3WOW

Crystal structure of human CK2a with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb3WOW/pdb

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


• Deposited: 2014-01-06 Released: 2015-02-04 
• Deposition Author(s): Kinoshita, T., Nakaniwa, T., Sekiguchi, Y., Sogabe, Y., Sakurai, A., Nakamura, S., Nakanishi, I., Shimada, K., Tanaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

A hydrophobic residue divergence of CK2a contribute to a species-dependent variation for apigenin binding mode but not for an ATP analogue

Kinoshita, T., Nakaniwa, T., Sekiguchi, Y., Sogabe, Y., Sakurai, A., Nakamura, S., Nakanishi, I., Shimada, K., Tanaka, M.

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: 41.41 kDa 
• Atom Count: 3,008 
• Modelled Residue Count: 334 
• 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  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
ANP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.242	α = 90
b = 78.46	β = 90
c = 82.389	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Kinoshita, T., Nakaniwa, T., Sekiguchi, Y., Sogabe, Y., Sakurai, A., Nakamura, S., Nakanishi, I., Shimada, K., Tanaka, M.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description