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Yorodumi- PDB-3ugl: Structural and functional characterization of an anesthetic bindi... -
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-Basic information
Entry | Database: PDB / ID: 3ugl | ||||||
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Title | Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta | ||||||
Components | Proteine kinase C delta type | ||||||
Keywords | METAL BINDING PROTEIN / Proteine kinase C delta / PHOSPHOTRANSFERASE / Anesthetic binding site | ||||||
Function / homology | Function and homology information DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / VEGFR2 mediated cell proliferation / Apoptotic cleavage of cellular proteins / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / SHC1 events in ERBB2 signaling / Effects of PIP2 hydrolysis / Interferon gamma signaling ...DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / VEGFR2 mediated cell proliferation / Apoptotic cleavage of cellular proteins / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / SHC1 events in ERBB2 signaling / Effects of PIP2 hydrolysis / Interferon gamma signaling / HuR (ELAVL1) binds and stabilizes mRNA / Calmodulin induced events / TIR domain binding / endolysosome / positive regulation of ceramide biosynthetic process / Role of phospholipids in phagocytosis / negative regulation of peptidyl-tyrosine phosphorylation / termination of signal transduction / negative regulation of filopodium assembly / protein kinase C / cellular response to hydroperoxide / D-aspartate import across plasma membrane / diacylglycerol-dependent serine/threonine kinase activity / CLEC7A (Dectin-1) signaling / negative regulation of glial cell apoptotic process / RHO GTPases Activate NADPH Oxidases / collagen metabolic process / negative regulation of actin filament polymerization / neutrophil activation / negative regulation of platelet aggregation / regulation of phosphorylation / cellular response to angiotensin / postsynaptic cytosol / B cell proliferation / insulin receptor substrate binding / immunoglobulin mediated immune response / : / negative regulation of insulin receptor signaling pathway / enzyme activator activity / Neutrophil degranulation / cell chemotaxis / post-translational protein modification / positive regulation of superoxide anion generation / positive regulation of D-glucose import / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of apoptotic signaling pathway / nuclear matrix / positive regulation of protein import into nucleus / cellular response to hydrogen peroxide / cellular senescence / cellular response to UV / cell-cell junction / cellular response to oxidative stress / peptidyl-serine phosphorylation / response to oxidative stress / positive regulation of MAPK cascade / intracellular signal transduction / defense response to bacterium / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.357 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. #1: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: Crystal structure of the cys2 activator binding domain of protein kinase C delta in complex with phorbol ester Authors: Zhang, G. / Kazanietz, M.G. / Blumberg, P.M. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ugl.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ugl.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ugl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ugl_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 3ugl_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 3ugl_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3ugl_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/3ugl ftp://data.pdbj.org/pub/pdb/validation_reports/ug/3ugl | HTTPS FTP |
-Related structure data
Related structure data | 3uejC 3ueyC 3uffC 3ugdC 3ugiC 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: 7376.554 Da / Num. of mol.: 2 / Fragment: C1B Subdomain of PKC delta, UNP residues 231-280 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 | #4: Chemical | #5: 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: 2.4 Å3/Da / Density % sol: 48.82 % |
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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 MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→10 Å / Num. all: 30362 / Num. obs: 28279 / % possible obs: 92.51 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PTQ Resolution: 1.357→9.986 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 16.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.422 Å2 / ksol: 0.546 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.357→9.986 Å
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Refine LS restraints |
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LS refinement shell |
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