1QNG

Plasmodium falciparum Cyclophilin complexed with Cyclosporin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Three-Dimensional Structure of a Plasmodium Falciparum Cyclophilin in Complex with the Potent Anti-Malarial Cyclosporin A

Peterson, M.R.Hall, D.R.Berriman, M.Leonard, G.A.Fairlamb, A.H.Hunter, W.N.

(2000) J.Mol.Biol. 298: 123

  • DOI: 10.1006/jmbi.2000.3633
  • Primary Citation of Related Structures:  1QNH

  • PubMed Abstract: 
  • Cyclosporin A (CsA) is a potent anti-malarial compound in vitro and in vivo in mice though better known for its immunosuppressive properties in humans. Crystal structures of wild-type and a double mutant Plasmodium falciparum cyclophilin (PfCyP19 and ...

    Cyclosporin A (CsA) is a potent anti-malarial compound in vitro and in vivo in mice though better known for its immunosuppressive properties in humans. Crystal structures of wild-type and a double mutant Plasmodium falciparum cyclophilin (PfCyP19 and mPfCyP19) complexed with CsA have been determined using diffraction terms to a resolution of 2.1 A (1 A=0.1 nm). The wild-type has a single PfCyP19/CsA complex per asymmetric unit in space group P1 and refined to an R-work of 0.15 and R-free of 0.19. An altered cyclophilin, with two accidental mutations, Phe120 to Leu in the CsA binding pocket and Leu171 to Trp at the C terminus, presents two complexes per asymmetric unit in the orthorhombic space group P2(1)2(1)2. This refined to an R-work of 0.18 and R-free 0.21. The mutations were identified from the crystallographic analysis and the C-terminal alteration helps to explain the different crystal forms obtained. PfCyP19 shares approximately 61 % sequence identity with human cyclophilin A (hCyPA) and the structures are similar, consisting of an eight-stranded antiparallel beta-barrel core capped by two alpha-helices. The fold creates a hydrophobic active-site, the floor of which is formed by side-chains of residues from four antiparallel beta-strands and the walls from loops and turns. We identified C-H.O hydrogen bonds between the drug and protein that may be an important feature of cyclophilins and suggest a general mode of interaction between hydrophobic molecules. Comparisons with cyclophilin-dipeptide complexes suggests that a specific C-H.O hydrogen bonding interaction may contribute to ligand binding. Residues Ser106, His99 and Asp130, located close to the active site and conserved in most cyclophilins, are arranged in a manner reminiscent of a serine protease catalytic triad. A Ser106Ala mutant was engineered to test the hypothesis that this triad contributes to CyP function. Mutant and wild-type enzymes were found to have similar catalytic properties.


    Related Citations: 
    • Detailed Characterization of a Cyclophilin from the Human Malaria Parasite Plasmodium Falciparum
      Berriman, M.,Fairlamb, A.H.
      (1998) Biochem.J. 334: 437


    Organizational Affiliation

    Department of Biochemistry The Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
A
170Plasmodium falciparumEC: 5.2.1.8
Find proteins for Q25756 (Plasmodium falciparum)
Go to UniProtKB:  Q25756
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLOSPORIN A
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
DCyclosporin ACyclic peptide / Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.460α = 61.08
b = 37.690β = 62.70
c = 37.990γ = 85.08
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2014-03-12
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2017-07-05
    Type: Data collection