6Z19

Crystal structure of P8C9 bound to CK2alpha

PDB DOI: https://doi.org/10.2210/pdb6Z19/pdb

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

Deposited: 2020-05-13 Released: 2021-05-26
Deposition Author(s): Atkinson, E., Iegre, J., Brear, P., Baker, D., Sore, H., Hyvonen, M., Spring, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.221
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK. spring@ch.cam.ac.uk.

Macromolecule Content

Total Structure Weight: 41.62 kDa
Atom Count: 3,223
Modelled Residue Count: 336
Deposited Residue Count: 336
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A [auth B]	328	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68400
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P2	B [auth C]	8	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	F [auth B], O [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth B] Focus chain O [auth B] Focus chain P [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	D [auth B], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]