Crystal structure of human cyclophilin D at 1.7 A resolution

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

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This is version 1.4 of the entry. See complete history


Crystal Engineering Yields Crystals of Cyclophilin D Diffracting to 1.7 A Resolution

Schlatter, D.Thoma, R.Kueng, E.Stihle, M.Mueller, F.Boroni, E.Hennig, M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 513-519

  • DOI: https://doi.org/10.1107/S0907444905003070
  • Primary Citation of Related Structures:  
    2BIT, 2BIU

  • PubMed Abstract: 

    In the pharmaceutical industry, knowledge of the three-dimensional structure of a specific target facilitates the drug-discovery process. Despite possessing favoured analytical properties such as high purity and monodispersion in light scattering, some proteins are not capable of forming crystals suitable for X-ray analysis. Cyclophilin D, an isoform of cyclophilin that is expressed in the mitochondria, was selected as a drug target for the treatment of cardiac disorders. As the wild-type enzyme defied all attempts at crystallization, protein engineering on the enzyme surface was performed. The K133I mutant gave crystals that diffracted to 1.7 A resolution using in-house X-ray facilities and were suitable for soaking experiments. The crystals were very robust and diffraction was maintained after soaking in 25% DMSO solution: excellent conditions for the rapid analysis of complex structures including crystallographic fragment screening.

  • Organizational Affiliation

    F. Hoffmann-La Roche Ltd, Pharmaceutical Research Discovery, CH-4070 Basel, Switzerland. daniel.schlatter@roche.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASEA [auth X]165Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
PHAROS:  P30405
GTEx:  ENSG00000108179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30405
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.165α = 90
b = 57.165β = 90
c = 87.227γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description