5ZXF | pdb_00005zxf

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a

• PDB DOI: https://doi.org/10.2210/pdb5ZXF/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-05-19 Released: 2018-08-22 
• Deposition Author(s): Cheng, X.Y., Su, Z.D., Pi, N., Cao, C.Z., Zhao, Z.T., Zhou, J.J., Chen, R., Kuang, Z.K., Huang, Y.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a

Cheng, X.Y., Su, Z.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.85 kDa 
• Atom Count: 797 
• Modeled Residue Count: 87 
• Deposited Residue Count: 87 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	87	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
PHAROS:  Q00987 GTEx:  ENSG00000135679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUT	B [auth A]	4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one C30 H30 Cl2 N4 O4 BDUHCSBCVGXTJM-WUFINQPMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB:  5ZXF	Ki: min: 6.4, max: 280 (nM) from 14 assay(s)
		Kd: min: 35, max: 700 (nM) from 4 assay(s)
		IC50: min: 10, max: 3.00e+4 (nM) from 15 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.575	α = 90
b = 43.222	β = 90
c = 53.853	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Cheng, X.Y., Su, Z.D., Pi, N., Cao, C.Z., Zhao, Z.T., Zhou, J.J., Chen, R., Kuang, Z.K., Huang, Y.Q.

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Funding Organization	Location	Grant Number
	China	2016ACA128

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references