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- PDB-6ynr: Crystal structure of the cAMP-dependent protein kinase A in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ynr | ||||||
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Title | Crystal structure of the cAMP-dependent protein kinase A in complex with 1,7-Naphthyridin-8-amine (soaked) and PKI (5-24) | ||||||
![]() | (cAMP-dependent protein kinase ...) x 2 | ||||||
![]() | TRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase | ||||||
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 / 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oebbeke, M. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses. Authors: Wienen-Schmidt, B. / Oebbeke, M. / Ngo, K. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.5 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.1 KB | Display | ![]() |
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Full document | ![]() | 766.4 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ynaC ![]() 6ynbC ![]() 6yncC ![]() 6yntC ![]() 6yqiC ![]() 6yqjC ![]() 6yqkC ![]() 6f14S 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
-CAMP-dependent protein kinase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 41113.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 219 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/O72.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/O72.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MPD / ( |
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#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-O72 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.2 mM PKA, 100 mM MBT (MES/Bis-Tris Puffer pH 6.9), 1 mM DTT, 0.1 mM EDTA, 75 mM LiCl, 0.2 mM Mega8, 0.5 mM PKI and 18-23% (v/v) Methanol. Soaking in buffer described above with 10% (v/v) ...Details: 0.2 mM PKA, 100 mM MBT (MES/Bis-Tris Puffer pH 6.9), 1 mM DTT, 0.1 mM EDTA, 75 mM LiCl, 0.2 mM Mega8, 0.5 mM PKI and 18-23% (v/v) Methanol. Soaking in buffer described above with 10% (v/v) 1,7-Naphthydrin-8-amine in DMSO (1M stock) and 30% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 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: 1.898→43.542 Å / Num. obs: 34597 / % possible obs: 99.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.63 Å2 / Rsym value: 0.056 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.9→2.01 Å / Mean I/σ(I) obs: 3.02 / Num. unique obs: 5482 / Rsym value: 0.496 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F14 Resolution: 1.9→43.54 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0631
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.54 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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