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- PDB-3sx9: 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: 3sx9 | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-132 | ||||||
![]() | Calmodulin-domain protein kinase 1 | ||||||
![]() | transferase/transferase inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase 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 / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Larson, E.T. / Merritt, E.A. | ||||||
![]() | ![]() 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: J.Med.Chem. / Year: 2012 Title: Development of Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitors with Potent Anti-Toxoplasma Activity. Authors: Johnson, S.M. / Murphy, R.C. / Geiger, J.A. / Derocher, A.E. / Zhang, Z. / Ojo, K.K. / Larson, E.T. / Perera, B.G. / Dale, E.J. / He, P. / Reid, M.C. / Fox, A.M. / Mueller, N.R. / Merritt, E. ...Authors: Johnson, S.M. / Murphy, R.C. / Geiger, J.A. / Derocher, A.E. / Zhang, Z. / Ojo, K.K. / Larson, E.T. / Perera, B.G. / Dale, E.J. / He, P. / Reid, M.C. / Fox, A.M. / Mueller, N.R. / Merritt, E.A. / Fan, E. / Parsons, M. / Van Voorhis, W.C. / Maly, D.J. #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. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / 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 | ![]() | 107.9 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sxfC ![]() 3t3uC ![]() 3t3vC ![]() 3upxC ![]() 3upzC ![]() 3uqfC ![]() 3uqgC ![]() 3v51C ![]() 3v5pC ![]() 3v5tC ![]() 3nyvS S: Starting model for refinement 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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Details | biological unit is the same as AU |
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Components
#1: Protein | Mass: 55226.914 Da / Num. of mol.: 1 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-BK7 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 26% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-132; frozen in LN2 after soaking in mother liquor supplemented with 10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2010 |
Diffraction measurement | Details: 1.00 degrees, 12.0 sec, detector distance 400.00 mm |
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 | Av R equivalents: 0.145 / Number: 50603 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 13349 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 9.802 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.506 / Rsym value: 0.857 / % possible all: 100 |
Cell measurement | Reflection used: 50603 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3NYV Resolution: 2.65→46.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.201 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
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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: 111.71 Å2 / Biso mean: 44.9889 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→46.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.638→2.706 Å / Total num. of bins used: 20
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