+Open data
-Basic information
Entry | Database: PDB / ID: 6cd6 | ||||||
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Title | Crystal Structure of the Human CAMKK1A in complex with GSK650394 | ||||||
Components | Calcium/calmodulin-dependent protein kinase kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Ca2+/calmodulin-dependent protein kinase / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / positive regulation of protein kinase activity / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...Ca2+/calmodulin-dependent protein kinase / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / positive regulation of protein kinase activity / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Santiago, A.S. / Counago, R.M. / Righetto, G.L. / Ramos, P.Z. / Silva, P.N.B. / Drewry, D. / Elkins, J.M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To be Published Title: Crystal Structure of the Human CAMKK1A in complex with GSK650394 Authors: Santiago, A.S. / Counago, R.M. / Righetto, G.L. / Ramos, P.Z. / Silva, P.N.B. / Drewry, D. / Elkins, J.M. / Massirer, K.B. / Arruda, P. / Edwards, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cd6.cif.gz | 220.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cd6.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 6cd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cd6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6cd6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6cd6_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 6cd6_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd6 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd6 | HTTPS FTP |
-Related structure data
Related structure data | 6ccfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 32702.705 Da / Num. of mol.: 4 / Fragment: UNP residues 124-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK1, CAMKKA / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 References: UniProt: Q8N5S9, Ca2+/calmodulin-dependent protein kinase #2: Chemical | ChemComp-DXV / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 33.75% PEG2000 MME, 0.15 M potassium thiocyanate, 0.1 M CHC buffer, pH 7.0, cryoprotectant: 30% polyethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2017 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.94 Å / Num. obs: 59443 / % possible obs: 98.8 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.046 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.152 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4575 / CC1/2: 0.893 / Rpim(I) all: 0.69 / Rrim(I) all: 1.344 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CCF Resolution: 2.2→19.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.255 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.247 / 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: 59.267 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→19.94 Å
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