7QUX

Crystal structure of P7C8 bound to CK2alpha

• PDB DOI: https://doi.org/10.2210/pdb7QUX/pdb

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


• Deposited: 2022-01-19 Released: 2022-12-28 
• Deposition Author(s): Atkinson, E., Iegre, J., Brear, P., Baker, D., Sore, H., Hyvonen, M., Spring, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

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.

Macromolecule Content

• Total Structure Weight: 43.59 kDa 
• Atom Count: 3,231 
• Modelled Residue Count: 338 
• Deposited Residue Count: 360 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	352	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
P7C8	B [auth D]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OUT (Subject of Investigation/LOI)	I [auth D]	CARBAMIC ACID C H3 N O2 KXDHJXZQYSOELW-UHFFFAOYSA-N
MG	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.204 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.461	α = 90
b = 63.25	β = 108.44
c = 58.672	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Atkinson, E., Iegre, J., Brear, P., Baker, D., Sore, H., Hyvonen, M., Spring, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary