3MA6 | pdb_00003ma6

Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1

• PDB DOI: https://doi.org/10.2210/pdb3MA6/pdb

• Classification: TRANSFERASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-23 Released: 2010-07-21 
• Deposition Author(s): Wernimont, A.K., Qiu, W., Amani, M., Artz, J.D., Hassani, A.A., Senisterra, G., Vedadi, M., Sibley, L.D., Lourido, S., Shokat, K., Zhang, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.286 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.255 (Depositor) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1

Wernimont, A.K., Qiu, W., Amani, M., Artz, J.D., Hassani, A.A., Senisterra, G., Vedadi, M., Sibley, L.D., Lourido, S., Shokat, K., Zhang, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Hui, R., Lin, Y.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.87 kDa 
• Atom Count: 4,214 
• Modeled Residue Count: 533 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A, B	298	Toxoplasma gondii	Mutation(s): 0  Gene Names: CDPK1, TGME49_101440 EC: 2.7.11.1
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
DXR	C [auth A], D [auth B]	3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine C16 H18 Br N5 FTICVONBLRGQJW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.286 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.255 (Depositor) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.329	α = 90
b = 145.923	β = 99.63
c = 52.111	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Wernimont, A.K., Qiu, W., Amani, M., Artz, J.D., Hassani, A.A., Senisterra, G., Vedadi, M., Sibley, L.D., Lourido, S., Shokat, K., Zhang, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary