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Open data
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Basic information
Entry | Database: PDB / ID: 5yv8 | ||||||
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Title | Structure of CaMKK2 in complex with CKI-002 | ||||||
![]() | Calcium/calmodulin-dependent protein kinase kinase 2 | ||||||
![]() | TRANSFERASE / ATP-BINDING / KINASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | ![]() positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / 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 ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niwa, H. / Handa, N. / Yokoyama, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yv9C ![]() 5yvaC ![]() 5yvbC ![]() 5yvcC ![]() 2zv2S 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: 33711.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase | ||||
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#2: Chemical | ChemComp-91L / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.49 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium cacodylate (pH 6.0), 0.2M Sodium acetate, 22% PEG 8000, 0.03M glycyl-glycyl-glycine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 33185 / % possible obs: 100 % / Redundancy: 7.4 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.097 / Rsym value: 0.09 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1621 / CC1/2: 0.769 / Rpim(I) all: 0.398 / Rrim(I) all: 1.082 / Rsym value: 1.005 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZV2 Resolution: 1.927→32.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.62 / Stereochemistry target values: ML Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.927→32.22 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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