5YWM | pdb_00005ywm

Crystal structure of CK2a2 form-1

• PDB DOI: https://doi.org/10.2210/pdb5YWM/pdb

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


• Deposited: 2017-11-29 Released: 2018-12-05 
• Deposition Author(s): Tsuyuguchi, M., Kinoshita, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human CK2a2 in a new crystal form at 1.89 angstrom resolution

Tsuyuguchi, M., Nakaniwa, T., Kinoshita, 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: 40.48 kDa 
• Atom Count: 2,799 
• Modeled Residue Count: 313 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha'	A [auth X]	339	Homo sapiens	Mutation(s): 0  Gene Names: CSNK2A2, CK2A2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens) Explore P19784  Go to UniProtKB:  P19784
PHAROS:  P19784 GTEx:  ENSG00000070770

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIO	D [auth X]	NICOTINIC ACID C6 H5 N O2 PVNIIMVLHYAWGP-UHFFFAOYSA-N
SO4	B [auth X], C [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.292	α = 90
b = 101.023	β = 90
c = 45.764	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Tsuyuguchi, M., Kinoshita, T.

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description