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Yorodumi- PDB-5izj: Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5izj | |||||||||
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Title | Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411 | |||||||||
Components |
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Keywords | TRANSFERASE / protein kinase / inhibitor / bisubstrate / oligoarginine / PKA | |||||||||
Function / homology | Function and homology information cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / PKA activation in glucagon signalling / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex ...cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / PKA activation in glucagon signalling / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / regulation of protein processing / renal water homeostasis / Hedgehog 'off' state / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of interleukin-2 production / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of proteasomal protein catabolic process / Ion homeostasis / negative regulation of smoothened signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / calcium channel complex / Anchoring of the basal body to the plasma membrane / Mitochondrial protein degradation / cellular response to epinephrine stimulus / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of calcium-mediated signaling / CD209 (DC-SIGN) signaling / regulation of heart rate / AURKA Activation by TPX2 / acrosomal vesicle / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / neural tube closure / Regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / positive regulation of insulin secretion / cytokine-mediated signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / mRNA processing / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / manganese ion binding / Factors involved in megakaryocyte development and platelet production / cellular response to heat / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / mitochondrial matrix / protein domain specific binding / protein phosphorylation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Pflug, A. / Enkvist, E. / Uri, A. / Engh, R.A. | |||||||||
Citation | Journal: Bioconjug.Chem. / Year: 2016 Title: Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions. Authors: Ivan, T. / Enkvist, E. / Viira, B. / Manoharan, G.B. / Raidaru, G. / Pflug, A. / Alam, K.A. / Zaccolo, M. / Engh, R.A. / Uri, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5izj.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5izj.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 5izj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5izj_validation.pdf.gz | 484.6 KB | Display | wwPDB validaton report |
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Full document | 5izj_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 5izj_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 5izj_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5izj ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5izj | HTTPS FTP |
-Related 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, 2 molecules AB
#1: Protein | Mass: 40808.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase |
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-Polypeptide(D) , 2 types, 2 molecules GF
#2: Polypeptide(D) | Mass: 671.861 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: C61H112N32O9 please find a complete description of the molecule in the LIGAND section Source: (synth.) Homo sapiens (human) |
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#3: Polypeptide(D) | Mass: 829.055 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: C61H112N32O9 please find a complete description of the molecule in the LIGAND section Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 639 molecules
#4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.4M lithium sulfate, 0.1M phosphate citrate pH 4.5, 17%-19% PEG 1.5K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.85→50 Å / Num. obs: 65758 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.67 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.9 Å / Rmerge(I) obs: 0.903 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.715 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.696 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→42.6 Å
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