3I79 | pdb_00003i79

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.258 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3I79

This is version 1.4 of the entry. See complete history

Literature

Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors.

Ojo, K.K.Larson, E.T.Keyloun, K.R.Castaneda, L.J.Derocher, A.E.Inampudi, K.K.Kim, J.E.Arakaki, T.L.Murphy, R.C.Zhang, L.Napuli, A.J.Maly, D.J.Verlinde, C.L.Buckner, F.S.Parsons, M.Hol, W.G.Merritt, E.A.Van Voorhis, W.C.

(2010) Nat Struct Mol Biol 17: 602-607

  • DOI: https://doi.org/10.1038/nsmb.1818
  • Primary Citation Related Structures: 
    3I79, 3I7B, 3I7C

  • PubMed Abstract: 

    New drugs are needed to treat toxoplasmosis. Toxoplasma gondii calcium-dependent protein kinases (TgCDPKs) are attractive targets because they are absent in mammals. We show that TgCDPK1 is inhibited by low nanomolar levels of bumped kinase inhibitors (BKIs), compounds inactive against mammalian kinases. Cocrystal structures of TgCDPK1 with BKIs confirm that the structural basis for selectivity is due to the unique glycine gatekeeper residue in the ATP-binding site. We show that BKIs interfere with an early step in T. gondii infection of human cells in culture. Furthermore, we show that TgCDPK1 is the in vivo target of BKIs because T. gondii expressing a glycine to methionine gatekeeper mutant enzyme show significantly decreased sensitivity to BKIs. Thus, design of selective TgCDPK1 inhibitors with low host toxicity may be achievable.


  • Organizational Affiliation
    • Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.

Macromolecule Content 

  • Total Structure Weight: 55.29 kDa 
  • Atom Count: 3,753 
  • Modeled Residue Count: 455 
  • Deposited Residue Count: 484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-domain protein kinase 1484Toxoplasma gondiiMutation(s): 0 
Gene Names: CDPK1
EC: 2.7.11.17 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii)
Explore Q9BJF5 
Go to UniProtKB:  Q9BJF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BJF5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.258 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.144α = 90
b = 71.861β = 102.98
c = 67.265γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations