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- PDB-5mhi: 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: 5mhi | |||||||||
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Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule (5-chloro-2-methoxyphenyl)methanamine | |||||||||
![]() | (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 / 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 | ![]() ![]() ![]() | |||||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | |||||||||
![]() | ![]() Title: A crystallographic fragment study with cAMP-dependent protein kinase A Authors: Siefker, C. / 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 | ![]() | 236 KB | Display | ![]() |
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PDB format | ![]() | 192.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n1dC ![]() 5n1eC ![]() 5n1fC ![]() 5n1gC ![]() 5n1hC ![]() 5n1kC ![]() 5n1lC ![]() 5n1mC ![]() 5n1nC ![]() 5n1oC ![]() 5n32C ![]() 5n36C ![]() 5n37C ![]() 5n39C ![]() 5n3aC ![]() 5n3bC ![]() 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
-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: 1993.318 Da / Num. of mol.: 1 / Fragment: UNP residues 12-30 / Source method: obtained synthetically / Details: cAMP-dependent protein kinase inhibitory peptide / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 307 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/7N9.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7N9.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MPD / ( | ||||
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#4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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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 PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2016 / Details: Silicon, active surface 50 nm Rh-coated |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.489→50 Å / Num. obs: 76142 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 1 / Rsym value: 0.038 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.489→1.58 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.7 / CC1/2: 0.9 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WIH Resolution: 1.489→45.475 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.42 / 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: 1.489→45.475 Å
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Refine LS restraints |
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LS refinement shell |
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