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Yorodumi- PDB-6z44: Crystal structure of the cAMP-dependent protein kinase A in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z44 | ||||||
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Title | Crystal structure of the cAMP-dependent protein kinase A in complex with phenol | ||||||
Components | cAMP-dependent protein kinase catalytic subunit alpha | ||||||
Keywords | TRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase | ||||||
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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base ...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 / 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 / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / 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: 1.38 Å | ||||||
Authors | Oebbeke, M. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Authors: Oebbeke, M. / Siefker, C. / Wagner, B. / Heine, 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 | 6z44.cif.gz | 260.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z44.ent.gz | 175 KB | Display | PDB format |
PDBx/mmJSON format | 6z44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z44_validation.pdf.gz | 692.8 KB | Display | wwPDB validaton report |
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Full document | 6z44_full_validation.pdf.gz | 692.7 KB | Display | |
Data in XML | 6z44_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 6z44_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/6z44 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/6z44 | HTTPS FTP |
-Related structure data
Related structure data | 5n33C 5n3cC 5n3dC 5n3eC 5n3hC 5n3jC 5n3qC 5n3sC 6snnC 6snxC 6soxC 6spmC 6spsC 6spuC 6spyC 6ypsC 6z08C 6zn0C 6f14S 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: 41113.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase | ||||||
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#2: Chemical | ChemComp-IPH / | ||||||
#3: Chemical | #4: Chemical | ChemComp-MRD / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking: ...Details: 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking: 100mM phenol in buffer described above and 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.379→48.705 Å / Num. obs: 74984 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.85 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.38→1.46 Å / Mean I/σ(I) obs: 3.07 / Num. unique obs: 11843 / Rsym value: 0.497 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F14 Resolution: 1.38→20.12 Å / SU ML: 0.0995 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.2211 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→20.12 Å
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Refine LS restraints |
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LS refinement shell |
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