7KJM

CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA)

• PDB DOI: https://doi.org/10.2210/pdb7KJM/pdb

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


• Deposited: 2020-10-26 Released: 2021-11-17 
• Deposition Author(s): Tolbert, W.D., Pazgier, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.210 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA)

Tolbert, W.D., Pazgier, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 23.72 kDa 
• Atom Count: 1,866 
• Modelled Residue Count: 193 
• 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
D-PMI-omega	B, D	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
IPA	F [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	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_002455	B, D	D-PMI-omega	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.210 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.355	α = 90
b = 38.451	β = 90
c = 138.022	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Tolbert, W.D., Pazgier, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI129769

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection