5JN2 | pdb_00005jn2

Crystal structure of TgCDPK1 bound to NVPACU106

• PDB DOI: https://doi.org/10.2210/pdb5JN2/pdb

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


• Deposited: 2016-04-29 Released: 2016-05-25 
• Deposition Author(s): El Bakkouri, M., Walker, J.R., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.269 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TgCDPK1 bound to NVPACU106

El Bakkouri, M., Walker, J.R., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lovato, D.V., 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: 60.08 kDa 
• Atom Count: 3,487 
• Modeled Residue Count: 450 
• Deposited Residue Count: 525 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	525	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6LO	B [auth A]	N-[(3-{4-amino-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}cyclobutyl)methyl]acetamide C26 H27 N5 O2 BUCAFRXFNHCHRU-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.269 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.142	α = 90
b = 72.473	β = 98.63
c = 65.101	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
BUSTER	refinement
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): El Bakkouri, M., Walker, J.R., Loppnau, P., Graslund, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description