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- PDB-4wg4: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 4wg4
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1613
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-UWB / non-specific serine/threonine protein kinase
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 UW1613
Authors: Merritt, E.A.
#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 / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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 / 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)55,6292
Polymers55,2271
Non-polymers4021
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.690, 73.180, 66.770
Angle α, β, γ (deg.)90.000, 99.750, 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-UWB / 3-(7-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 402.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 3350, 250 mM ammonium citrate, 2 mM EDTA, 5 mM DTT, 2 mM UW1613

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→48.93 Å / Num. obs: 20018 / % possible obs: 96.9 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Net I/σ(I): 8.2 / Num. measured all: 144096 / Scaling rejects: 39
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
2.3-2.387.21.7721.11388419280.5320.70296.3
8.91-48.936.80.05624.525133690.9960.02396.7

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Processing

Software
NameVersionClassification
MOSFLM0.1.26data reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementResolution: 2.3→48.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2407 / WRfactor Rwork: 0.1942 / FOM work R set: 0.7778 / SU B: 21.987 / SU ML: 0.237 / SU R Cruickshank DPI: 0.4707 / SU Rfree: 0.2605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1005 5 %RANDOM
Rwork0.2058 19012 --
obs0.2079 19012 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.25 Å2 / Biso mean: 55.429 Å2 / Biso min: 25.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0.36 Å2
2--0.08 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 2.3→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 30 48 3704
Biso mean--47.45 41.84 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193772
X-RAY DIFFRACTIONr_bond_other_d0.0010.023630
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9655083
X-RAY DIFFRACTIONr_angle_other_deg0.80538376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5875465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89124.581179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89915720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.571524
X-RAY DIFFRACTIONr_chiral_restr0.080.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_mcbond_it2.7533.5661831
X-RAY DIFFRACTIONr_mcbond_other2.7433.5641829
X-RAY DIFFRACTIONr_mcangle_it4.4445.3342287
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 68 -
Rwork0.364 1364 -
all-1432 -
obs--96.04 %
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)
14.43312.15020.40245.25250.38992.3622-0.2008-0.07060.2354-0.39760.02920.5068-0.2164-0.16080.17170.07680.0273-0.11330.09370.00030.2084-0.434-20.983-41.606
20.73670.2878-0.04430.71510.31662.19650.0315-0.0493-0.0359-0.05-0.09160.06660.0785-0.04580.06010.024-0.0082-0.06110.13380.02080.30655.495-21.321-26.203
31.4737-0.00560.3891.56420.18511.40360.0208-0.22840.12330.2451-0.0682-0.07380.067-0.18230.04740.0468-0.0276-0.04460.23910.00890.18965.678-14.72-7.99
40.1657-0.0821-0.05420.487-1.660210.7751-0.0401-0.03910.0208-0.087-0.03290.055-0.08510.05830.0730.1256-0.0222-0.07920.1338-0.01450.1756-11.298-0.89-42.513
53.75752.9430.45617.1008-1.22254.28780.1244-0.2396-0.3853-0.3397-0.24320.0536-0.11140.23130.11870.1430.0047-0.16840.0987-0.01210.2258-13.905-8.97-52.161
65.78561.4716-2.03510.5522-0.89784.13230.0071-0.0960.3113-0.0280.14410.0702-0.0773-0.1479-0.15120.0264-0.0297-0.05460.1759-0.05020.2706-16.8951.713-21.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 87
2X-RAY DIFFRACTION2A88 - 213
3X-RAY DIFFRACTION3A214 - 334
4X-RAY DIFFRACTION4A335 - 373
5X-RAY DIFFRACTION5A374 - 436
6X-RAY DIFFRACTION6A437 - 507

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