3V3B

Structure of the Stapled p53 Peptide Bound to Mdm2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the stapled p53 peptide bound to Mdm2.

Baek, S.Kutchukian, P.S.Verdine, G.L.Huber, R.Holak, T.A.Lee, K.W.Popowicz, G.M.

(2012) J.Am.Chem.Soc. 134: 103-106

  • DOI: 10.1021/ja2090367

  • PubMed Abstract: 
  • Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction tha ...

    Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction that restore the functional p53 constitute potential nongenotoxic anticancer agents with a novel mode of action. We present here a 2.0 Å resolution structure of the Mdm2 protein with a bound stapled p53 peptide. Such peptides, which are conformationally and proteolytically stabilized with all-hydrocarbon staples, are an emerging class of biologics that are capable of disrupting protein-protein interactions and thus have broad therapeutic potential. The structure represents the first crystal structure of an i, i + 7 stapled peptide bound to its target and reveals that rather than acting solely as a passive conformational brace, a staple can intimately interact with the surface of a protein and augment the binding interface.


    Organizational Affiliation

    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
88Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SAH-p53-8 stapled-peptide
C, D
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000857
Query on PRD_000857
CSAH-p53-8 stapled-peptidePeptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.400α = 90.00
b = 42.410β = 90.86
c = 50.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MAR345dtbdata collection
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-03-21
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2013-11-13
    Type: Other