3AMY | pdb_00003amy

Crystal structure of human CK2 alpha complexed with apigenin

• PDB DOI: https://doi.org/10.2210/pdb3AMY/pdb

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


• Deposited: 2010-08-25 Released: 2011-10-05 
• Deposition Author(s): Sekiguchi, Y., Nakaniwa, T., Kinoshita, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.340 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human CK2 alpha complexed with apigenin

Asada, N., Kitaura, K., Sekiguchi, Y., Nakaniwa, T., Kinoshita, T., Tada, T.

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: 40.81 kDa 
• Atom Count: 2,777 
• Modeled Residue Count: 318 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	340	Homo sapiens	Mutation(s): 0  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
AGI	B [auth A]	5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one C15 H10 O5 KZNIFHPLKGYRTM-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AGI	BindingDB:  3AMY	Ki: min: 440, max: 740 (nM) from 2 assay(s)
		IC50: min: 800, max: 800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.340 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.63	α = 90
b = 73.03	β = 90
c = 77.39	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Sekiguchi, Y., Nakaniwa, T., Kinoshita, T., Tada, T.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description