Macromolecule Content

Total Structure Weight: 34.92 kDa
Atom Count: 2430
Modelled Residue Count: 280
Deposited Residue Count: 291
Unique protein chains: 2

3LNJ

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

DOI: 10.2210/pdb3LNJ/pdb

Classification: LIGASE/LIGASE INHIBITOR
Mutation(s): No

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

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1002/anie.201000329
Primary Citation of Related Structures:
3LNJ

Macromolecules

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(by identity cutoff) | Structure

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
Find proteins for Q00987 (Homo sapiens) Explore Q00987 Go to UniProtKB: Q00987
NIH Common Fund Data Resources
PHAROS: Q00987 GTEx: ENSG00000135679
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E]	I [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C]	H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000808 Query on 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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-02-02
Released Date: 2010-03-09

Deposition Author(s):

Pazgier, M.

Lu, W.

Revision History (Full details and data files)

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

Prepare Data

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Deposit Data

Deposition Help & Resources

177426 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3LNJ

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

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

Entity ID: 1

NIH Common Fund Data Resources

Protein Feature View

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Entity ID: 2