3EOV

Crystal structure of cyclophilin from Leishmania donovani ligated with cyclosporin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 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 D Biol Crystallogr 65: 1187

  • DOI: 10.1107/S0907444909034234
  • Primary Citation of Related Structures:  
    3EOV

  • 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 immunosuppressive drug cyclosporin is known to have antiparasitic activity against a variety of pathogens ...

    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 Struct Biol Cryst Commun 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASEA, B172Leishmania donovaniMutation(s): 0 
Gene Names: CYP
EC: 5.2.1.8
UniProt
Find proteins for Q9U9R3 (Leishmania donovani)
Explore Q9U9R3 
Go to UniProtKB:  Q9U9R3
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN AC, D11Tolypocladium inflatumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
C, DL-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
C, DL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
C, DL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
C, DL-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
C, DPEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
C, DCyclosporin ACyclic peptide /  Immunosuppressant Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.81α = 90
b = 83.125β = 103.03
c = 73.58γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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