6HNW | pdb_00006hnw

Human protein kinase CK2 alpha in complex with coumestrol

• PDB DOI: https://doi.org/10.2210/pdb6HNW/pdb

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


• Deposited: 2018-09-17 Released: 2019-08-07 
• Deposition Author(s): Battistutta, R., Lolli, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Inhibitory Properties of ATP-Competitive Coumestrol and Boldine Are Correlated to Different Modulations of CK2 Flexibility.

Battistutta, R., Lolli, G.

(2019) J Nat Prod 82: 1014-1018

• PubMed: 30840451 
• DOI: https://doi.org/10.1021/acs.jnatprod.8b00889
• Primary Citation Related Structures: 
  6HNW, 6HNY


• PubMed Abstract: 
  

  Casein kinase 2 (CK2) is an anti-apoptotic cancer-sustaining protein kinase. Its crystallographic structures with the natural compounds coumestrol, a phytoestrogen, and boldine, an alkaloid, are reported. Coumestrol shows different inhibitory activity against the isolated catalytic α-subunit and the α ₂ β ₂ holoenzyme and is able to discriminate between two conformations of the hinge/αD region, whose intrinsic flexibility is a relevant selectivity determinant among kinases. Boldine explores a small cavity at the bottom of the ATP-binding pocket through a local deviation from planarity, a unique case among CK2 inhibitors. The two compounds have different impacts on protein flexibility, which correlate with their different properties.

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Organizational Affiliation: 
• Department of Chemical Sciences , University of Padua and Institute of Biomolecular Chemistry, National Research Council (CNR) , 35131 Padua , Italy.
Department of Cellular, Computational and Integrative Biology - CIBIO , University of Trento , Via Sommarive 9 , 38123 Povo (TN) , Italy.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.61 kDa 
• Atom Count: 3,018 
• Modeled Residue Count: 328 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	336	Homo sapiens	Mutation(s): 0  Gene Names: CSNK2A1, CK2A1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CUE	B [auth A]	Coumestrol C15 H8 O5 ZZIALNLLNHEQPJ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
CUE	BindingDB:  6HNW	Ki: min: 7670, max: 7670 (nM) from 2 assay(s)
		IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.329	α = 90
b = 46.274	β = 112.02
c = 63.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Battistutta, R., Lolli, G.

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description