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)

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
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Ligand Structure Quality Assessment

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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U5FKB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12C (Subject of Investigation/LOI) Query on 12C Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Alvarez-Martinez, C.E.

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

Revision History (Full details and data files)

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

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