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Yorodumi- PDB-6t28: Crystal structure of human calmodulin-dependent protein kinase 1D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t28 | ||||||
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Title | Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 19 (CS640) | ||||||
Components | Calcium/calmodulin-dependent protein kinase type 1D | ||||||
Keywords | TRANSFERASE / Inhibitor / Complex / Kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calcium/calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development ...regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calcium/calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development / calmodulin binding / inflammatory response / positive regulation of apoptotic process / protein serine kinase activity / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Kraemer, A. / Sorrell, F. / Butterworth, S. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesityin VivoMouse Model. Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. ...Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. / Box, C. / Kumar, J. / Grant, P. / Novitskaya, V. / Morgan, J. / Sorrell, F.J. / Redondo, C. / Kramer, A. / Harris, C.J. / Leighton, B. / Vickers, S.P. / Cheetham, S.C. / Kenyon, C. / Grabowska, A.M. / Overduin, M. / Berditchevski, F. / Weston, C.J. / Knapp, S. / Fischer, P.M. / Butterworth, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t28.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t28.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/6t28 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/6t28 | HTTPS FTP |
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-Related structure data
Related structure data | 6t29C 2jc6S S: Starting model for refinement C: citing same article (ref.) |
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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: 42972.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1D, CAMKID / Production host: Escherichia coli (E. coli) References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-M92 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.9 / Details: 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→33.8 Å / Num. obs: 34389 / % possible obs: 86.2 % / Redundancy: 4 % / CC1/2: 0.996 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.55→1.58 Å / Num. unique obs: 1829 / CC1/2: 0.806 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2jc6 Resolution: 1.55→31.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.103 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.081 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.177 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→31.78 Å
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Refine LS restraints |
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LS refinement shell |
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