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 

wwPDB Validation 3D Report Full Report


This is version 2.0 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: 10.1002/pro.2875

  • 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 rapamyc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP3
A
124Homo sapiensMutation(s): 0 
Gene Names: FKBP3 (FKBP25)
EC: 5.2.1.8
Find proteins for Q00688 (Homo sapiens)
Go to Gene View: FKBP3
Go to UniProtKB:  Q00688
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download SDF File 
Download CCD File 
A
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
JEF
Query on JEF

Download SDF File 
Download CCD File 
A
O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500)
JEFFAMINE
C30 H63 N O10
ICCXIDTYQFYPNV-RUMGZKRTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.784α = 90.00
b = 74.784β = 90.00
c = 44.618γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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