Crystal Structure of the N-terminal domain of human FKBP52

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.219 

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This is version 1.4 of the entry. See complete history


Structure of the N-terminal domain of human FKBP52.

Li, P.Ding, Y.Wu, B.Shu, C.Shen, B.Rao, Z.

(2003) Acta Crystallogr D Biol Crystallogr 59: 16-22

  • DOI: https://doi.org/10.1107/s0907444902017523
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    FKBP52 is a member of the FK506-binding protein family (FKBPs). The N-terminal domain of FKBP52 (FKBP52-N; residues 1-140) is responsible for peptidyl-prolyl isomerase activity and binding of FK506. Here, the crystal structure of FKBP52-N has been determined by molecular replacement to 2.4 A. FKBP52-N is defined by a six-stranded antiparallel beta-sheet wrapping with a right-handed twist around a short alpha-helix, an architecture similar to that of FKBP12. FKBP52-N is able to bind FK506 in a similar way to FKBP12. The variability in two loop regions (residues 70-76 and 108-127) is the principal reason for the specificity differences between FKBP52-N and FKBP12. The Pro120 change corresponding to Gly89 in FKBP12 limits the conformational adaptation between the loop (residues 108-127) and FK506 and decreases the FK506 affinity, while the Lys121 substitution corresponding to Ile90 of FKBP12 destroys a key interaction between FKBP52-N and calcineurin. It can be inferred from the locations of strictly conserved amino acids in the polypeptide chain that the maintenance of the overall conformation of the PPIase domains of FKBPs is essential for the PPIase activity. The N-terminal region and beta-sheets of FKBP52-N forms a hydrophobic patch which may be responsible for the binding of target proteins such as dynein or PAHX.

  • Organizational Affiliation

    MOE Laboratory of Protein Science and Laboratory of Structural Biology, Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
140Homo sapiensMutation(s): 0 
Gene Names: FKBP4
UniProt & NIH Common Fund Data Resources
Find proteins for Q02790 (Homo sapiens)
Explore Q02790 
Go to UniProtKB:  Q02790
PHAROS:  Q02790
GTEx:  ENSG00000004478 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02790
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.805α = 90
b = 58.362β = 98.31
c = 70.904γ = 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: 2002-12-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description