+Open data
-Basic information
Entry | Database: PDB / ID: 6bku | ||||||
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Title | Crystal Structure of the Human CAMKK2B bound to GSK650394 | ||||||
Components | Calcium/calmodulin-dependent protein kinase kinase 2 | ||||||
Keywords | TRANSFERASE / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase Inhibitor Complex | ||||||
Function / homology | Function and homology information positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / Activation of AMPK downstream of NMDARs / calcium-mediated signaling / cellular response to reactive oxygen species / MAPK cascade / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Ramos, P.Z. / Drewry, D. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Human CAMKK2B bound to GSK650394 Authors: Counago, R.M. / dos Reis, C.V. / de Souza, G.P. / Ramos, P.Z. / Drewry, D. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bku.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bku.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bku ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bku | HTTPS FTP |
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-Related structure data
Related structure data | 5uyjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33127.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK2, CAMKKB, KIAA0787 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-DXV / |
#3: Chemical | ChemComp-FMT / |
#4: 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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20% PEG smear medium, 0.2M sodium formate, 0.1M sodium-potassium phosphate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.97 Å / Num. obs: 20267 / % possible obs: 89.9 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.033 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1601 / CC1/2: 0.534 / Rpim(I) all: 0.579 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UYJ Resolution: 2→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.524 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 44.588 Å2
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Refinement step | Cycle: 1 / Resolution: 2→19.97 Å
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