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- PDB-5n3b: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -
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Basic information
Entry | Database: PDB / ID: 5n3b | ||||||
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Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 2-(pyridin-3-yl)ethanamine | ||||||
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![]() | TRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA | ||||||
Function / homology | ![]() 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 / axoneme / plasma membrane raft / 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 / phosphorylation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A crystallographic fragment study with cAMP-dependent protein kinase A Authors: Siefker, C. / Heine, A. / Klebe, G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.2 KB | Display | ![]() |
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PDB format | ![]() | 177.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 315.9 KB | Display | ![]() |
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Full document | ![]() | 317.5 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mhiC ![]() 5n1dC ![]() 5n1eC ![]() 5n1fC ![]() 5n1gC ![]() 5n1hC ![]() 5n1kC ![]() 5n1lC ![]() 5n1mC ![]() 5n1nC ![]() 5n1oC ![]() 5n32C ![]() 5n36C ![]() 5n37C ![]() 5n39C ![]() 5n3aC ![]() 5n3fC ![]() 5n3gC ![]() 5n3iC ![]() 5n3kC ![]() 5n3lC ![]() 5n3mC ![]() 5n3nC ![]() 5n3oC ![]() 5n3pC ![]() 5n3rC ![]() 5n3tC ![]() 5n7pC ![]() 4wihS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Details: Phosphorylation of S11, S140, T198 and S339 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-BJN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-Solution DTT EDTA LiCl Methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2016 / Details: Silicon |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 57234 / % possible obs: 98.4 % / Redundancy: 6.66 % / CC1/2: 0.99 / Rrim(I) all: 0.063 / Net I/σ(I): 18.31 |
Reflection shell | Resolution: 1.64→1.74 Å / Redundancy: 6.84 % / Mean I/σ(I) obs: 3.31 / Num. unique obs: 8697 / CC1/2: 0.88 / Rrim(I) all: 0.574 / % possible all: 93.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WIH Resolution: 1.64→45.74 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→45.74 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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