Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.80 kDa 
• Atom Count: 860 
• Residue Count: 95 
• Unique protein chains: 2

3JZS

Human MDM2 liganded with a 12mer peptide inhibitor (pDIQ)

• DOI: 10.2210/pdb3JZS/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-24 Released: 2009-11-10 
• Deposition Author(s): Schonbrunn, E., Phan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.253 
• R-Value Work: 0.215 

Literature

Structure-based design of high affinity peptides inhibiting the interaction of p53 with MDM2 and MDMX.

Phan, J., Li, Z., Kasprzak, A., Li, B., Sebti, S., Guida, W., Schonbrunn, E., Chen, J.

(2010) J Biol Chem 285: 2174-2183

• PubMed: 19910468 
• DOI: 10.1074/jbc.M109.073056
• Structures With Same Primary Citation


• PubMed Abstract: 
  

MDM2 and MDMX function as key regulators of p53 by binding to its N terminus, inhibiting its transcriptional activity, and promoting degradation. MDM2 and MDMX overexpression or hyperactivation directly contributes to the loss of p53 function during the development of nearly 50% of human cancers. Recent studies showed that disrupting p53-MDM2 and p53-MDMX interactions can lead to robust activation of p53 but also revealed a need to develop novel dual specific or MDMX-specific inhibitors. Using phage display we identified a 12-residue peptide (pDI) with inhibitory activity against MDM2 and MDMX. The co-crystal structures of the pDI and a single mutant derivative (pDI6W) liganded with the N-terminal domains of human MDMX and MDM2 served as the basis for the design of 11 distinct pDI-derivative peptides that were tested for inhibitory potential. The best derivative (termed pDIQ) contained four amino acid substitutions and exhibited a 5-fold increase in potency over the parent peptide against both MDM2 (IC(50) = 8 nm) and MDMX (IC(50) = 110 nm). Further structural studies revealed key molecular features enabling the high affinity binding of the pDIQ to these proteins. These include large conformational changes of the pDIQ to reach into a hydrophobic site unique to MDMX. The findings suggest new strategies toward the rational design of small molecule inhibitors efficiently targeting MDMX.

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Organizational Affiliation: 

Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase Mdm2	A	86	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987 GTEx  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
pDIQ peptide (12mer)	P	12	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	P	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.253 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.81	α = 90
b = 50.593	β = 90
c = 39.204	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-24 
• Released Date: 2009-11-10 
Deposition Author(s): Schonbrunn, E., Phan, J.

Revision History 

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance