3NYV | pdb_00003nyv

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DTQClick on this verticalbar to view details

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
Find similar proteins by: 
(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
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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DTQClick on this verticalbar to view details

View more in-depth experimental data
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