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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.243 (Depositor), 0.253 (DCC)
R-Value Work:
0.218 (Depositor), 0.226 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZXF

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Cheng, X.Y., Su, Z.D.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUT Query on NUT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB: 5ZXF	Ki: min: 6.4, max: 150 (nM) from 11 assay(s)
		Kd: min: 20, max: 700 (nM) from 3 assay(s)
		IC50: min: 10, max: 3.00e+4 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.243 (Depositor), 0.253 (DCC)
R-Value Work: 0.218 (Depositor), 0.226 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	2016ACA128

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.