7ROX | pdb_00007rox

BthTX-I complexed with inhibitor MMV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.198 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.167 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ROX

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural and functional studies of a snake venom phospholipase A 2 -like protein complexed to an inhibitor from Tabernaemontana catharinensis.

Borges, R.J.Cardoso, F.F.de Carvalho, C.de Marino, I.Pereira, P.S.Soares, A.M.Dal-Pai-Silva, M.Uson, I.Fontes, M.R.M.

(2023) Biochimie 206: 105-115

  • DOI: https://doi.org/10.1016/j.biochi.2022.10.011
  • Primary Citation Related Structures: 
    7ROX

  • PubMed Abstract: 

    Snake envenomation is an ongoing global health problem and tropical neglected disease that afflicts millions of people each year. The only specific treatment, antivenom, has several limitations that affects its proper distribution to the victims and its efficacy against local effects, such as myonecrosis. The main responsible for this consequence are the phospholipases A 2 (PLA 2 ) and PLA 2 -like proteins, such as BthTX-I from Bothrops jararacussu. Folk medicine resorts to plants such as Tabernaemontana catharinensis to palliate these and other snakebite effects. Here, we evaluated the effect of its root bark extract and one of its isolated compounds, 12-methoxy-4-methyl-voachalotine (MMV), against the in vitro paralysis and muscle damage induced by BthTX-I. Secondary and quaternary structures of BthTX-I were not modified by the interaction with MMV. Instead, this compound interacted in an unprecedented way with the region inside the toxin hydrophobic channel and promoted a structural change in Val31, loop 58-71 and Membrane Disruption Site. Thus, we hypothesize that MMV inhibits PLA 2 -like proteins by preventing entrance of fatty acid into the hydrophobic channel. These data may explain the traditional use of T. catharinensis extract and confirm MMV as a promising candidate to complement antivenom or a structural guide to develop more effective inhibitors.


  • Organizational Affiliation
    • Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, 18618-689, Brazil; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, 08028, Spain. Electronic address: rafael.borges@unesp.br.

Macromolecule Content 

  • Total Structure Weight: 27.92 kDa 
  • Atom Count: 2,078 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog bothropstoxin-I
A, B
121Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for Q90249 (Bothrops jararacussu)
Explore Q90249 
Go to UniProtKB:  Q90249
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90249
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
85O
(Subject of Investigation/LOI)

Query on 85O



Download:Ideal Coordinates CCD File
C [auth A]12-methoxy-Nb-methylvoachalotine
C24 H31 N2 O4
LXYOQAOPFZZHKS-ROHZQTCMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.167 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.92α = 90
b = 104.92β = 90
c = 64.44γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil16/24191-8
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil302883/2017-7

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary