiMutation(s): 0 
Find proteins for P58399 (Bothrops pirajai)
Go to UniProtKB:  P58399
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download SDF File 
Download CCD File 
A, B
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DHC
Query on DHC

Download SDF File 
Download CCD File 
A, B
CAFFEIC ACID
3,4-DIHYDROXYCINNAMIC ACID
C9 H8 O4
QAIPRVGONGVQAS-DUXPYHPUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.647 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.233α = 90.00
b = 72.082β = 102.08
c = 44.644γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil2009/10905-5
FAPESPBrazil2014/17864-8

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references