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- PDB-9hw6: Toxoplasma gondii GSK3b bound to LY2090314 and disulphide bonded ... -

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Basic information

Entry
Database: PDB / ID: 9hw6
TitleToxoplasma gondii GSK3b bound to LY2090314 and disulphide bonded through the C223 residue
Components(Putative cell-cycle-associated protein kinase GSK) x 2
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
: / PHOSPHATE ION / Putative cell-cycle-associated protein kinase GSK
Similarity search - Component
Biological speciesToxoplasma gondii RH (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSwale, C. / Diaz-Martin, S. / Bowler, M.W.
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 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)173,02010
Polymers170,7794
Non-polymers2,2406
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.910, 161.730, 83.280
Angle α, β, γ (deg.)90.000, 92.210, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 27 through 61 or resid 66...
d_2ens_1(chain "B" and (resid 27 through 61 or resid 66...
d_3ens_1(chain "D" and (resid 27 through 61 or resid 66...
d_4ens_1(chain "F" and (resid 27 through 91 or resid 102...
d_1ens_2chain "C"
d_2ens_2chain "E"
d_3ens_2chain "G"
d_4ens_2chain "X"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRGLNGLNAA27 - 6127 - 61
d_12ens_1LYSLYSGLUGLUAA66 - 9166 - 91
d_13ens_1ARGARGLEULEUAA102 - 183102 - 183
d_14ens_1ILEILETHRTHRAA193 - 237193 - 237
d_15ens_1VALVALPROPROAA239 - 365239 - 365
d_16ens_2A1IYFA1IYFA1IYFA1IYFAE401
d_21ens_1THRTHRGLNGLNBB27 - 6127 - 61
d_22ens_1LYSLYSGLUGLUBB66 - 9166 - 91
d_23ens_1ARGARGLEULEUBB102 - 183102 - 183
d_24ens_1ILEILETHRTHRBB193 - 237193 - 237
d_25ens_1VALVALPROPROBB239 - 365239 - 365
d_26ens_2A1IYFA1IYFA1IYFA1IYFBG402
d_31ens_1THRTHRGLNGLNDC27 - 6127 - 61
d_32ens_1LYSLYSGLUGLUDC66 - 9166 - 91
d_33ens_1ARGARGTHRTHRDC102 - 237102 - 237
d_34ens_1VALVALPROPRODC239 - 365239 - 365
d_36ens_2A1IYFA1IYFA1IYFA1IYFDI402
d_41ens_1THRTHRGLUGLUFD27 - 9127 - 91
d_42ens_1ARGARGLEULEUFD102 - 183102 - 183
d_43ens_1ILEILETHRTHRFD193 - 237193 - 237
d_44ens_1VALVALPROPROFD239 - 365239 - 365
d_45ens_2A1IYFA1IYFA1IYFA1IYFFJ401

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.998716452714, 0.0499534369401, -0.00837264688997), (0.0478612829161, 0.984836919857, 0.166749929191), (0.0165754238468, 0.16613517215, -0.985963670679)69.5159018248, -5.32813016649, 41.9286876462
2given(-0.999868352219, 0.0114322591931, 0.0115144118975), (-0.0126916699366, -0.993166150717, -0.116016889221), (0.0101093889937, -0.11614775297, 0.993180497057)32.2109311052, -32.7557974288, -2.05547603785
3given(0.999105158417, -0.0405749299971, 0.0119397437351), (-0.0400338544725, -0.998293310602, -0.0425177198727), (0.0136445198085, 0.0420016792858, -0.999024367078)-36.0789617172, -33.3577651983, 40.0680202958
4given(0.999902820006, -0.00973741812478, -0.00997663436498), (-0.0103941447063, -0.997628454757, -0.0680399001745), (-0.00929044136804, 0.0681369866387, -0.997632717362)-36.158170462, -34.2990934034, 41.4137190042
5given(-0.999884988496, 0.0110473576539, 0.0103906529257), (-0.0123701936213, -0.990448291878, -0.137328654788), (0.00877428567615, -0.137441394801, 0.990471036884)33.2853037449, -32.5895655174, -2.61904328222
6given(-0.999175765722, 0.0392075026646, 0.0105147957077), (0.040437944923, 0.984004050635, 0.173495823994), (-0.00354426358646, 0.173778019518, -0.984778471601)68.8430026452, -4.9254222876, 42.7150771507

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Components

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


Mass: 42734.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii RH (eukaryote) / Gene: TGGT1_265330 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A125YY75, tau-protein kinase
#2: Protein Putative cell-cycle-associated protein kinase GSK


Mass: 42654.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii RH (eukaryote) / Gene: TGGT1_265330 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A125YY75, tau-protein kinase
#3: Chemical
ChemComp-A1IYF / 3-(6-fluoranyl-10-piperidin-1-ylcarbonyl-1,10-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4,6,8(13)-tetraen-3-yl)-4-imidazo[1,2-a]pyridin-3-yl-pyrrole-2,5-dione


Mass: 512.535 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H25FN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
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: 3.03 Å3/Da / Density % sol: 59.4 % / Description: Elongated rod like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% MPD, 9% PEG 6000, 0.1M HEPES

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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: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.9→45.48 Å / Num. obs: 40947 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.85 Å2 / CC1/2: 0.96 / Net I/σ(I): 4.86
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
3-9.326.87370150.941
2.9-31.539320.551

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.48 Å / SU ML: 0.414 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 1996 4.88 %
Rwork0.204 38914 -
obs0.2068 40910 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.57 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10578 0 162 0 10740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011110996
X-RAY DIFFRACTIONf_angle_d1.296614927
X-RAY DIFFRACTIONf_chiral_restr0.06521642
X-RAY DIFFRACTIONf_plane_restr0.01651896
X-RAY DIFFRACTIONf_dihedral_angle_d17.09644115
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.05276920453
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.991577425596
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.21088619257
ens_2d_2GBX-RAY DIFFRACTIONTorsion NCS0.095941488174
ens_2d_3GBX-RAY DIFFRACTIONTorsion NCS0.0903470564881
ens_2d_4GBX-RAY DIFFRACTIONTorsion NCS0.170757201271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.32931440.3062783X-RAY DIFFRACTION98.72
2.97-3.050.31761450.26722750X-RAY DIFFRACTION98.4
3.05-3.140.33181420.25912758X-RAY DIFFRACTION98.74
3.14-3.240.30851530.25242802X-RAY DIFFRACTION99.03
3.24-3.360.32861420.25442793X-RAY DIFFRACTION98.85
3.36-3.490.33051350.24932719X-RAY DIFFRACTION97.37
3.49-3.650.28031410.21862762X-RAY DIFFRACTION98.31
3.65-3.850.24651420.20362774X-RAY DIFFRACTION98.31
3.85-4.090.23461390.18512766X-RAY DIFFRACTION97.81
4.09-4.40.24911450.17752783X-RAY DIFFRACTION98.69
4.4-4.840.26731330.16732803X-RAY DIFFRACTION98.99
4.84-5.540.24891480.19152813X-RAY DIFFRACTION99.26
5.54-6.980.23441450.20192807X-RAY DIFFRACTION99.16
6.98-45.480.19021420.1692801X-RAY DIFFRACTION97.64

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