+Open data
-Basic information
Entry | Database: PDB / ID: 5t5t | ||||||
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Title | AMPK bound to allosteric activator | ||||||
Components |
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Keywords | TRANSFERASE / AMPK / Kinase / allostery / activator | ||||||
Function / homology | Function and homology information eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [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 / regulation of bile acid secretion / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / : / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / protein kinase regulator activity / bile acid signaling pathway / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / positive regulation of protein localization / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / fatty acid homeostasis / positive regulation of adipose tissue development / cellular response to nutrient levels / negative regulation of lipid catabolic process / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / cellular response to glucose starvation / response to UV / energy homeostasis / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / positive regulation of glucose import / regulation of circadian rhythm / response to gamma radiation / cellular response to glucose stimulus / response to hydrogen peroxide / ADP binding / Wnt signaling pathway / fatty acid biosynthetic process / autophagy / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to xenobiotic stimulus / rhythmic process / cellular response to prostaglandin E stimulus / glucose metabolic process / glucose homeostasis / cellular response to hypoxia / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / non-specific serine/threonine protein kinase / negative regulation of translation / protein kinase activity / nuclear speck / apical plasma membrane / response to xenobiotic stimulus / protein phosphorylation / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / neuronal cell body / positive regulation of cell population proliferation / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / signal transduction Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.46 Å | ||||||
Authors | Calabrese, M.F. / Kurumbail, R.G. | ||||||
Citation | Journal: J. Pharmacol. Exp. Ther. / Year: 2017 Title: Selective Activation of AMPK beta 1-Containing Isoforms Improves Kidney Function in a Rat Model of Diabetic Nephropathy. Authors: Salatto, C.T. / Miller, R.A. / Cameron, K.O. / Cokorinos, E. / Reyes, A. / Ward, J. / Calabrese, M.F. / Kurumbail, R.G. / Rajamohan, F. / Kalgutkar, A.S. / Tess, D.A. / Shavnya, A. / Genung, ...Authors: Salatto, C.T. / Miller, R.A. / Cameron, K.O. / Cokorinos, E. / Reyes, A. / Ward, J. / Calabrese, M.F. / Kurumbail, R.G. / Rajamohan, F. / Kalgutkar, A.S. / Tess, D.A. / Shavnya, A. / Genung, N.E. / Edmonds, D.J. / Jatkar, A. / Maciejewski, B.S. / Amaro, M. / Gandhok, H. / Monetti, M. / Cialdea, K. / Bollinger, E. / Kreeger, J.M. / Coskran, T.M. / Opsahl, A.C. / Boucher, G.G. / Birnbaum, M.J. / DaSilva-Jardine, P. / Rolph, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t5t.cif.gz | 351.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t5t.ent.gz | 280.8 KB | Display | PDB format |
PDBx/mmJSON format | 5t5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t5t_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5t5t_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5t5t_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 5t5t_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/5t5t ftp://data.pdbj.org/pub/pdb/validation_reports/t5/5t5t | HTTPS FTP |
-Related structure data
Related structure data | 4qfgS S: Starting model for refinement |
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Similar structure data |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57779.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Production host: Escherichia coli (E. coli) References: UniProt: P54645, 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: 23055.291 Da / Num. of mol.: 1 / Mutation: S108D, Q109H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80386 |
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#3: Protein | Mass: 37434.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkag1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80385 |
-Non-polymers , 6 types, 10 molecules
#4: Chemical | ChemComp-STU / | ||||||||
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#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-75O / | #8: Chemical | #9: Chemical | ChemComp-ADP / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 100 mM trisodium citrate, 500 mM ammonium sulfate, 900 mM lithium sulfate, and 4% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→50 Å / Num. obs: 25312 / % possible obs: 99.8 % / Redundancy: 14.8 % / Biso Wilson estimate: 93.57 Å2 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 3.45→3.57 Å / Redundancy: 15 % / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QFG Resolution: 3.46→40.93 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397 / SU Rfree Cruickshank DPI: 0.399
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Displacement parameters | Biso max: 225.67 Å2 / Biso mean: 125.23 Å2 / Biso min: 59.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.46→40.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.46→3.6 Å / Total num. of bins used: 13
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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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