3FAP

ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 

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This is version 1.2 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:  
    2FAP, 1NSG, 4FAP, 3FAP

  • 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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-BINDING PROTEIN A107Homo sapiensMutation(s): 0 
Gene Names: HUMAN HIPPOCAMPAL CDNA LIBRARY SOURCE 8 (CLONTECH, PALO ALTO, CA), FKBP1A, FKBP1, FKBP12
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
NIH Common Fund Data Resources
PHAROS:  P62942
GTEx:  ENSG00000088832
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FKBP12-RAPAMYCIN ASSOCIATED PROTEIN B94Homo sapiensMutation(s): 0 
Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
NIH Common Fund Data Resources
PHAROS:  P42345
GTEx:  ENSG00000198793
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARD
Query on ARD
Download Ideal Coordinates CCD File 
A
C15-(R)-METHYLTHIENYL RAPAMYCIN
C55 H81 N O12 S
SDSGJAIFUCCAOV-MSLSVLDMSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.4α = 90
b = 51.72β = 90
c = 101.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1999-05-06 
  • Released Date: 2000-09-13 
    • Deposition Author(s): Liang, J., Clardy, J.

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance