9EED | pdb_00009eed

The Hanks-type kinase PknS from Xanthomonas citri bound to CHIR-124

• PDB DOI: https://doi.org/10.2210/pdb9EED/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas citri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-11-19 Released: 2025-11-26 
• Deposition Author(s): Lima, L.P., Alvarez-Martinez, C.E., Massirer, K.B., Counago, R.M.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The Hanks-type kinase PknS from Xanthomonas citri bound to CHIR-124

Lima, L.P., Alvarez-Martinez, C.E., Massirer, K.B., Counago, R.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.02 kDa 
• Atom Count: 2,114 
• Modeled Residue Count: 273 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinase domain protein	A	364	Xanthomonas citri	Mutation(s): 1  Gene Names: pknB, XAC3562_900036
UniProt
Find proteins for A0A0U5FKB2 (Xanthomonas citri pv. citri) Explore A0A0U5FKB2  Go to UniProtKB:  A0A0U5FKB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
12C (Subject of Investigation/LOI)	B [auth A]	4-[(3S)-1-AZABICYCLO[2.2.2]OCT-3-YLAMINO]-3-(1H-BENZIMIDAZOL-2-YL)-6-CHLOROQUINOLIN-2(1H)-ONE C23 H22 Cl N5 O MOVBBVMDHIRCTG-LJQANCHMSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.713	α = 90
b = 76.713	β = 90
c = 58.923	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Lima, L.P., Alvarez-Martinez, C.E., Massirer, K.B., Counago, R.M.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release