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- PDB-4m84: 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: 4m84 | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1455 | ||||||
![]() | Calmodulin-domain protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Merritt, E.A. | ||||||
![]() | ![]() 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. #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. / Buckner, F.S. / Parsons, M. / Hol, W.G. / Merritt, E.A. / Van Voorhis, W.C. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204 KB | Display | ![]() |
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PDB format | ![]() | 163.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4onaC ![]() 3sx9S 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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Unit cell |
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Components
#1: Protein | Mass: 55226.914 Da / Num. of mol.: 1 / Fragment: residues 30-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-21E / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1455, 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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 7, 2013 |
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: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.998→48.673 Å / Num. obs: 28948 / % possible obs: 94.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SX9 Resolution: 1.998→48.67 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2548 / WRfactor Rwork: 0.1982 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8093 / SU B: 11.43 / SU ML: 0.156 / SU R Cruickshank DPI: 0.2318 / SU Rfree: 0.1995 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.199 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.14 Å2 / Biso mean: 54.6328 Å2 / Biso min: 25.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.998→48.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 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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