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- PDB-1dsy: C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dsy | ||||||
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Title | C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE | ||||||
![]() | PROTEIN KINASE C, ALPHA TYPE | ||||||
![]() | TRANSFERASE / CALCIUM++ / PHOSPHOLIPID BINDING PROTEIN / CALCIUM-BINDING PROTEIN / PHOSPHATIDYLSERINE / PROTEIN KINASE C | ||||||
Function / homology | ![]() Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling ...Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ / positive regulation of angiotensin-activated signaling pathway / desmosome assembly / positive regulation of dense core granule biogenesis / histone H3T6 kinase activity / cone photoreceptor outer segment / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / regulation of receptor-mediated endocytosis / ooplasm / RET signaling / central nervous system neuron axonogenesis / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / cellular response to carbohydrate stimulus / regulation of response to osmotic stress / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / regulation of muscle contraction / positive regulation of macrophage differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / alphav-beta3 integrin-PKCalpha complex / regulation of the force of heart contraction / induction of positive chemotaxis / negative regulation of glucose import / presynaptic cytosol / positive regulation of synapse assembly / negative regulation of MAPK cascade / regulation of synaptic vesicle exocytosis / muscle cell cellular homeostasis / response to corticosterone / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / Trafficking of GluR2-containing AMPA receptors / calyx of Held / positive regulation of cell adhesion / intercalated disc / positive regulation of blood vessel endothelial cell migration / positive regulation of bone resorption / chondrocyte differentiation / response to mechanical stimulus / regulation of peptidyl-tyrosine phosphorylation / positive regulation of endothelial cell proliferation / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of mitotic cell cycle / response to interleukin-1 / intrinsic apoptotic signaling pathway / neutrophil chemotaxis / post-translational protein modification / ciliary basal body / negative regulation of protein phosphorylation / stem cell differentiation / response to reactive oxygen species / mitochondrial membrane / positive regulation of smooth muscle cell proliferation / peptidyl-threonine phosphorylation / establishment of protein localization / response to organic cyclic compound / response to toxic substance / response to peptide hormone / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of angiogenesis / integrin binding / apical part of cell / response to estradiol / angiogenesis / response to ethanol / cell population proliferation / learning or memory / positive regulation of ERK1 and ERK2 cascade / negative regulation of translation / cell adhesion / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / lipid binding / dendrite / perinuclear region of cytoplasm / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Verdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C. | ||||||
![]() | ![]() Title: Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine. Authors: Verdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 464.5 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16240.451 Da / Num. of mol.: 1 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05696, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-PSF / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.32 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8K, POTASSIUM PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 5950 / Num. obs: 5610 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Num. unique all: 562 / % possible all: 95.1 |
Reflection | *PLUS Num. measured all: 17072 |
Reflection shell | *PLUS % possible obs: 95.1 % |
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Processing
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Refinement | Resolution: 2.6→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→18 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.233 / Rfactor Rwork: 0.195 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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