3EOV

Crystal structure of cyclophilin from Leishmania donovani ligated with cyclosporin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of Cyclophilin from Leishmania Donovani Bound to Cyclosporin at 2.6 A Resolution: Correlation between Structure and Thermodynamic Data.

Venugopal, V.Datta, A.K.Bhattacharyya, D.Dasgupta, D.Banerjee, R.

(2009) Acta Crystallogr.,Sect.D 65: 1187

  • DOI: 10.1107/S0907444909034234

  • PubMed Abstract: 
  • Drug development against Leishmania donovani, the pathogen that causes visceral leishmaniasis in humans, is currently an active area of research given the widespread prevalence of the disease and the emergence of resistant strains. The immunosuppress ...

    Drug development against Leishmania donovani, the pathogen that causes visceral leishmaniasis in humans, is currently an active area of research given the widespread prevalence of the disease and the emergence of resistant strains. The immunosuppressive drug cyclosporin is known to have antiparasitic activity against a variety of pathogens. The receptor for cyclosporin is the protein cyclophilin, which is a ubiquitous peptidylprolyl isomerase. The crystal structure of cyclophilin from L. donovani complexed with cyclosporin has been solved at 2.6 A resolution. The thermodynamic parameters of the interaction have been determined using spectroscopic and calorimetric techniques. A detailed effort has been made to predict the thermodynamic parameters of binding from computations based on the three-dimensional crystal structure. These results were in good agreement with the corresponding experimental values. Furthermore, the structural and biophysical results have been discussed in the context of leishmanial drug resistance and could also set the stage for the design of potent non-immunosuppressive antileishmanials.


    Related Citations: 
    • Structure of Cyclophilin from Leishmania Donovani at 1.97 A Resolution.
      Venugopal, V.,Sen, B.,Datta, A.K.,Banerjee, R.
      (2007) Acta Crystallogr.,Sect.F 63: 60
    • Lack of Abundance of Cytoplasmic Cyclosporin A- Binding Protein Renders Free-Living Leishmania Donovani Resistant to Cyclosporin A.
      Dutta, M.,Delhi, P.,Sinha, K.M.,Banerjee, R.,Datta, A.K.
      (2001) J.Biol.Chem. 276: 19294


    Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Bidhannagar, Kolkata 700 064, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
A, B
172Leishmania donovaniGene Names: CYP
EC: 5.2.1.8
Find proteins for Q9U9R3 (Leishmania donovani)
Go to UniProtKB:  Q9U9R3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLOSPORIN A
C, D
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
C,DCyclosporin ACyclic peptide / Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.810α = 90.00
b = 83.125β = 103.03
c = 73.580γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other