4MVF | pdb_00004mvf

Crystal Structure of Plasmodium falciparum CDPK2 complexed with inhibitor staurosporine

• PDB DOI: https://doi.org/10.2210/pdb4MVF/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Plasmodium falciparum K1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-24 Released: 2014-09-03 
• Deposition Author(s): Lauciello, L., Pernot, L., Scapozza, L., Perozzo, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: in silico

Literature

P. falciparum Calcium-Dependent Protein Kinase 2 (PfCDPK2): First Crystal Structure and Virtual Ligand Screening

Lauciello, L., Pernot, L., Bottegoni, G., Bisson, W., Scapozza, L., Perozzo, 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: 58.81 kDa 
• Atom Count: 3,563 
• Modeled Residue Count: 408 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 2	A	506	Plasmodium falciparum K1	Mutation(s): 0  Gene Names: CDPK2, CPK2, PFF0520w EC: 2.7.11.1
UniProt
Find proteins for O15865 (Plasmodium falciparum (isolate K1 / Thailand)) Explore O15865  Go to UniProtKB:  O15865

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	B [auth A]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.15	α = 90
b = 92.25	β = 90
c = 97.78	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Lauciello, L., Pernot, L., Scapozza, L., Perozzo, R.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description