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- PDB-4m84: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 4m84
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1455
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


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-21E / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.998 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
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5362
Polymers55,2271
Non-polymers3091
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.120, 73.180, 66.010
Angle α, β, γ (deg.)90.000, 99.770, 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: residues 30-507
Source method: isolated from a genetically manipulated source
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-21E / 5-amino-1-tert-butyl-3-(quinolin-2-yl)-1H-pyrazole-4-carboxamide


Mass: 309.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 40.69 %
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 UW1455, 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: BL14-1 / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 7, 2013
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: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.998→48.673 Å / Num. obs: 28948 / % possible obs: 94.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SX9

3sx9


Resolution: 1.998→48.67 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2548 / WRfactor Rwork: 0.1982 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8093 / SU B: 11.43 / SU ML: 0.156 / SU R Cruickshank DPI: 0.2318 / SU Rfree: 0.1995 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1448 5 %RANDOM
Rwork0.198 ---
obs0.201 28905 94.19 %-
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: 139.14 Å2 / Biso mean: 54.6328 Å2 / Biso min: 25.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20.56 Å2
2--0.58 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.998→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 23 86 3807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193832
X-RAY DIFFRACTIONr_bond_other_d0.0020.023680
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9765173
X-RAY DIFFRACTIONr_angle_other_deg0.7943.0028492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51624.945182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2121521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_mcbond_it1.9873.0431869
X-RAY DIFFRACTIONr_mcbond_other1.9873.0431868
X-RAY DIFFRACTIONr_mcangle_it2.9834.5542338
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 70 -
Rwork0.316 1430 -
all-1500 -
obs--66.46 %
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)
15.045-2.22871.08054.424-1.3583.1788-0.2397-0.02280.2210.58-0.0032-0.4354-0.34960.04260.24290.0913-0.0006-0.08220.0964-0.03570.15814.7816.62472.755
20.9368-0.34470.45451.3889-0.81762.60260.05640.1168-0.0504-0.0072-0.1316-0.12610.2330.21120.07510.02650.0224-0.01570.1787-0.00130.266414.15614.20157.283
32.4931-0.20340.17563.3552-0.38641.68970.01840.30780.0219-0.4424-0.098-0.02860.18770.21530.07970.08010.0474-0.02640.2646-0.02450.140510.73822.10640.916
45.5853.50624.9092.20493.08074.32750.1898-0.46360.26840.1115-0.34060.19480.236-0.44720.15081.27360.07910.1251.00890.15781.063121.9221.52833.04
50.9506-0.10060.52180.73790.86474.1245-0.12870.07240.01660.2285-0.0051-0.12610.0738-0.14470.13380.10690.0287-0.04750.18780.040.249929.92430.64268.623
610.08110.39830.60816.8489-1.60045.82570.24890.2592-0.608-0.019-0.15780.21540.1779-0.2765-0.09110.21680.0058-0.1630.1737-0.0490.222932.1926.48482.909
74.9694-1.4039-2.55061.66931.4874.87530.0134-0.01640.27930.17770.2012-0.0154-0.11030.0587-0.21450.04870.0312-0.02890.18170.04110.287835.03737.32955.415
820.928215.415-12.286728.89930.281712.2576-0.2506-0.7588-0.6668-1.7486-0.43910.0848-0.82570.55780.68970.5772-0.1334-0.14520.10550.07060.094219.57915.51963.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 99
2X-RAY DIFFRACTION2A100 - 211
3X-RAY DIFFRACTION3A212 - 313
4X-RAY DIFFRACTION4A314 - 320
5X-RAY DIFFRACTION5A321 - 383
6X-RAY DIFFRACTION6A384 - 432
7X-RAY DIFFRACTION7A433 - 507
8X-RAY DIFFRACTION8A601

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