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- PDB-6c9h: non-phosphorylated AMP-activated protein kinase bound to pharmaco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c9h | |||||||||||||||||||||||||||
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Title | non-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734 | |||||||||||||||||||||||||||
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![]() | TRANSFERASE / AMPK / activator / R734 | |||||||||||||||||||||||||||
Function / homology | ![]() negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / nucleotide-activated protein kinase complex / : / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of hepatocyte apoptotic process / tau-protein kinase / protein kinase regulator activity / bile acid and bile salt transport / cellular response to ethanol / protein localization to lipid droplet / negative regulation of TOR signaling / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / cAMP-dependent protein kinase activity / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / tau-protein kinase activity / positive regulation of protein localization / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / cellular response to nutrient levels / positive regulation of protein kinase activity / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / response to UV / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / negative regulation of insulin receptor signaling pathway / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to gamma radiation / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / tau protein binding / regulation of circadian rhythm / ADP binding / Wnt signaling pathway / fatty acid biosynthetic process / autophagy / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to prostaglandin E stimulus / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / response to hypoxia / protein kinase activity / nuclear speck / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / chromatin binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Yan, Y. / Zhou, X.E. / Novick, S. / Shaw, S.J. / Li, Y. / Hitoshi, Y. / Brunzelle, J.S. / Griffin, P.R. / Xu, H.E. / Melcher, K. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states. Authors: Yan, Y. / Zhou, X.E. / Novick, S.J. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.2 KB | Display | ![]() |
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PDB format | ![]() | 307.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 46.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c9fC ![]() 6c9gC ![]() 6c9jC ![]() 4rerS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57165.641 Da / Num. of mol.: 1 / Mutation: S108D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase |
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-5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC
#2: Protein | Mass: 23071.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 37626.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 85 molecules ![](data/chem/img/R34.gif)
![](data/chem/img/STU.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/STU.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-R34 / | ||
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#5: Chemical | ChemComp-STU / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 54649 / % possible obs: 99.7 % / Redundancy: 33.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.571 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.65→2.73 Å / Rmerge(I) obs: 0.716 / Num. unique obs: 4387 / CC1/2: 0.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RER Resolution: 2.65→49.884 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→49.884 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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