+Open data
-Basic information
Entry | Database: PDB / ID: 5yvb | ||||||
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Title | Structure of CaMKK2 in complex with CKI-011 | ||||||
Components | Calcium/calmodulin-dependent protein kinase kinase 2 | ||||||
Keywords | TRANSFERASE / ATP-BINDING / KINASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/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 ...regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/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: 2.02 Å | ||||||
Authors | Niwa, H. / Handa, N. / Yokoyama, S. | ||||||
Citation | Journal: J.Mol.Graph.Model. / Year: 2020 Title: Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method. Authors: Takaya, D. / Niwa, H. / Mikuni, J. / Nakamura, K. / Handa, N. / Tanaka, A. / Yokoyama, S. / Honma, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yvb.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yvb.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yvb_validation.pdf.gz | 751.9 KB | Display | wwPDB validaton report |
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Full document | 5yvb_full_validation.pdf.gz | 753.7 KB | Display | |
Data in XML | 5yvb_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 5yvb_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/5yvb ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yvb | HTTPS FTP |
-Related structure data
Related structure data | 5yv8C 5yv9C 5yvaC 5yvcC 2zv2S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33711.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMKK2, CAMKKB, KIAA0787 / Plasmid: PX070406-05 / Production host: CELL-FREE SYNTHESIS (others) References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase |
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-Non-polymers , 5 types, 219 molecules
#2: Chemical | ChemComp-92C / ( | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-CL / | #6: 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: 3.25 Å3/Da / Density % sol: 62.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium cocodylate pH 6.5, 0.2M ammonium acetate, 32% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 29365 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.104 / Rsym value: 0.096 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1422 / CC1/2: 0.659 / Rpim(I) all: 0.44 / Rrim(I) all: 1.199 / Rsym value: 1.114 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZV2 Resolution: 2.02→38.773 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 21.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→38.773 Å
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Refine LS restraints |
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LS refinement shell |
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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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