9TFX | pdb_00009tfx

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha isoform 1 in complex with inositol hexakisphosphate (InsP6)

PDB DOI: https://doi.org/10.2210/pdb9TFX/pdb

Classification: CELL CYCLE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-27 Released: 2025-12-10
Deposition Author(s): Sturm, K., Hothorn, M.
Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.208 (Depositor), 0.208 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

An inositol pyrophosphate interaction screen provides insight into the regulation of plant casein kinase II.

Sturm, K., Pri-Tal, O., Rico-Resendiz, F., Verma, Y., Richter, A., Chen, H., Broger, L., Hothorn, L.A., Fiedler, D., Panse, V.G., Hothorn, M.

To be published.

Macromolecule Content

Total Structure Weight: 41.73 kDa
Atom Count: 3,073
Modeled Residue Count: 337
Deposited Residue Count: 344
Unique protein chains: 1

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-1	A [auth AAAA]	344	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CKA1, At5g67380, K8K14.10 EC: 2.7.11.1
UniProt
Find proteins for Q08467 (Arabidopsis thaliana) Explore Q08467 Go to UniProtKB: Q08467
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08467
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP Query on IHP Download Ideal Coordinates CCD File SDF format, chain B [auth AAAA] MOL2 format, chain B [auth AAAA] mmCIF format, chain B [auth AAAA]	B [auth AAAA]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain B [auth AAAA] Interactions & Density Focus chain B [auth AAAA]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain C [auth AAAA] MOL2 format, chain C [auth AAAA] mmCIF format, chain C [auth AAAA]	C [auth AAAA]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain C [auth AAAA] Interactions & Density Focus chain C [auth AAAA]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth AAAA] SDF format, chain E [auth AAAA] SDF format, chain D [auth AAAA] MOL2 format, chain F [auth AAAA] MOL2 format, chain E [auth AAAA] MOL2 format, chain D [auth AAAA] mmCIF format, chain F [auth AAAA] mmCIF format, chain E [auth AAAA] mmCIF format, chain D [auth AAAA]	D [auth AAAA], E [auth AAAA], F [auth AAAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAAA] Focus chain E [auth AAAA] Focus chain F [auth AAAA] Interactions & Density Focus chain D [auth AAAA] Focus chain E [auth AAAA] Focus chain F [auth AAAA]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth AAAA] SDF format, chain G [auth AAAA] MOL2 format, chain H [auth AAAA] MOL2 format, chain G [auth AAAA] mmCIF format, chain H [auth AAAA] mmCIF format, chain G [auth AAAA]	G [auth AAAA], H [auth AAAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth AAAA] Focus chain H [auth AAAA] Interactions & Density Focus chain G [auth AAAA] Focus chain H [auth AAAA]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth AAAA] SDF format, chain J [auth AAAA] SDF format, chain K [auth AAAA] SDF format, chain L [auth AAAA] MOL2 format, chain I [auth AAAA] MOL2 format, chain J [auth AAAA] MOL2 format, chain K [auth AAAA] MOL2 format, chain L [auth AAAA] mmCIF format, chain I [auth AAAA] mmCIF format, chain J [auth AAAA] mmCIF format, chain K [auth AAAA] mmCIF format, chain L [auth AAAA]	I [auth AAAA], J [auth AAAA], K [auth AAAA], L [auth AAAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth AAAA] Focus chain J [auth AAAA] Focus chain K [auth AAAA] Focus chain L [auth AAAA] Interactions & Density Focus chain I [auth AAAA] Focus chain J [auth AAAA] Focus chain K [auth AAAA] Focus chain L [auth AAAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.208 (Depositor), 0.208 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.903	α = 90
b = 63.897	β = 90
c = 97.211	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Sturm, K.

Hothorn, M.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	818696
Swiss National Science Foundation	Switzerland	CRSII5_209412
Howard Hughes Medical Institute (HHMI)	United States	55008733