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

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Basic information

Entry
Database: PDB / ID: 4yjn
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1639
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-UW4 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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: Acs Med.Chem.Lett. / Year: 2015
Title: SAR Studies of 5-Aminopyrazole-4-carboxamide Analogues as Potent and Selective Inhibitors of Toxoplasma gondii CDPK1.
Authors: Huang, W. / Ojo, K.K. / Zhang, Z. / Rivas, K. / Vidadala, R.S. / Scheele, S. / DeRocher, A.E. / Choi, R. / Hulverson, M.A. / Barrett, L.K. / Bruzual, I. / Siddaramaiah, L.K. / Kerchner, K.M. ...Authors: Huang, W. / Ojo, K.K. / Zhang, Z. / Rivas, K. / Vidadala, R.S. / Scheele, S. / DeRocher, A.E. / Choi, R. / Hulverson, M.A. / Barrett, L.K. / Bruzual, I. / Siddaramaiah, L.K. / Kerchner, K.M. / Kurnick, M.D. / Freiberg, G.M. / Kempf, D. / Hol, W.G. / Merritt, E.A. / Neckermann, G. / de Hostos, E.L. / Isoherranen, N. / Maly, D.J. / Parsons, M. / Doggett, J.S. / 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.M.J. / Buckner, F.S. / Parsons, M. / Hol, W.G.J. / Merritt, E.A. / Van Voorhis, W.C.
#2: 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, E. / Geiger, J.A. / Scheele, S. / Choi, R. / Reid, M.C. / Keyloun, K. / Parsons, M. / Merritt, E.A. / Maly, D.J. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Fan, E.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _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 1.4Sep 27, 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)55,6062
Polymers55,2271
Non-polymers3791
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.300, 72.640, 65.710
Angle α, β, γ (deg.)90.000, 99.720, 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
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: CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-UW4 / 5-amino-1-tert-butyl-3-[2-(cyclobutyloxy)quinolin-6-yl]-1H-pyrazole-4-carboxamide


Mass: 379.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1639

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI 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: 2.6→72.64 Å / Num. obs: 12536 / % possible obs: 90.6 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.097 / Net I/σ(I): 5.1 / Num. measured all: 72119 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.6-2.725.51.7491.1858415480.4020.80192.4
9.01-72.645.90.0671118123070.9960.03186

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Blu-Icedata collection
Aimless0.1.26data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ONA

4ona


Resolution: 2.6→64.77 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2554 / WRfactor Rwork: 0.2193 / FOM work R set: 0.7862 / SU B: 33.625 / SU ML: 0.329 / SU R Cruickshank DPI: 0.3841 / SU Rfree: 0.3837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 610 4.9 %RANDOM
Rwork0.2148 ---
obs0.2164 11891 89.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.32 Å2 / Biso mean: 56.735 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å20.68 Å2
2---1.32 Å2-0 Å2
3---2.46 Å2
Refinement stepCycle: final / Resolution: 2.6→64.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 28 29 3725
Biso mean--41.08 35.12 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193803
X-RAY DIFFRACTIONr_bond_other_d0.0010.023660
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9665128
X-RAY DIFFRACTIONr_angle_other_deg0.85438446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.804179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7315727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3131522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02844
X-RAY DIFFRACTIONr_mcbond_it1.3582.6361853
X-RAY DIFFRACTIONr_mcbond_other1.3572.6361854
X-RAY DIFFRACTIONr_mcangle_it2.333.952318
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 44 -
Rwork0.387 884 -
all-928 -
obs--90.54 %
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)
14.84912.95021.5217.62972.09724.3765-0.0988-0.07610.3515-0.4841-0.07580.136-0.5059-0.03260.17460.19690.0466-0.12730.28880.04530.1712.0893-19.5327-40.6823
21.56030.08530.39022.49281.313.61450.0732-0.1195-0.06910.0856-0.12610.11340.1893-0.26740.05290.0303-0.021-0.04690.22240.05730.14586.0611-18.2851-17.5657
31.746-0.01490.69172.24-0.31583.1614-0.13460.16020.0775-0.3481-0.02890.1501-0.0964-0.11970.16340.0725-0.0384-0.03020.3105-0.07210.3083-10.8765-6.8887-33.3185
48.74542.532.93426.01962.43567.5390.3762-0.2257-0.5620.4035-0.1524-0.69270.03230.5475-0.22380.5870.062-0.06260.47230.00760.6643-9.8479-11.235-50.8038
52.52391.9525-0.97742.92432.54298.94810.1633-0.01140.5388-0.0079-0.48540.63730.4475-0.83620.32220.90290.0832-0.11380.6602-0.00360.7198-20.2057-6.9096-47.7077
66.71331.4423-2.48113.2653-1.04747.26280.1404-0.18310.7141-0.03860.18480.1326-0.52920.0022-0.32520.0844-0.0067-0.05490.2182-0.0270.2136-16.64862.7004-20.4144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 94
2X-RAY DIFFRACTION2A95 - 312
3X-RAY DIFFRACTION3A313 - 379
4X-RAY DIFFRACTION4A380 - 412
5X-RAY DIFFRACTION5A413 - 441
6X-RAY DIFFRACTION6A442 - 507

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