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- PDB-5n33: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n33 | ||||||
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Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 3-amino-5-(trifluoromethyl)-1H-pyridin-2-one | ||||||
![]() | (cAMP-dependent protein kinase ...) x 2 | ||||||
![]() | 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 / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / protein kinase A catalytic subunit binding / 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 / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.5 KB | Display | ![]() |
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PDB format | ![]() | 194.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 352.4 KB | Display | ![]() |
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Full document | ![]() | 355.1 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n3cC ![]() 5n3dC ![]() 5n3eC ![]() 5n3hC ![]() 5n3jC ![]() 5n3qC ![]() 5n3sC ![]() 6snnC ![]() 6snxC ![]() 6soxC ![]() 6spmC ![]() 6spsC ![]() 6spuC ![]() 6spyC ![]() 6ypsC ![]() 6z08C ![]() 6z44C ![]() 6zn0C ![]() 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
-CAMP-dependent protein kinase ... , 2 types, 2 molecules AB
#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 / Fragment: UNP residues 12-30 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 326 molecules ![](data/chem/img/8JW.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-8JW / |
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#4: Chemical | ChemComp-MPD / ( |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2016 / Details: Silicon, active surface |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. obs: 84316 / % possible obs: 99.2 % / Redundancy: 6.25 % / CC1/2: 0.99 / Rrim(I) all: 0.066 / Net I/σ(I): 14.92 |
Reflection shell | Resolution: 1.43→1.52 Å / Redundancy: 6.23 % / Mean I/σ(I) obs: 2.64 / Num. unique obs: 12943 / CC1/2: 0.9 / Rrim(I) all: 0.526 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WIH Resolution: 1.434→41.913 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.434→41.913 Å
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Refine LS restraints |
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LS refinement shell |
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