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- PDB-3v5t: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3v5t
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1299
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / calcium-binding / ATP-binding / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane
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 ...: / 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-UW9 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMerritt, E.A. / Larson, E.T.
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: 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: 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.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G. ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G.J. / Buckner, F.S. / Napuli, A.J. / White, C.A. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)55,6452
Polymers55,2271
Non-polymers4191
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.350, 72.210, 67.310
Angle α, β, γ (deg.)90.000, 103.360, 90.000
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, 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-UW9 / 1-[(2S)-2-(dimethylamino)-3-methylbutyl]-3-(6-ethoxynaphthalen-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 418.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 225 mM ammonium citrate, 5 mM DTT, 2 mM UW1299, 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: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 2011
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
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 5 / Number: 105225 / Rsym value: 0.126 / D res high: 2.131 Å / D res low: 36.105 Å / Num. obs: 25308 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.7436.199.310.0470.0474
4.776.7410010.0690.0694.1
3.894.7710010.060.064.2
3.373.8910010.0820.0824.2
3.013.3710010.1210.1214.2
2.753.0110010.2110.2114.2
2.552.7510010.3620.3624.2
2.382.5510010.530.534.2
2.252.3810010.7530.7534.2
2.132.2599.811.0271.0274.1
ReflectionResolution: 2.131→36.105 Å / Num. all: 25308 / Num. obs: 25308 / % possible obs: 100 % / Redundancy: 4.2 % / Rsym value: 0.126 / Net I/σ(I): 5.9
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.13-2.254.10.71518136871.02799.8
2.25-2.384.20.91437134600.753100
2.38-2.554.21.41370332900.53100
2.55-2.754.221262830210.362100
2.75-3.014.23.51181928270.211100
3.01-3.374.25.31065225420.121100
3.37-3.894.28.2935322410.082100
3.89-4.774.210.6799119150.06100
4.77-6.744.19620514960.069100
6.74-36.105412.533228290.04799.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→34.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2672 / WRfactor Rwork: 0.2067 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7626 / SU B: 18.314 / SU ML: 0.219 / SU R Cruickshank DPI: 0.2894 / SU Rfree: 0.2295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1308 5.2 %RANDOM
Rwork0.2115 ---
obs0.2146 25282 99.92 %-
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: 107.74 Å2 / Biso mean: 58.4376 Å2 / Biso min: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å22.33 Å2
2---1.61 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.13→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 31 44 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023701
X-RAY DIFFRACTIONr_bond_other_d0.0010.022492
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9764996
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0016084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92824.97165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7411517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
LS refinement shellResolution: 2.131→2.186 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 105 -
Rwork0.325 1725 -
all-1830 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: 16.583 Å / Origin y: 22.62 Å / Origin z: 59.577 Å
111213212223313233
T0.0855 Å20.0127 Å2-0.0299 Å2-0.124 Å2-0.0195 Å2--0.0286 Å2
L0.3 °2-0.0189 °20.1723 °2-0.6681 °20.0266 °2--0.1567 °2
S0.0119 Å °-0.0079 Å °0.0137 Å °0.0224 Å °-0.0008 Å °-0.0959 Å °0.0112 Å °-0.0223 Å °-0.0111 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 507
2X-RAY DIFFRACTION1A700

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