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

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Basic information

Entry
Database: PDB / ID: 3nyv
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with non-specific inhibitor WHI-P180
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase inhibitor / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / 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
4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.88 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
Journal: To be Published
Title: Binding modes of non-specific inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from T. gondii and C. parvum
Authors: Larson, E.T. / Ojo, K.K. / Kim, J.E. / Verlinde, C.L.M.J. / Buckner, F.S. / Hol, W.G.J. / Merritt, E.A. / Van Voorhis, W.C.
#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: ACS Med.Chem.Lett. / Year: 2010
Title: Discovery of potent and selective inhibitors of 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
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,2752
Polymers55,9771
Non-polymers2971
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.272, 72.297, 67.174
Angle α, β, γ (deg.)90.000, 103.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55977.227 Da / Num. of mol.: 1 / Fragment: TgCDPK1, residues 30-507
Source method: isolated from a genetically manipulated source
Details: residues 1-29 were replaced with a 3C cleavable His-tag; tag was cleaved prior to crystallization
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AAG53993, 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-DTQ / 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE


Mass: 297.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM WHI-P180; frozen directly in LN2, pH 6.5, 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: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 36621 / % possible obs: 99.2 % / Observed criterion σ(I): 5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Χ2: 1.072 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.88-1.954.10.4812.2934011.22692.8
1.95-2.034.20.3273.3236781.08599.9
2.03-2.124.20.234.4936611.142100
2.12-2.234.20.1477.1936671.046100
2.23-2.374.20.1198.4436531.08899.9
2.37-2.554.20.0841237061.017100
2.55-2.814.30.06415.4736921.034100
2.81-3.214.30.0423.1436891.02100
3.21-4.054.20.03227.0837151.08399.9
4.05-504.20.02332.193759199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3i7c

3i7c


Resolution: 1.88→43.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.153 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1873 5.1 %RANDOM
Rwork0.1726 ---
obs0.1751 36601 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.9 Å2 / Biso mean: 37.7362 Å2 / Biso min: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å21.16 Å2
2---0.87 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.88→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 22 230 3926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223786
X-RAY DIFFRACTIONr_bond_other_d0.0010.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9765094
X-RAY DIFFRACTIONr_angle_other_deg0.85336406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0835462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45324.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
X-RAY DIFFRACTIONr_mcbond_it2.22842278
X-RAY DIFFRACTIONr_mcbond_other0.7214936
X-RAY DIFFRACTIONr_mcangle_it3.42863678
X-RAY DIFFRACTIONr_scbond_it4.19361508
X-RAY DIFFRACTIONr_scangle_it6.382101412
LS refinement shellResolution: 1.88→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 128 -
Rwork0.202 2547 -
all-2675 -
obs--98.2 %
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)
12.24-1.20091.10894.6126-1.48643.7939-0.1197-0.11140.10740.42430.0412-0.0846-0.2451-0.00720.07850.1431-0.0096-0.04330.1467-0.01160.131913.569615.125673.8118
20.7108-0.27920.51181.2494-0.61491.61620.0146-0.01760.0507-0.0106-0.0677-0.08910.06510.03940.05310.0951-0.0022-0.00860.1122-0.00970.12588.813913.960258.4228
31.1912-0.20570.0952.24870.46021.31550.06780.13340.055-0.3968-0.0567-0.13840.02480.1297-0.01110.13260.02570.00610.1120.00130.05718.019520.947940.4456
40.7416-0.18440.34650.79610.32277.9411-0.1036-0.07580.05030.29110.1412-0.1469-0.2019-0.1716-0.03760.14190.0677-0.0410.0977-0.00340.136925.109634.747575.4909
52.0858-2.50160.88653.2845-2.28795.73590.07040.0194-0.0397-0.1143-0.01410.05740.0894-0.0053-0.05630.15090.0205-0.08450.0942-0.00020.074130.177226.399184.1625
65.4335-1.1416-1.0470.67851.06443.2487-0.04630.13090.16070.0120.02890.1256-0.18910.00480.01740.0771-0.002-0.00260.08770.02410.149730.549737.962553.3718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 89
2X-RAY DIFFRACTION2A90 - 214
3X-RAY DIFFRACTION3A215 - 334
4X-RAY DIFFRACTION4A335 - 373
5X-RAY DIFFRACTION5A374 - 440
6X-RAY DIFFRACTION6A441 - 507

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