3NYV

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with non-specific inhibitor WHI-P180

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Binding modes of non-specific inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from T. gondii and C. parvum

Larson, E.T., Ojo, K.K., Kim, J.E., Verlinde, C.L.M.J., Buckner, F.S., Hol, W.G.J., Merritt, E.A., Van Voorhis, W.C.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-domain protein kinase 1484Toxoplasma gondiiMutation(s): 0 
Gene Names: AAG53993, 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
DTQ
Query on DTQ
Download Ideal Coordinates CCD File 
B [auth A]4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE
C16 H15 N3 O3
BNDYIYYKEIXHNK-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.272α = 90
b = 72.297β = 103.61
c = 67.174γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    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: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection
  • Version 1.5: 2024-11-27
    Changes: Structure summary