3IS5

Crystal structure of CDPK kinase domain from toxoplasma Gondii, TGME49_018720


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of CDPK kinase domain from toxoplasma Gondii, TGME49_018720

Wernimont, A.K.Artz, J.D.Senisterra, G.MacKenzie, F.Hutchinson, A.Kozieradzki, I.Cossar, D.Bochkarev, A.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Weigelt, J.Hui, R.Lin, Y.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-dependent protein kinase
A, B, C, D, E
A, B, C, D, E, F
285Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_018720
EC: 2.7.11.17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
L [auth B]
O [auth C]
R [auth D]
AA [auth F],
G [auth A],
L [auth B],
O [auth C],
R [auth D],
V [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F]
I [auth A]
K [auth A]
N [auth B]
S [auth D]
BA [auth F],
I [auth A],
K [auth A],
N [auth B],
S [auth D],
T [auth D],
W [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
P [auth C],
Y [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
M [auth B]
Q [auth C]
U [auth D]
X [auth E]
J [auth A],
M [auth B],
Q [auth C],
U [auth D],
X [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.973α = 90
b = 113.973β = 90
c = 153.471γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description