5D75

Crystal structure of Human FKBD25 in complex with FK506

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

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This is version 2.1 of the entry. See complete history. 


Literature

Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506.

Prakash, A., Rajan, S., Yoon, H.S.

(2016) Protein Sci 25: 905-910

  • DOI: https://doi.org/10.1002/pro.2875
  • Primary Citation of Related Structures:  
    5D75

  • PubMed Abstract: 

    Human FKBP25 (hFKBP25) is a nuclear immunophilin and interacts with several nuclear proteins, hence involving in many nuclear events. Similar to other FKBPs, FK506 binding domain (FKBD) of hFKBP25 also binds to immunosuppressive drugs such as rapamycin and FK506, albeit with a lower affinity for the latter. The molecular basis underlying this difference in affinity could not be addressed due to the lack of the crystal structure of hFKBD25 in complex with FK506. Here, we report the crystal structure of hFKBD25 in complex with FK506 determined at 1.8 Å resolution and its comparison with the hFKBD25-rapamycin complex, bringing out the microheterogeneity in the mode of interaction of these drugs, which could possibly explain the lower affinity for FK506.

    • Organizational Affiliation: 

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP3124Homo sapiensMutation(s): 0 
Gene Names: FKBP3, FKBP25
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q00688 (Homo sapiens)
Explore Q00688 
Go to UniProtKB:  Q00688
PHAROS:  Q00688
GTEx:  ENSG00000100442 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00688
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5
Download Ideal Coordinates CCD File 
B [auth A]8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
JEF
Query on JEF
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500)
C30 H63 N O10
ICCXIDTYQFYPNV-RUMGZKRTSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FK5 Binding MOAD:  5D75 Ki: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.784α = 90
b = 74.784β = 90
c = 44.618γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 2.0: 2018-10-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description