3Q9W

Crystal structure of human CK2 alpha in complex with emodin at pH 8.5

• PDB DOI: https://doi.org/10.2210/pdb3Q9W/pdb

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


• Deposited: 2011-01-10 Released: 2012-01-11 
• Deposition Author(s): Battistutta, R., Ranchio, A., Papinutto, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Structural and functional analysis of the flexible regions of the catalytic alpha-subunit of protein kinase CK2

Papinutto, E., Ranchio, A., Lolli, G., Pinna, L.A., Battistutta, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.71 kDa 
• Atom Count: 3,139 
• Modelled 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
EMO	B [auth A]	3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE C15 H10 O5 RHMXXJGYXNZAPX-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
EMO	BindingDB:  3Q9W	Ki: min: 1500, max: 1900 (nM) from 3 assay(s)
		IC50: min: 580, max: 2000 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.337	α = 90
b = 45.619	β = 111.88
c = 62.613	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Battistutta, R., Ranchio, A., Papinutto, E.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description