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Yorodumi- PDB-6you: Crystal structure of the cAMP-dependent protein kinase A in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6you | ||||||
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Title | Crystal structure of the cAMP-dependent protein kinase A in complex with Pyrido[3,2-d]pyrimidin-4-amine (soaked) | ||||||
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 / regulation of osteoblast differentiation / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / 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 / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Oebbeke, M. / 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 | 6you.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6you.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 6you.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6you_validation.pdf.gz | 730.9 KB | Display | wwPDB validaton report |
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Full document | 6you_full_validation.pdf.gz | 731 KB | Display | |
Data in XML | 6you_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6you_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/6you ftp://data.pdbj.org/pub/pdb/validation_reports/yo/6you | HTTPS FTP |
-Related structure data
Related structure data | 6f14SC 6y05C 6y0bC 6y2oC 6y2uC 6y89C 6yotC 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: 41193.746 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-P4Q / |
#3: 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: 2.2 Å3/Da / Density % sol: 44.13 % |
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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 |
-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: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→45.805 Å / Num. obs: 37845 / % possible obs: 98.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.69 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.92 |
Reflection shell | Resolution: 1.73→1.83 Å / Mean I/σ(I) obs: 2.74 / Num. unique obs: 5976 / Rsym value: 0.49 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F14 Resolution: 1.73→45.8 Å / SU ML: 0.1758 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6117
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→45.8 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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