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Yorodumi- PDB-6bfa: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bfa | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1553 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / bumped kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / protein kinase activity / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Merritt, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2016 Title: Development of an Orally Available and Central Nervous System (CNS) Penetrant Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitor with Minimal Human Ether-a-go-go-Related ...Title: Development of an Orally Available and Central Nervous System (CNS) Penetrant Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitor with Minimal Human Ether-a-go-go-Related Gene (hERG) Activity for the Treatment of Toxoplasmosis. Authors: Vidadala, R.S. / Rivas, K.L. / Ojo, K.K. / Hulverson, M.A. / Zambriski, J.A. / Bruzual, I. / Schultz, T.L. / Huang, W. / Zhang, Z. / Scheele, S. / DeRocher, A.E. / Choi, R. / Barrett, L.K. / ...Authors: Vidadala, R.S. / Rivas, K.L. / Ojo, K.K. / Hulverson, M.A. / Zambriski, J.A. / Bruzual, I. / Schultz, T.L. / Huang, W. / Zhang, Z. / Scheele, S. / DeRocher, A.E. / Choi, R. / Barrett, L.K. / Siddaramaiah, L.K. / Hol, W.G. / Fan, E. / Merritt, E.A. / Parsons, M. / Freiberg, G. / Marsh, K. / Kempf, D.J. / Carruthers, V.B. / Isoherranen, N. / Doggett, J.S. / Van Voorhis, W.C. / Maly, D.J. #1: 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 | 6bfa.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bfa.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bfa_validation.pdf.gz | 668.4 KB | Display | wwPDB validaton report |
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Full document | 6bfa_full_validation.pdf.gz | 674.9 KB | Display | |
Data in XML | 6bfa_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6bfa_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/6bfa ftp://data.pdbj.org/pub/pdb/validation_reports/bf/6bfa | HTTPS FTP |
-Related 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 BL21(DE3) (bacteria) References: UniProt: Q9BJF5, UniProt: A0A0F7UUA6*PLUS, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-UW5 / |
#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: 2.05 Å3/Da / Density % sol: 40.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 24% PEG3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1533 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97944 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→36.23 Å / Num. obs: 10998 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.296 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.325 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MODEL Resolution: 2.8→36.23 Å / SU B: 48.32 / SU ML: 0.434 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.478 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 69.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→36.23 Å
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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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