+Open data
-Basic information
Entry | Database: PDB / ID: 6e4u | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of AMPK bound to activator | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / Kinase / AMPK / activator / allostery / TRANSFERASE-ACTIVATOR complex | ||||||
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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / [acetyl-CoA carboxylase] 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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / [acetyl-CoA carboxylase] 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 / import into nucleus / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / cellular response to organonitrogen compound / protein kinase regulator activity / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / nucleotide-activated protein kinase complex / cellular response to ethanol / protein localization to lipid droplet / bile acid signaling pathway / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / negative regulation of tubulin deacetylation / AMP-activated protein kinase activity / positive regulation of protein localization / tau-protein kinase activity / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / cellular response to glucose starvation / positive regulation of autophagy / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / energy homeostasis / response to UV / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / ADP binding / cellular response to glucose stimulus / response to gamma radiation / positive regulation of glucose import / response to hydrogen peroxide / regulation of circadian rhythm / cellular response to hydrogen peroxide / Wnt signaling pathway / autophagy / neuron cellular homeostasis / cellular response to prostaglandin E stimulus / response to estrogen / fatty acid biosynthetic process / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / response to xenobiotic stimulus / apical plasma membrane / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / chromatin binding / positive regulation of cell population proliferation / chromatin / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.27 Å | ||||||
Authors | Calabrese, M.F. / Kurumbail, R.G. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of ...Title: Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (AMPK). Authors: Ryder, T.F. / Calabrese, M.F. / Walker, G.S. / Cameron, K.O. / Reyes, A.R. / Borzilleri, K.A. / Delmore, J. / Miller, R. / Kurumbail, R.G. / Ward, J. / Kung, D.W. / Brown, J.A. / Edmonds, D. ...Authors: Ryder, T.F. / Calabrese, M.F. / Walker, G.S. / Cameron, K.O. / Reyes, A.R. / Borzilleri, K.A. / Delmore, J. / Miller, R. / Kurumbail, R.G. / Ward, J. / Kung, D.W. / Brown, J.A. / Edmonds, D.J. / Eng, H. / Wolford, A.C. / Kalgutkar, A.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6e4u.cif.gz | 342.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6e4u.ent.gz | 284.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e4u ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e4u | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 |
---|
-5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC
#2: Protein | Mass: 23097.242 Da / Num. of mol.: 1 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 |
---|---|
#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 / | ||||||
---|---|---|---|---|---|---|---|
#5: Chemical | ChemComp-HU7 / | ||||||
#6: Chemical | ChemComp-CL / #7: Chemical | #8: Chemical | ChemComp-ADP / | #9: Chemical | ChemComp-SO4 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.27→107.82 Å / Num. obs: 29561 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 91.45 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 3.27→3.39 Å / Rmerge(I) obs: 0.643 / Num. unique all: 1836 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.27→107.82 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.882 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.215 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.393 / SU Rfree Blow DPI: 0.368 / SU Rfree Cruickshank DPI: 0.371 Details: Data collection and scaling were performed to 3.27 A. Final refinement was to 3.35 A
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 210.52 Å2 / Biso mean: 100.67 Å2 / Biso min: 42.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.27→107.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.27→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|