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Yorodumi- PDB-3uey: Structural and functional characterization of an anesthetic bindi... -
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-Basic information
Entry | Database: PDB / ID: 3uey | ||||||
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Title | Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase Cdelta | ||||||
Components | Protein kinase C delta type | ||||||
Keywords | METAL BINDING PROTEIN / PROTEINE KINASE Cdelta / PHOSPHOTRANSFERASE / ANESTHETIC BINDING SITE | ||||||
Function / homology | Function and homology information DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / Effects of PIP2 hydrolysis / HuR (ELAVL1) binds and stabilizes mRNA ...DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / Effects of PIP2 hydrolysis / HuR (ELAVL1) binds and stabilizes mRNA / Interferon gamma signaling / Calmodulin induced events / TIR domain binding / endolysosome / positive regulation of ceramide biosynthetic process / negative regulation of peptidyl-tyrosine phosphorylation / Role of phospholipids in phagocytosis / termination of signal transduction / negative regulation of filopodium assembly / protein kinase C / cellular response to hydroperoxide / negative regulation of glial cell apoptotic process / collagen metabolic process / CLEC7A (Dectin-1) signaling / D-aspartate import across plasma membrane / diacylglycerol-dependent serine/threonine kinase activity / RHO GTPases Activate NADPH Oxidases / negative regulation of actin filament polymerization / neutrophil activation / regulation of phosphorylation / negative regulation of platelet aggregation / cellular response to angiotensin / postsynaptic cytosol / B cell proliferation / immunoglobulin mediated immune response / enzyme activator activity / insulin receptor substrate binding / positive regulation of apoptotic signaling pathway / positive regulation of protein dephosphorylation / negative regulation of insulin receptor signaling pathway / Neutrophil degranulation / post-translational protein modification / cell chemotaxis / positive regulation of superoxide anion generation / regulation of actin cytoskeleton organization / positive regulation of glucose import / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cellular response to hydrogen peroxide / nuclear matrix / positive regulation of protein import into nucleus / cellular response to UV / cell-cell junction / cellular senescence / cellular response to oxidative stress / peptidyl-serine phosphorylation / response to oxidative stress / positive regulation of MAPK cascade / protein kinase activity / intracellular signal transduction / defense response to bacterium / cell cycle / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / mitochondrion / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 Å | ||||||
Authors | Shanmugasundararaj, S. / Stehle, T. / Miller, K.W. | ||||||
Citation | Journal: Biophys.J. / Year: 2012 Title: Structural and Functional Characterization of an Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta Authors: Shanmugasundararaj, S. / Das, J. / Sandberg, W.S. / Zhou, X. / Wang, D. / Messing, R.O. / Bruzik, K.S. / Stehle, T. / Miller, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uey.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uey.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 3uey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3uey ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3uey | HTTPS FTP |
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-Related structure data
Related structure data | 3uejC 3uffC 3ugdC 3ugiC 3uglC 1ptqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7360.555 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280 / Mutation: Y236F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcd, Pkcd / Production host: Escherichia coli (E. coli) / References: UniProt: P28867, protein kinase C #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #4: 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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 20% PEG 3350 in 0.2 M ammonium sulfate and 25 mM HEPES pH 7.2. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2004 |
Radiation | Monochromator: SI(111) CHANNEL CULT MONOCHROMAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→10 Å / Num. all: 33077 / Num. obs: 31416 / % possible obs: 95.47 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PTQ Resolution: 1.301→9.986 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 22.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.885 Å2 / ksol: 0.51 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.301→9.986 Å
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Refine LS restraints |
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LS refinement shell |
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