6YZH

Crystal structure of P8C9 bound to CK2alpha

• PDB DOI: https://doi.org/10.2210/pdb6YZH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-07 Released: 2021-05-19 
• Deposition Author(s): Atkinson, E., Iegre, J., Brear, P., Baker, D., Sore, H., Hyvonen, M., Spring, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Development of small cyclic peptides targeting the CK2 alpha / beta interface.

Atkinson, E.L., Iegre, J., D'Amore, C., Brear, P., Salvi, M., Hyvonen, M., Spring, D.R.

(2022) Chem Commun (Camb) 58: 4791-4794

• PubMed: 35343996 
• DOI: https://doi.org/10.1039/d2cc00707j
• Primary Citation of Related Structures:  
  6YZH, 6Z19, 7QUX


• PubMed Abstract: 
  

  In this work, an iterative cycle of enzymatic assays, X-ray crystallography, molecular modelling and cellular assays were used to develop a functionalisable chemical probe for the CK2α/β PPI. The lead peptide, P8C9, successfully binds to CK2α at the PPI site, is easily synthesisable and functionalisable, highly stable in serum and small enough to accommodate further optimisation.

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Organizational Affiliation: 

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 48.47 kDa 
• Atom Count: 3,481 
• Modelled Residue Count: 354 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	398	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P8C9	B [auth D]	10	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
Q2E	B [auth D]	L-PEPTIDE LINKING	C12 H14 N2 O2 S		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.374	α = 90
b = 65.019	β = 111.2
c = 59.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Atkinson, E., Iegre, J., Brear, P., Baker, D., Sore, H., Hyvonen, M., Spring, D.

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-03-29
  Changes: Database references
• Version 2.0: 2023-07-19
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.1: 2024-02-07
  Changes: Refinement description
• Version 4.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary