8J81

MDM2 bound with a peptoid

• PDB DOI: https://doi.org/10.2210/pdb8J81/pdb

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


• Deposited: 2023-04-28 Released: 2024-05-01 
• Deposition Author(s): Yokomine, M., Fukuda, Y., Ago, H., Matsuura, H., Ueno, G., Nagatoishi, S., Yamamoto, M., Tsumoto, K., Jumpei, M., Sando, S.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.190 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

A structural and physicochemical study of how a peptoid binds to a protein

Yokomine, M., Jumpei, M., Fukuda, Y., Ueda, T., Takeuchi, K., Suzuki, K., Maeda, S., Ago, H., Matsuura, H., Ueno, G., Yamamoto, M., Senoo, A., Nagatoishi, S., Tsumoto, K., Sando, S.

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 Evidence: isothermal titration calorimetry, surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 12.61 kDa 
• Atom Count: 945 
• Modelled Residue Count: 87 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	100	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
GTEx:  ENSG00000135679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UAC (Subject of Investigation/LOI)	B [auth A]	(2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide C45 H65 Cl N8 O6 GPZUKWJTFXMPJR-ZTTXAYQISA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.190 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.521	α = 90
b = 45.815	β = 90
c = 63.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Yokomine, M., Fukuda, Y., Ago, H., Matsuura, H., Ueno, G., Nagatoishi, S., Yamamoto, M., Tsumoto, K., Jumpei, M., Sando, S.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101070
Japan Science and Technology	Japan	JPMJCR21N5
Japan Science and Technology	Japan	JPMJPR21AF
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121033

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release