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- PDB-5w91: Toxoplasma Gondii CDPK1 in complex with inhibitor LZH118 -

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Basic information

Entry
Database: PDB / ID: 5w91
TitleToxoplasma Gondii CDPK1 in complex with inhibitor LZH118
ComponentsCalmodulin-domain protein kinase 1
Keywordstransferase/transferase inhibitor / CDPK / PARASITOLOGY / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / transferase-transferase inhibitor complex
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9XP / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEl Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Toxoplasma Gondii CDPK1 in complex with inhibitor LZH118
Authors: El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R. / ...Authors: El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5843
Polymers55,2271
Non-polymers3572
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.908, 73.230, 65.709
Angle α, β, γ (deg.)90.000, 98.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55226.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Plasmid: PET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9BJF5
#2: Chemical ChemComp-9XP / 1-tert-butyl-N~3~-(3-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,4-diamine


Mass: 316.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17ClN6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.7 % / Mosaicity: 0.34 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG8K, 0.2M NaCl, 0.1M Hepes pH7.5, 10 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→48.59 Å / Num. obs: 17646 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Rrim(I) all: 0.071 / Net I/σ(I): 15.3 / Num. measured all: 72491 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4940.8350.5820.4770.96499.2
8.98-48.593.60.0220.9990.0130.02694.2

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFG

4ifg


Resolution: 2.4→39.76 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9102 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.469 / SU Rfree Blow DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 845 4.79 %RANDOM
Rwork0.2086 ---
obs0.2107 17628 99.7 %-
Displacement parametersBiso max: 152.74 Å2 / Biso mean: 62.48 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.1752 Å20 Å23.0529 Å2
2--2.9391 Å20 Å2
3----5.1143 Å2
Refinement stepCycle: final / Resolution: 2.4→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 23 73 3520
Biso mean--50.07 53.64 -
Num. residues----451
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1482SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1054HARMONIC5
X-RAY DIFFRACTIONt_it6767HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion475SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7054SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6767HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12178HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion14.43
LS refinement shellResolution: 2.4→2.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.322 133 4.72 %
Rwork0.2483 2683 -
all0.2516 2816 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: 40.2917 Å / Origin y: -10.0205 Å / Origin z: 90.7482 Å
111213212223313233
T-0.0725 Å20.0687 Å20.0153 Å2--0.1123 Å20.0127 Å2---0.1193 Å2
L1.0449 °20.2423 °20.2767 °2-1.3055 °2-0.0232 °2--0.8577 °2
S-0.0018 Å °0.147 Å °-0.0941 Å °0.0008 Å °-0.0861 Å °-0.1479 Å °0.1604 Å °0.0769 Å °0.0878 Å °
Refinement TLS groupSelection details: { A|* }

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