7C44 | pdb_00007c44

Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a

PDB DOI: https://doi.org/10.2210/pdb7C44/pdb

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

Deposited: 2020-05-15 Released: 2020-06-17
Deposition Author(s): Cheng, X.Y., Zhang, B.L., Kuang, Z.K., Yang, J., Li, Z.C., Yu, J.P., Zhao, Z.T., Cao, C.Z., Su, Z.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)

Starting Models: experimental
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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 the p53-binding domain of human MdmX protein in complex with Nutlin3a

Cheng, X.Y., Zhang, B.L., Kuang, Z.K., Yang, J., Li, Z.C., Yu, J.P., Zhao, Z.T., Cao, C.Z., Su, Z.D.

To be published.

Macromolecule Content

Total Structure Weight: 11.89 kDa
Atom Count: 857
Modeled Residue Count: 96
Deposited Residue Count: 96
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Mdm4	A	96	Homo sapiens	Mutation(s): 0 Gene Names: MDM4, MDMX
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens) Explore O15151 Go to UniProtKB: O15151
PHAROS: O15151 GTEx: ENSG00000198625
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15151
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] 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]
O4B Query on O4B Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB: 7C44	Ki: min: 1599, max: 6.90e+4 (nM) from 2 assay(s)
		Kd: 6500 (nM) from 1 assay(s)
		IC50: 4300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.265 (Depositor), 0.264 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.47	α = 90
b = 47.47	β = 90
c = 91.19	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description