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Yorodumi- PDB-5ot3: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -
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-Basic information
Entry | Database: PDB / ID: 5ot3 | ||||||
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Title | Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp191 and RKp117 | ||||||
Components | (cAMP-dependent protein kinase ...) x 2 | ||||||
Keywords | TRANSFERASE / Complex / peptidic ligand | ||||||
Function / homology | Function and homology information regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / 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 protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Mueller, J.M. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Omega / Year: 2019 Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ot3.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ot3.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 5ot3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ot3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ot3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ot3_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5ot3_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5ot3 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5ot3 | HTTPS FTP |
-Related structure data
Related structure data | 5nw8C 5o0eC 5o5mC 5ol3C 5ouaC 5ousC 6egwC 6eh0C 6eh2C 6em2C 6em6C 6em7C 6emaC 6ertC 6eruC 6ervC 6erwC 6esaC 6i2aC 6i2bC 6i2cC 6i2dC 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
-CAMP-dependent protein kinase ... , 2 types, 2 molecules AD
#1: Protein | Mass: 41193.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P25321, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 1989.177 Da / Num. of mol.: 1 / Fragment: UNP Residues 6-23 / Source method: obtained synthetically Details: cAMP-dependent protein kinase inhibitor with A17RBS mutation Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS |
-Sugars , 1 types, 1 molecules
#5: Sugar | ChemComp-RIP / |
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-Non-polymers , 4 types, 95 molecules
#3: Chemical | ChemComp-9LQ / [ |
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#4: Chemical | ChemComp-MPD / ( |
#6: Chemical | ChemComp-CL / |
#7: Water | ChemComp-HOH / |
-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: 49.07 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM RKp117, 20 % v/v methanol/water in reservoir |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.886 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→42.007 Å / Num. obs: 25374 / % possible obs: 99.9 % / Redundancy: 7.63 % / CC1/2: 0.999 / Rsym value: 0.06 / Net I/σ(I): 20.68 |
Reflection shell | Resolution: 2.04→2.16 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.86 / Num. unique obs: 4008 / CC1/2: 0.912 / Rsym value: 0.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→42.007 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→42.007 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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