5UMM

CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3

• PDB DOI: https://doi.org/10.2210/pdb5UMM/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2017-01-27 Released: 2018-01-31 
• Deposition Author(s): Pazgier, M., Gohain, N., Tolbert, W.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.231 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for p53 activation

Pazgier, M., Gohain, N., Tolbert, W.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.21 kDa 
• Atom Count: 1,646 
• Modelled Residue Count: 187 
• Deposited Residue Count: 194 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, C	85	Homo sapiens	Mutation(s): 0  EC: 2.3.2.27
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
PEPTIDE INHIBITOR M3	B, D	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.231 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.567	α = 90
b = 87.895	β = 92.3
c = 36.576	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Pazgier, M., Gohain, N., Tolbert, W.D.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Advisory, Author supporting evidence, Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2020-10-21
  Changes: Database references, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description