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- PDB-3v51: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3v51
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor RM-1-176
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-I76 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6712
Polymers55,2271
Non-polymers4441
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.317, 72.619, 67.356
Angle α, β, γ (deg.)90.000, 103.900, 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-I76 / 3-{6-[(3-chlorobenzyl)oxy]naphthalen-2-yl}-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 443.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22ClN5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 40.78 %
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 RM-1-176, 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: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2010
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: 1.948→39.398 Å / Num. all: 32294 / Num. obs: 32294 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rsym value: 0.068 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.0540.6731.11769544660.67393
2.05-2.184.30.4051.91939545080.40598.8
2.18-2.334.10.2792.71712741540.27997.5
2.33-2.514.30.1794.21719539630.17999.2
2.51-2.754.20.1236.11530736220.12398.6
2.75-3.084.20.07410.11359832550.07497.9
3.08-3.564.20.04714.81227329270.04798.6
3.56-4.364.20.03419.51010924330.03497.8
4.36-6.164.10.03119.6771218990.03197.7
6.16-39.3984.10.02621.4433810670.02697.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→37.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2183 / WRfactor Rwork: 0.1829 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8451 / SU B: 8.713 / SU ML: 0.122 / SU R Cruickshank DPI: 0.194 / SU Rfree: 0.1645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1664 5.2 %RANDOM
Rwork0.1965 ---
obs0.1985 32270 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.3 Å2 / Biso mean: 36.7158 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.74 Å2
2---0.09 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 32 76 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023765
X-RAY DIFFRACTIONr_bond_other_d0.0010.022581
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9795071
X-RAY DIFFRACTIONr_angle_other_deg0.8443.0016291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0885462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9324.857175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33815710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7191520
X-RAY DIFFRACTIONr_chiral_restr0.070.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 108 -
Rwork0.34 1963 -
all-2071 -
obs--86.54 %
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)
11.9552-0.92251.13132.0808-0.72642.8661-0.1171-0.07040.16090.3320.0197-0.2081-0.31470.02410.09740.07940.0026-0.05350.0418-0.01160.157511.89316.26673.286
20.7599-0.41620.60981.2355-0.77592.8713-0.01040.01570.0224-0.0118-0.0778-0.15210.1030.14780.08810.00830.0043-0.01940.069100.19029.05414.00458.238
31.7053-0.3517-0.06422.54170.5091.85380.09590.14620.0937-0.3966-0.0587-0.19970.01850.1494-0.03730.0780.0252-0.00250.10720.00320.14877.59921.22940.538
40.52290.09861.030.72070.673411.9246-0.146-0.10620.00810.27210.2179-0.1382-0.3817-0.2592-0.07190.18820.1255-0.06890.198-0.00810.303125.07134.73676.003
57.8164-2.2142.96277.4816-2.53446.0211-0.01240.1424-0.4068-0.29150.34320.76410.279-0.4253-0.33080.1363-0.0134-0.13650.16420.03730.32425.59323.41885.137
61.1435-1.22552.49871.3373-3.027913.39440.23930.25170.3364-0.2317-0.3413-0.36330.06980.80710.1020.47870.0663-0.09630.3630.07730.465733.79529.13980.538
76.1823-1.8772-1.41931.51250.91133.2233-0.00880.17230.22730.08550.04670.0799-0.2122-0.0135-0.03790.0412-0.0013-0.01950.09330.01220.253330.15338.19453.225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 94
2X-RAY DIFFRACTION2A95 - 214
3X-RAY DIFFRACTION3A215 - 334
4X-RAY DIFFRACTION4A335 - 375
5X-RAY DIFFRACTION5A376 - 413
6X-RAY DIFFRACTION6A414 - 442
7X-RAY DIFFRACTION7A443 - 507

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