5W8R | pdb_00005w8r

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

• PDB DOI: https://doi.org/10.2210/pdb5W8R/pdb

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


• Deposited: 2017-06-22 Released: 2017-07-19 
• 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., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.249 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI

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., Structural Genomics Consortium (SGC)

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: 55.58 kDa 
• Atom Count: 3,753 
• Modeled Residue Count: 456 
• 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 EC: 2.7.11.1
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5  Go to UniProtKB:  Q9BJF5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9XV	B [auth A]	1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine C16 H18 Cl N5 VYDBKDXQXXHCLQ-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9XV	BindingDB:  5W8R	IC50: min: 3.38, max: 3.4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.249 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.024	α = 90
b = 72.944	β = 99.3
c = 65.546	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
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., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Source and taxonomy
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description