5W9E

Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186

• PDB DOI: https://doi.org/10.2210/pdb5W9E/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-23 Released: 2017-08-02 
• Deposition Author(s): El Bakkouri, M., Lovato, D., Loppnau, P., Lin, Y.H., Rutaganaria, F., Lopez, M.S., Shokat, L., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Sibley, D., Hui, R., Walker, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.249 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186

El Bakkouri, M., Lovato, D., Loppnau, P., Lin, Y.H., Rutaganaria, F., Lopez, M.S., Shokat, L., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Sibley, D., Hui, R., Walker, J.R.

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)

Macromolecule Content

• Total Structure Weight: 55.56 kDa 
• Atom Count: 3,590 
• Modelled Residue Count: 451 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	484	Toxoplasma gondii	Mutation(s): 0  Gene Names: CDPK1
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5  Go to UniProtKB:  Q9BJF5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YJ	B [auth A]	1-tert-butyl-3-[(3-chlorophenyl)sulfanyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine C15 H16 Cl N5 S PNPUVQZAAVTLKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.249 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.997	α = 90
b = 72.802	β = 98.57
c = 64.595	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data collection
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): El Bakkouri, M., Lovato, D., Loppnau, P., Lin, Y.H., Rutaganaria, F., Lopez, M.S., Shokat, L., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Sibley, D., Hui, R., Walker, J.R.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references