1FAP | pdb_00001fap

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.299 (Depositor) 
  • R-Value Work: 
    0.193 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FAP

This is version 1.3 of the entry. See complete history

Literature

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: 239-242

  • DOI: https://doi.org/10.1126/science.273.5272.239
  • Primary Citation Related Structures: 
    1FAP

  • PubMed Abstract: 

    Rapamycin, a potent immunosuppressive agent, binds two proteins: the FK506-binding protein (FKBP12) and the FKBP-rapamycin-associated protein (FRAP). A crystal structure of the ternary complex of human FKBP12, rapamycin, and the FKBP12-rapamycin-binding (FRB) domain of human FRAP at a resolution of 2.7 angstroms revealed the two proteins bound together as a result of the ability of rapamycin to occupy two different hydrophobic binding pockets simultaneously. The structure shows extensive interactions between rapamycin and both proteins, but fewer interactions between the proteins. The structure of the FRB domain of FRAP clarifies both rapamycin-independent and -dependent effects observed for mutants of FRAP and its homologs in the family of proteins related to the ataxia-telangiectasia mutant gene product, and it illustrates how a small cell-permeable molecule can mediate protein dimerization.


  • Organizational Affiliation
    • Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.

Macromolecule Content 

  • Total Structure Weight: 24.24 kDa 
  • Atom Count: 1,727 
  • Modeled Residue Count: 202 
  • Deposited Residue Count: 202 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FK506-BINDING PROTEIN107Homo sapiensMutation(s): 0 
Gene Names: HUMAN HIPPOCAMPAL CDNA LIBRARY
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FRAP95Homo sapiensMutation(s): 0 
Gene Names: HUMAN HIPPOCAMPAL CDNA LIBRARY
EC: 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
PHAROS:  P42345
GTEx:  ENSG00000198793 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42345
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RAP

Query on RAP



Download:Ideal Coordinates CCD File
C [auth A]RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.299 (Depositor) 
  • R-Value Work:  0.193 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.63α = 90
b = 52.14β = 90
c = 102.53γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-23
    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: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other