4QOX | pdb_00004qox

Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500

• PDB DOI: https://doi.org/10.2210/pdb4QOX/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-06-20 Released: 2014-09-03 
• Deposition Author(s): Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500

Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V.

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: 62.52 kDa 
• Atom Count: 3,701 
• Modelled Residue Count: 462 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 4	A	537	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: CDPK4, CPK4, PF07_0072 EC: 2.7.11.1
UniProt
Find proteins for Q8IBS5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IBS5  Go to UniProtKB:  Q8IBS5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXR	C [auth A]	3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine C16 H18 Br N5 FTICVONBLRGQJW-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.289	α = 90
b = 75.967	β = 90
c = 92.688	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Wernimont, A.K., Walker, J.R., Hutchinson, A., Seitova, A., He, H., Loppnau, P., Neculai, M., Amani, M., Lin, Y.H., Ravichandran, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Lovato, D.V., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations