9WXC | pdb_00009wxc

Crystal structure of C-terminal truncated calcium-dependent protein kinase 3 (CPK3) from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb9WXC/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-25 Released: 2026-10-07 
• Deposition Author(s): Zhao, S.-Y., Hu, H.-F., Luo, Z.P., Lv, J., Wu, J.-W., Wang, Z.-X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Structural insights into inhibition and activation mechanism of plant calcium-dependent protein kinases

Zhao, S.-Y., Hu, H.-F., Luo, Z.P., Lv, J., Liu, Y.-N., Wu, J.-W., Wang, Z.-X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 136.64 kDa 
• Atom Count: 7,946 
• Modeled Residue Count: 956 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 3	A, B, C	404	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CPK3, CDPK6, At4g23650, F9D16.120 EC: 2.7.11.1
UniProt
Find proteins for Q42479 (Arabidopsis thaliana) Explore Q42479  Go to UniProtKB:  Q42479

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth A], F [auth B], G [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.192 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.994	α = 106.062
b = 73.112	β = 102.404
c = 76.481	γ = 113.145

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Zhao, S.-Y., Hu, H.-F., Luo, Z.P., Lv, J., Wu, J.-W., Wang, Z.-X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release