6MQD

Myotoxin II from Bothrops moojeni complexed with Rosmarinic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Search for efficient inhibitors of myotoxic activity induced by ophidian phospholipase A2-like proteins using functional, structural and bioinformatics approaches.

Salvador, G.H.M.Cardoso, F.F.Gomes, A.A.Cavalcante, W.L.G.Gallacci, M.Fontes, M.R.M.

(2019) Sci Rep 9: 510-510

  • DOI: https://doi.org/10.1038/s41598-018-36839-6
  • Primary Citation of Related Structures:  
    6MQD, 6MQF

  • PubMed Abstract: 

    Ophidian accidents are considered an important neglected tropical disease by the World Health Organization. Particularly in Latin America, Bothrops snakes are responsible for the majority of the snakebite envenomings that are not efficiently treated by conventional serum therapy. Thus, the search for simple and efficient inhibitors to complement this therapy is a promising research area, and a combination of functional and structural assays have been used to test candidate ligands against specific ophidian venom compounds. Herein, we tested a commercial drug (acetylsalicylic acid, ASA) and a plant compound with antiophidian properties (rosmarinic acid, RA) using myographic, crystallographic and bioinformatics experiments with a phospholipase A 2 -like toxin, MjTX-II. MjTX-II/RA and MjTX-II/ASA crystal structures were solved at high resolution and revealed the presence of ligands bound to different regions of the toxin. However, in vitro myographic assays showed that only RA is able to prevent the myotoxic effects of MjTX-II. In agreement with functional results, molecular dynamics simulations showed that the RA molecule remains tightly bound to the toxin throughout the calculations, whereas ASA molecules tend to dissociate. This approach aids the design of effective inhibitors of PLA 2 -like toxins and, eventually, may complement serum therapy.


  • Organizational Affiliation

    Depto. de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog 2
A, B
122Bothrops moojeniMutation(s): 0 
UniProt
Find proteins for Q9I834 (Bothrops moojeni)
Explore Q9I834 
Go to UniProtKB:  Q9I834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I834
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ROA
Query on ROA

Download Ideal Coordinates CCD File 
C [auth A](2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid
C18 H16 O8
DOUMFZQKYFQNTF-WUTVXBCWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.076α = 90
b = 65.839β = 90
c = 90.42γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description