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

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Basic information

Entry
Database: PDB / ID: 3upz
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumpless BKI analog UW1243
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / 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-B5A / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionNov 18, 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)55,4592
Polymers55,2271
Non-polymers2321
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.270, 72.790, 67.290
Angle α, β, γ (deg.)90.000, 103.490, 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
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-B5A / 1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 232.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 0.250 M ammonium citrate, 5 mM DTT, 2.3 mM UW1243, 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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 16, 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
ReflectionResolution: 2.2→37.158 Å / Num. all: 22898 / Num. obs: 22898 / % possible obs: 99.1 % / Redundancy: 4 % / Rsym value: 0.084 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.323.70.4981.31137431160.49893.6
2.32-2.464.10.411.81300831780.41100
2.46-2.634.10.312.41223029900.31100
2.63-2.844.10.213.41147327940.21100
2.84-3.114.10.1295.61050625540.129100
3.11-3.484.10.0769.3960623410.076100
3.48-4.024.10.05312.6847220600.053100
4.02-4.924.10.03916.8716917440.039100
4.92-6.964.10.05510.6551613560.055100
6.96-37.1583.90.02226.730117650.02299.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2442 / WRfactor Rwork: 0.1809 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8375 / SU B: 15.016 / SU ML: 0.18 / SU R Cruickshank DPI: 0.3249 / SU Rfree: 0.2353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1171 5.1 %RANDOM
Rwork0.191 ---
obs0.1941 22879 99.03 %-
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: 118.42 Å2 / Biso mean: 53.7697 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å21.49 Å2
2---1.94 Å20 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 17 65 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023783
X-RAY DIFFRACTIONr_bond_other_d0.0010.022630
X-RAY DIFFRACTIONr_angle_refined_deg0.891.9755096
X-RAY DIFFRACTIONr_angle_other_deg0.7613.0016414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.435469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30524.804179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59715730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0821522
X-RAY DIFFRACTIONr_chiral_restr0.0510.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 79 -
Rwork0.293 1379 -
all-1458 -
obs--89.12 %
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)
13.7799-1.07561.05164.3024-0.70122.0029-0.0905-0.03850.17720.2770.0575-0.0019-0.2876-0.11380.0330.14190.0075-0.01990.086-0.01840.024710.4516.23372.847
20.79880.00580.66791.2224-0.62412.48860.0244-0.0575-0.0427-0.0725-0.0901-0.13640.09670.13190.06570.05080.0068-0.01080.05910.01240.04669.93512.04957.335
32.16430.0488-0.12722.91630.64581.95830.0790.11820.0324-0.4094-0.0662-0.194-0.02030.1578-0.01280.09530.02080.01460.07050.01240.02188.54122.19842.144
40.337-0.5458-1.35461.84274.118722.2308-0.0578-0.0671-0.13150.21450.0985-0.058-0.3054-0.015-0.04060.10190.0533-0.0240.12080.03770.1424.32334.03968.202
54.5267-2.50310.33577.84310.55054.9730.0059-0.02440.1364-0.20910.12730.0831-0.0032-0.1563-0.13320.31390.0434-0.11040.19670.00830.124828.44927.85186.427
68.0024-2.2079-2.02312.54932.00693.702-0.0267-0.00090.26890.22070.16140.0793-0.14960.153-0.13470.1254-0.0040.00460.07640.02620.091331.0337.38354.644
712.63525.9952-0.8583114.7056-45.955831.9546-0.2662-0.17330.2039-1.2691-0.5834-0.7490.51030.19650.84960.0380.0150.00560.0672-0.00730.02717.564115.960961.7548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 99
2X-RAY DIFFRACTION2A100 - 203
3X-RAY DIFFRACTION3A204 - 334
4X-RAY DIFFRACTION4A335 - 363
5X-RAY DIFFRACTION5A364 - 435
6X-RAY DIFFRACTION6A436 - 507
7X-RAY DIFFRACTION7A1

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