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Yorodumi- PDB-5n3e: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n3e | ||||||
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Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 6-dimethylaminopyridine-3-carboxylic acid | ||||||
Components | (cAMP-dependent protein kinase ...Protein kinase A) x 2 | ||||||
Keywords | TRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA | ||||||
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 / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / 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 / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / 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 / protein kinase A catalytic subunit binding / 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 / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.529 Å | ||||||
Authors | Siefker, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n3e.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n3e.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 5n3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/5n3e ftp://data.pdbj.org/pub/pdb/validation_reports/n3/5n3e | HTTPS FTP |
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-Related structure data
Related structure data | 5n33C 5n3cC 5n3dC 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 (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
-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.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS |
-Non-polymers , 4 types, 244 molecules
#3: Chemical | ChemComp-46L / |
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#4: Chemical | ChemComp-MPD / ( |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 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: 1.53→50 Å / Num. obs: 69062 / % possible obs: 98 % / Redundancy: 7.13 % / CC1/2: 0.99 / Rrim(I) all: 0.045 / Net I/σ(I): 23.19 |
Reflection shell | Resolution: 1.53→1.62 Å / Redundancy: 7.28 % / Mean I/σ(I) obs: 3.46 / Num. unique obs: 10849 / CC1/2: 0.91 / Rrim(I) all: 0.547 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WIH Resolution: 1.529→45.538 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.29 / 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: 1.529→45.538 Å
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Refine LS restraints |
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LS refinement shell |
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