4K06 | pdb_00004k06

Crystal structure of MTX-II from Bothrops brazili venom complexed with polyethylene glycol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4K06

This is version 1.2 of the entry. See complete history

Literature

Structural bases for a complete myotoxic mechanism: Crystal structures of two non-catalytic phospholipases A2-like from Bothrops brazili venom.

Fernandes, C.A.H.Comparetti, E.J.Borges, R.J.Huancahuire-Vega, S.Ponce-Soto, L.A.Marangoni, S.Soares, A.M.Fontes, M.R.M.

(2013) Biochim Biophys Acta 1834: 2772-2781

  • DOI: https://doi.org/10.1016/j.bbapap.2013.10.009
  • Primary Citation Related Structures: 
    4K06, 4K09

  • PubMed Abstract: 

    Bothrops brazili is a snake found in the forests of the Amazonian region whose commercial therapeutic anti-bothropic serum has low efficacy for local myotoxic effects, resulting in an important public health problem in this area. Catalytically inactive phospholipases A2-like (Lys49-PLA2s) are among the main components from Bothrops genus venoms and are capable of causing drastic myonecrosis. Several studies have shown that the C-terminal region of these toxins, which includes a variable combination of positively charged and hydrophobic residues, is responsible for their activity. In this work we describe the crystal structures of two Lys49-PLA2s (BbTX-II and MTX-II) from B. brazili venom and a comprehensive structural comparison with several Lys49-PLA2s. Based on these results, two independent sites of interaction were identified between protein and membrane which leads to the proposition of a new myotoxic mechanism for bothropic Lys49-PLA2s composed of five different steps. This proposition is able to fully explain the action of these toxins and may be useful to develop efficient inhibitors to complement the conventional antivenom administration.


  • Organizational Affiliation
    • Dep. de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu and Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq, Brazil.

Macromolecule Content 

  • Total Structure Weight: 28.8 kDa 
  • Atom Count: 2,164 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MTX-II
A, B
121Bothrops braziliMutation(s): 0 
UniProt
Find proteins for I6L8L6 (Bothrops brazili)
Explore I6L8L6 
Go to UniProtKB:  I6L8L6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6L8L6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
G [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
7PE

Query on 7PE



Download:Ideal Coordinates CCD File
J [auth B]2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.01α = 90
b = 71.414β = 102.5
c = 44.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary