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- PDB-4ona: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 4ona
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1517
ComponentsCalmodulin-domain protein kinase 1
KeywordsTransferase/Transferase Inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / 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-UW1 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMerritt, E.A.
Citation
Journal: ACS Med Chem Lett / Year: 2014
Title: Potent and selective inhibitors of CDPK1 from T. gondii and C. parvum based on a 5-aminopyrazole-4-carboxamide scaffold.
Authors: Zhang, Z. / Ojo, K.K. / Vidadala, R. / Huang, W. / Geiger, J.A. / Scheele, S. / Choi, R. / Reid, M.C. / Keyloun, K.R. / Rivas, K. / Siddaramaiah, L.K. / Comess, K.M. / Robinson, K.P. / ...Authors: Zhang, Z. / Ojo, K.K. / Vidadala, R. / Huang, W. / Geiger, J.A. / Scheele, S. / Choi, R. / Reid, M.C. / Keyloun, K.R. / Rivas, K. / Siddaramaiah, L.K. / Comess, K.M. / Robinson, K.P. / Merta, P.J. / Kifle, L. / Hol, W.G. / Parsons, M. / Merritt, E.A. / Maly, D.J. / Verlinde, C.L. / Van Voorhis, W.C. / Fan, E.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors.
Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C. ...Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C.L. / Buckner, F.S. / Parsons, M. / Hol, W.G. / Merritt, E.A. / Van Voorhis, W.C.
#2: 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.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 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)55,5802
Polymers55,2271
Non-polymers3531
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.270, 72.631, 67.200
Angle α, β, γ (deg.)90.00, 102.36, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Fragment: UNP residues 30-507
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, 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-UW1 / 5-amino-1-tert-butyl-3-(7-ethoxyquinolin-3-yl)-1H-pyrazole-4-carboxamide


Mass: 353.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1517, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→48.7 Å / Num. obs: 17101 / % possible obs: 95.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.493.10.0191.4196.7
8.98-48.73.70.01923.11100

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M84

4m84


Resolution: 2.4→48.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 21.342 / SU ML: 0.233 / SU R Cruickshank DPI: 0.8912 / Cross valid method: THROUGHOUT / ESU R: 0.889 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24795 859 5 %RANDOM
Rwork0.1873 ---
obs0.19028 16218 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å21.8 Å2
2---2.55 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 26 43 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193821
X-RAY DIFFRACTIONr_bond_other_d0.0010.023668
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9655158
X-RAY DIFFRACTIONr_angle_other_deg0.78238459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51624.916179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8391521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6962.8251871
X-RAY DIFFRACTIONr_mcbond_other1.6952.8251872
X-RAY DIFFRACTIONr_mcangle_it2.7594.2352340
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3143.111950
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 63 -
Rwork0.272 1207 -
obs--97.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6681.82741.36397.38871.3644.0264-0.15340.18930.148-0.41450.0990.0583-0.35550.24620.05440.1999-0.0039-0.03230.12740.04850.10744.9815-18.1364-40.5885
20.8844-0.0631.52942.2128-0.2845.18150.01460.0459-0.03830.0718-0.00160.20750.0469-0.2567-0.01290.08470.01130.02620.1019-0.00730.20095.8958-21.9946-24.5016
34.362-0.1796-0.18056.4403-0.59844.0564-0.0085-0.14970.07760.41780.03980.13650.0271-0.1486-0.03130.0956-0.02820.02320.0731-0.02970.0419.2088-11.7301-10.0456
41.74170.28251.54964.8763-6.802921.0481-0.0494-0.1901-0.1516-0.3411-0.26530.03851.15470.570.31460.09430.06250.090.1899-0.04980.3044-7.3728-8.7486-23.0449
58.83082.6147-1.769515.0982-0.10027.7868-0.16440.46870.1956-0.80450.31190.4869-0.0356-0.1122-0.14750.5918-0.0857-0.15080.3678-0.02610.4506-13.3201-6.3589-53.6337
69.69153.4629-1.8164.8229-3.41257.3068-0.0120.02080.3472-0.18590.13340.0591-0.2582-0.2334-0.12150.15050.02470.03490.1191-0.02550.262-14.91493.1028-22.1795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 99
2X-RAY DIFFRACTION2A100 - 204
3X-RAY DIFFRACTION3A205 - 313
4X-RAY DIFFRACTION4A314 - 364
5X-RAY DIFFRACTION5A365 - 435
6X-RAY DIFFRACTION6A436 - 507

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