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- PDB-3v5t: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v5t | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1299 | ||||||
![]() | Calmodulin-domain protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / calcium-binding / ATP-binding / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Merritt, E.A. / Larson, E.T. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.9 KB | Display | ![]() |
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PDB format | ![]() | 153.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 696.2 KB | Display | ![]() |
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Full document | ![]() | 700.3 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sx9C ![]() 3sxfC ![]() 3t3uC ![]() 3t3vC ![]() 3upxC ![]() 3upzC ![]() 3uqfC ![]() 3uqgC ![]() 3v51C ![]() 3v5pC C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-UW9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% PEG 3350, 225 mM ammonium citrate, 5 mM DTT, 2 mM UW1299, pH 7.5, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: 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 wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.2 % / Av σ(I) over netI: 5 / Number: 105225 / Rsym value: 0.126 / D res high: 2.131 Å / D res low: 36.105 Å / Num. obs: 25308 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.131→36.105 Å / Num. all: 25308 / Num. obs: 25308 / % possible obs: 100 % / Redundancy: 4.2 % / Rsym value: 0.126 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.01 / Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.74 Å2 / Biso mean: 58.4376 Å2 / Biso min: 29.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→34.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.131→2.186 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.583 Å / Origin y: 22.62 Å / Origin z: 59.577 Å
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Refinement TLS group |
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