5Z02

Crystal structure of HIS6-tagged Mdm2 with nutlin-3a

PDB DOI: https://doi.org/10.2210/pdb5Z02/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-12-18 Released: 2018-01-03
Deposition Author(s): Su, Z.D., Cheng, X.Y., Chen, R., Pi, N.
Funding Organization(s): Hubei University of Tehnology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.254
R-Value Work: 0.226
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of HIS6-tagged Mdm2 with nutlin-3a

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

To be published.

Macromolecule Content

Total Structure Weight: 13.54 kDa
Atom Count: 802
Modelled Residue Count: 88
Deposited Residue Count: 110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	110	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 (Subject of Investigation/LOI) Query on NUT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 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: 5Z02	Ki: min: 6.4, max: 140 (nM) from 11 assay(s)
		Kd: min: 35, max: 700 (nM) from 3 assay(s)
		IC50: min: 10, max: 3.00e+4 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.254
R-Value Work: 0.226
R-Value Observed: 0.227
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.5	α = 90
b = 42.99	β = 90
c = 54.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BUCCANEER	phasing
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Hubei University of Tehnology	China	--

Revision History (Full details and data files)

Version 1.0: 2018-01-03
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.