1FKJ

ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSANT COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin.

Wilson, K.P.Yamashita, M.M.Sintchak, M.D.Rotstein, S.H.Murcko, M.A.Boger, J.Thomson, J.A.Fitzgibbon, M.J.Black, J.R.Navia, M.A.

(1995) Acta Crystallogr D Biol Crystallogr 51: 511-521

  • DOI: 10.1107/S0907444994014514
  • Primary Citation of Related Structures:  
    1FKL, 1FKK, 1FKJ

  • PubMed Abstract: 
  • FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase activity ...

    FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase activity of calcineurin. Rapamycin (sirolimus), which is itself an immunosuppressant by a different mechanism, completes with FK506 for binding to FKBP12 and thereby acts as an antagonist of calcineurin inhibition. We have solved the X-ray structure of unliganded FKBP12 and of FKBP12 in complex with FK506 and with rapamycin; these structures show localized differences in conformation and mobility in those regions of the protein that are known, by site-directed mutagenesis, to be involved in calcineurin inhibition. A comparison of 16 additional X-ray structures of FKBP12 in complex with FKBP12-binding ligands, where those structures were determined from different crystal forms with distinct packing arrangements, lends significance to the observed structural variability and suggests that it represents an intrinsic functional characteristic of the protein. Similar differences have been observed for FKBP12 before, but were considered artifacts of crystal-packing interactions. We suggest that immunosuppressive ligands express their differential effects in part by modulating the conformation of FKBP12, in agreement with mutagenesis experiments on the protein, and not simply through differences in the ligand structures themselves.


    Related Citations: 
    • X-Ray Structure of Calcineurin Inhibited by the Immunophilin-Immunosuppressant Fkbp12-Fk506 Complex
      Griffith, J.P., Kim, J.L., Kim, E.E., Sintchak, M.D., Thomson, J.A., Fitzgibbon, M.J., Fleming, M.A., Caron, P.R., Hsiao, K., Navia, M.A.
      (1995) Cell 82: 507
    • Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes. Crystallographic and Functional Analysis
      Rotonda, J., Burbaum, J.J., Chan, H.K., Marcy, A.I., Becker, J.W.
      (1993) J Biol Chem 268: 7607
    • Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818
      Becker, J.W., Rotonda, J., Mckeever, B.M., Chan, H.K., Marcy, A.I., Wiederrecht, G., Hermes, J.D., Springer, J.P.
      (1993) J Mol Biol 268: 11335
    • Atomic Structures of Human Immunophilin Fkbp-12 Complexes with Fk506 and Rapamycin
      Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J.
      (1993) J Mol Biol 229: 105
    • Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
      Van Duyne, G.D., Standaert, R.F., Schreiber, S.L., Clardy, J.
      (1991) J Am Chem Soc 113: 7433
    • Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex
      Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J.
      (1991) Science 252: 839

    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139-4211, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FK506 BINDING PROTEIN A107Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
NIH Common Fund Data Resources
PHAROS:  P62942
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download Ideal Coordinates CCD File 
A
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FK5IC50:  14   nM  BindingDB
FK5IC50:  2.299999952316284   nM  BindingDB
FK5EC50:  0.8999999761581421   nM  BindingDB
FK5Ki:  0.4000000059604645   nM  BindingDB
FK5IC50:  1000   nM  BindingDB
FK5Kd:  0.20000000298023224   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.1α = 90
b = 58.1β = 90
c = 55.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MANUFACTURERdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance