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Yorodumi- PDB-6y0b: Crystal structure of the cAMP-dependent protein kinase A cocrysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y0b | ||||||
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Title | Crystal structure of the cAMP-dependent protein kinase A cocrystallized with quinazolin-4-amine and PKI (5-24) | ||||||
Components |
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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 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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Oebbeke, M. / Wienen-Schmidt, B. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Fragment based drug design - Small chemical changes of fragments effecting big changes in binding Authors: Oebbeke, M. / Wienen-Schmidt, B. / Gerber, H.-D. / 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 | 6y0b.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y0b.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 6y0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y0b_validation.pdf.gz | 732.8 KB | Display | wwPDB validaton report |
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Full document | 6y0b_full_validation.pdf.gz | 733.5 KB | Display | |
Data in XML | 6y0b_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6y0b_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0b ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0b | HTTPS FTP |
-Related structure data
Related structure data | 6f14SC 6y05C 6y2oC 6y2uC 6y89C 6yotC 6youC 7axtC 7axvC 7axwC 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 Details: The first aminoacid (G) is numbered as -2 -> Therefore Methionine is number 0. The last aminoacid is number 350. Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA 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: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248 |
#3: Chemical | ChemComp-1LQ / |
#4: Chemical | ChemComp-DMS / |
#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: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM quinazolin-4-amine in DMSO, 0.5 mM PKI (5-24) and 22 % methanol (v/v)0.003 mL drop volume, 0. ...Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM quinazolin-4-amine in DMSO, 0.5 mM PKI (5-24) and 22 % methanol (v/v)0.003 mL drop volume, 0.5 mL reservoir volume |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→45.47 Å / Num. obs: 51100 / % possible obs: 90.3 % / Redundancy: 4.1 % / Rsym value: 0.046 / Net I/σ(I): 17.67 |
Reflection shell | Resolution: 1.64→1.74 Å / Num. unique obs: 6824 / Rsym value: 0.522 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F14 Resolution: 1.71→45.47 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.1265
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→45.47 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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