6GXY

Tryparedoxin from Trypanosoma brucei in complex with CFT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes.

Wagner, A.Le, T.A.Brennich, M.Klein, P.Bader, N.Diehl, E.Paszek, D.Weickhmann, A.K.Dirdjaja, N.Krauth-Siegel, R.L.Engels, B.Opatz, T.Schindelin, H.Hellmich, U.A.

(2019) Angew. Chem. Int. Ed. Engl. 58: 3640-3644

  • DOI: 10.1002/anie.201810470
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from ...

    Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from Trypanosoma brucei is the essential oxidoreductase in the parasite's hydroperoxide-clearance cascade. In vitro and in vivo functional assays show that a small, selective inhibitor efficiently inhibits Tpx. With X-ray crystallography, SAXS, analytical SEC, SEC-MALS, MD simulations, ITC, and NMR spectroscopy, we show how covalent binding of this monofunctional inhibitor leads to Tpx dimerization. Intra- and intermolecular inhibitor-inhibitor, protein-protein, and inhibitor-protein interactions stabilize the dimer. The behavior of this efficient antitrypanosomal molecule thus constitutes an exquisite example of chemically induced dimerization with a small, monovalent ligand that can be exploited for future drug design.


    Organizational Affiliation

    Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Johann-Joachim-Becherweg 31, 55128, Mainz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryparedoxin
A, B, C
146Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for O77404 (Trypanosoma brucei brucei)
Go to UniProtKB:  O77404
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFN
Query on FFN

Download SDF File 
Download CCD File 
A, B, C
5-(4-fluorophenyl)-2-methyl-3~{H}-thieno[2,3-d]pyrimidin-4-one
C13 H9 F N2 O S
PEYKEBUFADUZJK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.630α = 90.00
b = 96.009β = 96.57
c = 48.276γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references