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Yorodumi- PDB-4wg3: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wg3 | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1610 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / bumped kinase inhibitor / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | Function and homology information phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Merritt, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1610 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wg3.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wg3.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/4wg3 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/4wg3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-UWA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 28% PEG 3350, 250 mM ammonium citrate, 2 mM EDTA, 5 mM DTT, 2 mM UW1610 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→65.27 Å / Num. obs: 21941 / % possible obs: 95.7 % / Redundancy: 7.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.068 / Net I/σ(I): 8.2 / Num. measured all: 166095 / Scaling rejects: 52 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.2→65.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2132 / WRfactor Rwork: 0.1729 / FOM work R set: 0.7161 / SU B: 24.649 / SU ML: 0.258 / SU R Cruickshank DPI: 0.3743 / SU Rfree: 0.2296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.55 Å2 / Biso mean: 59.487 Å2 / Biso min: 27.71 Å2
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Refinement step | Cycle: final / Resolution: 2.2→65.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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