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- PDB-9hvx: Toxoplasma gondii GSK3b bound to LY2090314 -

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Basic information

Entry
Database: PDB / ID: 9hvx
TitleToxoplasma gondii GSK3b bound to LY2090314
ComponentsPutative cell-cycle-associated protein kinase GSK
KeywordsTRANSFERASE / GSK3b Cell signalling kinase
Function / homology
Function and homology information


tau-protein kinase / cell differentiation / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / cytoplasm
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Putative cell-cycle-associated protein kinase GSK
Similarity search - Component
Biological speciesToxoplasma gondii RH (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDiaz-Martin, S. / Bowler, M.W. / Swale, C.
Funding support France, 5items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE35-0010-01 France
Agence Nationale de la Recherche (ANR)ANR-21-CE15-0002-01 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0024 France
Agence Nationale de la Recherche (ANR)ANR-19-CE15-0026 France
Fondation pour la Recherche Medicale (FRM)EQU202103012571 France
CitationJournal: Nat Commun / Year: 2025
Title: Structural and functional characterization of TgGSK3, a druggable kinase in Toxoplasma gondii
Authors: Diaz-Martin, S. / Swale, C. / Bellini, V. / Dobrescu, I. / Wenker, J. / Bernier-Pinchart, M.P. / Braun, L. / Tollec, A. / Belmudes, L. / Corrao, C. / Coute, Y. / Mas, C. / Laurent, F. / ...Authors: Diaz-Martin, S. / Swale, C. / Bellini, V. / Dobrescu, I. / Wenker, J. / Bernier-Pinchart, M.P. / Braun, L. / Tollec, A. / Belmudes, L. / Corrao, C. / Coute, Y. / Mas, C. / Laurent, F. / Bowler, M.W. / Hakimi, M.A. / Bougdour, A.
History
DepositionJan 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cell-cycle-associated protein kinase GSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6795
Polymers40,0961
Non-polymers5834
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-19 kcal/mol
Surface area15230 Å2
Unit cell
Length a, b, c (Å)56.000, 120.840, 49.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

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Components

#1: Protein Putative cell-cycle-associated protein kinase GSK


Mass: 40096.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii RH (eukaryote) / Strain: RH / Gene: TGGT1_265330 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A125YY75, tau-protein kinase
#2: Chemical ChemComp-A1IYH / 3-(6-fluoranyl-10-piperidin-1-ylcarbonyl-1,10-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13),11-pentaen-3-yl)-4-imidazo[1,2-a]pyridin-3-yl-pyrrole-2,5-dione


Mass: 510.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H23FN6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Description: Rose petal morphology, the crystals are tainted in orange due to presence of the LY2090314 inhibitor.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.1→46.16 Å / Num. obs: 20469 / % possible obs: 99.81 % / Redundancy: 5.93 % / CC1/2: 0.99 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
2.38-6.2315.3172370.961
2.1-2.381.432320.561

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.16 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1999 9.77 %1999
Rwork0.1983 ---
obs0.2033 20463 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 41 118 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082690
X-RAY DIFFRACTIONf_angle_d0.9993651
X-RAY DIFFRACTIONf_dihedral_angle_d13.298364
X-RAY DIFFRACTIONf_chiral_restr0.05404
X-RAY DIFFRACTIONf_plane_restr0.007461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3751400.34881301X-RAY DIFFRACTION98
2.15-2.210.36141380.30411270X-RAY DIFFRACTION100
2.21-2.280.33381410.26551310X-RAY DIFFRACTION100
2.28-2.350.30951400.24941284X-RAY DIFFRACTION100
2.35-2.430.29421410.24491301X-RAY DIFFRACTION100
2.43-2.530.29381410.23581309X-RAY DIFFRACTION100
2.53-2.650.26521400.21261293X-RAY DIFFRACTION100
2.65-2.790.26681440.2191334X-RAY DIFFRACTION100
2.79-2.960.27861420.22151298X-RAY DIFFRACTION100
2.96-3.190.24221410.20171308X-RAY DIFFRACTION100
3.19-3.510.25341440.1831329X-RAY DIFFRACTION100
3.51-4.020.22391440.15181333X-RAY DIFFRACTION100
4.02-5.060.19191490.14411365X-RAY DIFFRACTION100
5.06-46.160.22691540.19881429X-RAY DIFFRACTION100

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