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Yorodumi- PDB-3dne: cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dne | ||||||
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Title | cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24 | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ATP-binding / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Transferase / cAMP / Protein kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of protein import into nucleus / molecular function inhibitor activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / molecular adaptor activity / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Schiffer, A. / Wendt, K.U. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008 Title: Crystallography-independent determination of ligand binding modes Authors: Orts, J. / Tuma, J. / Reese, M. / Grimm, S.K. / Monecke, P. / Bartoschek, S. / Schiffer, A. / Wendt, K.U. / Griesinger, C. / Carlomagno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dne.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dne.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dne ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dne | HTTPS FTP |
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-Related 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: 40707.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: Inhibitory Fragment, UNP residues 6-25 / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P61926 |
#3: Chemical | ChemComp-LL1 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 2 AND 3 IN THE DATABASE, KAPCA_BOVIN. N286D IS CONFLICT OF KAPCA_BOVIN. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 15% Methanol, 75mM LiCl, 30mM MesBisTris, 1mM DTT, 0.2mM EDTA, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2008 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 30051 / Num. obs: 29885 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 98.9 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→18.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.919 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.438 Å2
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Refinement step | Cycle: LAST / Resolution: 2→18.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 Å / Total num. of bins used: 20
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