4FAP

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: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.184 

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.,Sect.D 55: 736-744

  • Primary Citation of Related Structures:  

  • 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 associate ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506-BINDING PROTEIN
A
107Homo sapiensMutation(s): 0 
Gene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FKBP12-RAPAMYCIN ASSOCIATED PROTEIN
B
94Homo sapiensMutation(s): 0 
Gene Names: MTOR (FRAP, FRAP1, FRAP2, RAFT1, RAPT1)
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Go to Gene View: MTOR
Go to UniProtKB:  P42345
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARD
Query on ARD

Download SDF File 
Download CCD File 
A
C15-(R)-METHYLTHIENYL RAPAMYCIN
RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C55 H81 N O12 S
SDSGJAIFUCCAOV-MSLSVLDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.400α = 90.00
b = 52.100β = 90.00
c = 102.560γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
UCSD-systemdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description