9I13 | pdb_00009i13

Human protein kinase CK2 alpha in complex with TN19

• PDB DOI: https://doi.org/10.2210/pdb9I13/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2025-02-26 
• Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Lolli, G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Switching off CK2-mediated activation of survivin offers new therapeutic opportunities in neuroblastoma

Cazzanelli, G., Dalle Vedove, A., Broso, F., Burigotto, M., Zasso, J., Aiello, G., Zonta, F., Astolfi, A., Barreca, M.L., Ruzzene, M., Tiberi, L., Fava, L.L., Quattrone, A., Lolli, G.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40 kDa 
• Atom Count: 3,067 
• Modeled Residue Count: 328 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	328	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IYY (Subject of Investigation/LOI)	D [auth A]	(2~{Z},5~{Z})-2-(3-fluorophenyl)imino-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-1,3-thiazolidin-4-one C17 H13 F N2 O3 S SRBXBEVOYNFMHC-NVNXTCNLSA-N
SO4	B [auth A], C [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.491	α = 90
b = 46.613	β = 111.75
c = 63.412	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Lolli, G.

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Funding Organization	Location	Grant Number
Other government		PoC Road to Market 2023

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release