3LNJ

Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)

• PDB DOI: https://doi.org/10.2210/pdb3LNJ/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2010-02-02 Released: 2010-03-09 
• Deposition Author(s): Pazgier, M., Lu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

A left-handed solution to peptide inhibition of the p53-MDM2 interaction.

Liu, M., Pazgier, M., Li, C., Yuan, W., Li, C., Lu, W.

(2010) Angew Chem Int Ed Engl 49: 3649-3652

• PubMed: 20449836 
• DOI: https://doi.org/10.1002/anie.201000329
• Primary Citation of Related Structures:  
  3LNJ


• PubMed Abstract: 
  

  [Image: see text] Throwing tumors a left hook punch: The oncoprotein MDM2 negatively regulates the activity and stability of the tumor suppressor protein p53, and is an important molecular target for anticancer therapy. Mirror image phage display identifies a high-affinity D-peptide ligand of MDM2 that can be developed into a potent and protease-resistant p53 activator with potential antitumor activity.

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Organizational Affiliation: 

Institute of Human Virology, University of Maryland School of Medicine, 725 W. Lombard St., Baltimore, MD 21201, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.92 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 280 
• Deposited Residue Count: 291 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, C, E	85	N/A	Mutation(s): 0  EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-peptide inhibitor	B, D, F	12	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000808	B, D, F	D-peptide inhibitor	Oligopeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.976	α = 90
b = 213.478	β = 90
c = 45.536	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Pazgier, M., Lu, W.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary