1NSG

THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution.

Liang, J.Choi, J.Clardy, J.

(1999) Acta Crystallogr D Biol Crystallogr 55: 736-744

  • DOI: 10.1107/s0907444998014747
  • Primary Citation of Related Structures:  
    4FAP, 1NSG, 3FAP, 2FAP

  • PubMed Abstract: 
  • The structure of the FKBP12-rapamycin-FRB ternary complex has now been refined at 2.2 A resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12-rapamycin binding (FRB) domain of FKBP12-rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity ...

    The structure of the FKBP12-rapamycin-FRB ternary complex has now been refined at 2.2 A resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12-rapamycin binding (FRB) domain of FKBP12-rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity. The conformation of rapamycin in the ternary complex is very similar to that observed in the FKBP12-rapamycin binary complex, with an r.m.s. difference of only 0.30 A. However, a slight (9 degrees ) rotation repositions the FRB-binding face of rapamycin in the ternary complex. There are extensive rapamycin-protein interactions and relatively few interactions between the two protein partners FKBP12 and FRB, these interactions mainly involving residues in the 40s and 80s loops of FKBP12 and alpha1 and alpha4 of FRB. The high-resolution refinement has revealed the crucial role of several buried waters in the formation of the ternary complex.


    Related Citations: 
    • Structure of the Fkbp12-Rapamycin Complex Interacting with the Binding Domain of Human Frap
      Choi, J., Chen, J., Schreiber, S.L., Clardy, J.
      (1996) Science 273: 239

    Organizational Affiliation

    Department of Chemistry, Cornell University, Ithaca, New York 14853-1301, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-BINDING PROTEINA107Homo sapiensMutation(s): 0 
Gene Names: HUMAN HIPPOCAMPAL CDNA LIBRARYFKBP1AFKBP1FKBP12
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FKBP-RAPAMYCIN ASSOCIATED PROTEIN (FRAP)B94Homo sapiensMutation(s): 0 
Gene Names: HUMAN HIPPOCAMPAL CDNA LIBRARYMTORFRAPFRAP1FRAP2RAFT1RAPT1
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
NIH Common Fund Data Resources
PHAROS:  P42345
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAD
Query on RAD

Download Ideal Coordinates CCD File 
C [auth A]C49-METHYL RAPAMYCIN
C52 H81 N O13
GPZGXSFHPLUMHE-JQEUAWNDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RADEC50:  200   nM  BindingDB
RADKi:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.3α = 90
b = 52.4β = 90
c = 102γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-09-18
    Changes: Derived calculations