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- PDB-4wg5: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 4wg5
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1647
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


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-UW3 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMerritt, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089441 United States
Citation
Journal: to be published
Title: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1647
Authors: Merritt, E.A. / Maly, D.J. / Ojo, K.K. / Zhang, Z. / Fan, E. / Van Voorhis, W.C.
#1: 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.
#2: 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.
#3: 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
DepositionSep 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)55,6322
Polymers55,2271
Non-polymers4051
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.190, 72.950, 67.880
Angle α, β, γ (deg.)90.000, 102.480, 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 / Fragment: UNP residues 30-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-UW3 / 5-amino-3-[7-(cyclobutyloxy)quinolin-3-yl]-1-cyclohexyl-1H-pyrazole-4-carboxamide


Mass: 405.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 3350, 250 mM ammonium citrate, 2 mM EDTA, 5 mM DTT, 2 mM UW1647

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→66.28 Å / Num. obs: 19342 / % possible obs: 94.5 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.068 / Net I/σ(I): 6.7 / Num. measured all: 91536 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.394.71.1651.5942019880.6390.57693.6
8.61-66.284.80.06214.918633860.9970.0393.7

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Processing

Software
NameVersionClassification
MOSFLM0.2.14data reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementResolution: 2.3→66.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2653 / WRfactor Rwork: 0.2202 / FOM work R set: 0.7472 / SU B: 22.485 / SU ML: 0.257 / SU R Cruickshank DPI: 0.5942 / SU Rfree: 0.2821 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 936 4.8 %RANDOM
Rwork0.2204 18391 --
obs0.2223 18391 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.37 Å2 / Biso mean: 52.386 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å2-0 Å22.3 Å2
2---0.18 Å2-0 Å2
3---2.88 Å2
Refinement stepCycle: final / Resolution: 2.3→66.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 30 66 3819
Biso mean--26.03 37.62 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193848
X-RAY DIFFRACTIONr_bond_other_d0.0020.023708
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9795182
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0038571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91424.973183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16115742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
X-RAY DIFFRACTIONr_mcbond_it1.5811.9161866
X-RAY DIFFRACTIONr_mcbond_other1.581.9161865
X-RAY DIFFRACTIONr_mcangle_it2.6692.8692334
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 68 -
Rwork0.331 1303 -
all-1371 -
obs--91.89 %
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)
15.29222.44751.259310.16242.05394.5846-0.0974-0.05190.2229-0.3130.06830.5887-0.1713-0.17530.02920.30570.0267-0.12630.140.03660.180517.56-21.279-8.585
21.5663-0.38610.44952.7420.42254.44890.00950.07150.1137-0.0639-0.02350.17310.0042-0.16410.0140.2945-0.0068-0.09410.0533-0.00530.156223.772-21.376.614
35.1799-0.8594-0.32675.5562-0.32833.2157-0.0599-0.41780.09160.63590.04980.0580.1386-0.15760.01010.3817-0.0137-0.07950.1049-0.00520.028826.318-14.03924.504
41.7031-0.18660.64562.9989-2.39038.3712-0.0813-0.1325-0.1312-0.347-0.02760.02410.4713-0.06360.1090.2835-0.0134-0.02470.1656-0.03540.29578.618-8.5474.249
512.79831.00232.33715.7553-0.4085.0155-0.03450.178-0.0119-0.265-0.0741-0.18430.00540.34660.10860.8137-0.0227-0.0980.3764-0.07210.40697.464-10.511-20.221
61.50591.47630.2762.03550.399510.7592-0.04880.30280.153-0.3063-0.10250.53420.2497-0.89590.15130.8403-0.0544-0.15710.4982-0.09580.7277-2.122-7.286-16.099
78.42431.5477-1.90812.9834-1.78156.22050.0518-0.36230.5017-0.01890.10540.0519-0.34830.1136-0.15710.2820.0023-0.07930.0875-0.03330.16681.9342.45411.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 86
2X-RAY DIFFRACTION2A87 - 211
3X-RAY DIFFRACTION3A212 - 313
4X-RAY DIFFRACTION4A314 - 372
5X-RAY DIFFRACTION5A373 - 411
6X-RAY DIFFRACTION6A412 - 440
7X-RAY DIFFRACTION7A441 - 507

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