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Yorodumi- PDB-4yjn: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yjn | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1639 | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Merritt, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2015 Title: SAR Studies of 5-Aminopyrazole-4-carboxamide Analogues as Potent and Selective Inhibitors of Toxoplasma gondii CDPK1. Authors: Huang, W. / Ojo, K.K. / Zhang, Z. / Rivas, K. / Vidadala, R.S. / Scheele, S. / DeRocher, A.E. / Choi, R. / Hulverson, M.A. / Barrett, L.K. / Bruzual, I. / Siddaramaiah, L.K. / Kerchner, K.M. ...Authors: Huang, W. / Ojo, K.K. / Zhang, Z. / Rivas, K. / Vidadala, R.S. / Scheele, S. / DeRocher, A.E. / Choi, R. / Hulverson, M.A. / Barrett, L.K. / Bruzual, I. / Siddaramaiah, L.K. / Kerchner, K.M. / Kurnick, M.D. / Freiberg, G.M. / Kempf, D. / Hol, W.G. / Merritt, E.A. / Neckermann, G. / de Hostos, E.L. / Isoherranen, N. / Maly, D.J. / Parsons, M. / Doggett, J.S. / Van Voorhis, W.C. / Fan, E. #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: 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, E. / Geiger, J.A. / Scheele, S. / Choi, R. / Reid, M.C. / Keyloun, K. / Parsons, M. / Merritt, E.A. / Maly, D.J. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Fan, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yjn.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yjn.ent.gz | 161.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/4yjn ftp://data.pdbj.org/pub/pdb/validation_reports/yj/4yjn | HTTPS FTP |
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-Related structure data
Related structure data | 4onaS S: Starting model for refinement |
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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 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: CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BJF5 |
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#2: Chemical | ChemComp-UW4 / |
#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: 2.06 Å3/Da / Density % sol: 40.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1639 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.6→72.64 Å / Num. obs: 12536 / % possible obs: 90.6 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.097 / Net I/σ(I): 5.1 / Num. measured all: 72119 / Scaling rejects: 32 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ONA Resolution: 2.6→64.77 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2554 / WRfactor Rwork: 0.2193 / FOM work R set: 0.7862 / SU B: 33.625 / SU ML: 0.329 / SU R Cruickshank DPI: 0.3841 / SU Rfree: 0.3837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / 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: 151.32 Å2 / Biso mean: 56.735 Å2 / Biso min: 17.53 Å2
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Refinement step | Cycle: final / Resolution: 2.6→64.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 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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