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- PDB-3sx9: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3sx9
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-132
ComponentsCalmodulin-domain protein kinase 1
Keywordstransferase/transferase inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase inhibitor / transferase-transferase inhibitor complex
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / calcium ion binding / ATP binding
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 / Phosphorylase Kinase; 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-BK7 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsLarson, E.T. / Merritt, E.A.
Citation
Journal: J.Med.Chem. / Year: 2012
Title: Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1.
Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / ...Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / Verlinde, C.L. / Fan, E. / Van Voorhis, W.C. / Maly, D.J. / Merritt, E.A.
#1: Journal: J.Med.Chem. / Year: 2012
Title: Development of Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitors with Potent Anti-Toxoplasma Activity.
Authors: Johnson, S.M. / Murphy, R.C. / Geiger, J.A. / Derocher, A.E. / Zhang, Z. / Ojo, K.K. / Larson, E.T. / Perera, B.G. / Dale, E.J. / He, P. / Reid, M.C. / Fox, A.M. / Mueller, N.R. / Merritt, E. ...Authors: Johnson, S.M. / Murphy, R.C. / Geiger, J.A. / Derocher, A.E. / Zhang, Z. / Ojo, K.K. / Larson, E.T. / Perera, B.G. / Dale, E.J. / He, P. / Reid, M.C. / Fox, A.M. / Mueller, N.R. / Merritt, E.A. / Fan, E. / Parsons, M. / Van Voorhis, W.C. / Maly, D.J.
#2: Journal: ACS Med Chem Lett / Year: 2010
Title: Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii.
Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,6292
Polymers55,2271
Non-polymers4021
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.281, 72.475, 67.267
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as AU

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Components

#1: Protein Calmodulin-domain protein kinase 1 / Calmodulin-domain protein kinase / putative


Mass: 55226.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-29 were replaced with a cleavable His-tag plus linker during cloning; tag was cleaved prior to crystallization
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AAG53993, CDPK1, TGGT1_059880, TGVEG_042030 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-BK7 / 3-(6-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine / RM-1-132


Mass: 402.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 40.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 26% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-132; frozen in LN2 after soaking in mother liquor supplemented with 10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2010
Diffraction measurementDetails: 1.00 degrees, 12.0 sec, detector distance 400.00 mm
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionAv R equivalents: 0.145 / Number: 50603
ReflectionResolution: 2.65→50 Å / Num. obs: 13349 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 9.802
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.506 / Rsym value: 0.857 / % possible all: 100
Cell measurementReflection used: 50603

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.6.0095refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3NYV

3nyv


Resolution: 2.65→46.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.201 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 677 5.1 %RANDOM
Rwork0.1971 ---
obs0.1996 13331 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 111.71 Å2 / Biso mean: 44.9889 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å21.65 Å2
2---2.11 Å20 Å2
3---2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 30 26 3720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223793
X-RAY DIFFRACTIONr_bond_other_d0.0050.022628
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.975101
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0026398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.325464
X-RAY DIFFRACTIONr_chiral_restr0.050.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
LS refinement shellResolution: 2.638→2.706 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 35 -
Rwork0.279 856 -
all-891 -
obs--92.62 %

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