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Yorodumi- PDB-5nw8: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -
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-Basic information
Entry | Database: PDB / ID: 5nw8 | ||||||
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Title | Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp032 and Fasudil | ||||||
Components |
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Keywords | TRANSFERASE / Complex / peptidic ligand / ribose | ||||||
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 / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / 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 / 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 / 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: 2.086 Å | ||||||
Authors | Mueller, J.M. / Heine, A. / Klebe, G. | ||||||
Funding support | 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 | 5nw8.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nw8.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nw8_validation.pdf.gz | 772.9 KB | Display | wwPDB validaton report |
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Full document | 5nw8_full_validation.pdf.gz | 772.7 KB | Display | |
Data in XML | 5nw8_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5nw8_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/5nw8 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/5nw8 | HTTPS FTP |
-Related structure data
Related structure data | 5o0eC 5o5mC 5ol3C 5ot3C 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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD
#1: Protein | Mass: 40998.551 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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P25321, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 1903.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with S14RBS mutation / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48 |
#5: Sugar | ChemComp-RIP / |
-Non-polymers , 3 types, 182 molecules
#3: Chemical | ChemComp-MPD / ( |
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#4: Chemical | ChemComp-M77 / |
#6: 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: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 5 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 Fasudil x HCl, 16 % v/v methanol/water in reservoir |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.086→42.209 Å / Num. obs: 23612 / % possible obs: 98 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rsym value: 0.075 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.09→2.21 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.95 / Num. unique obs: 3709 / CC1/2: 0.91 / Rsym value: 0.375 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.086→42.209 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.086→42.209 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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