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Yorodumi- PDB-5n1d: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -
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-Basic information
Entry | Database: PDB / ID: 5n1d | ||||||
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Title | cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule N-methyl-1-(5-pyridin-3-yloxyfuran-2-yl)methanamine | ||||||
Components |
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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 / 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 | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 Å | ||||||
Authors | Siefker, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n1d.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n1d.ent.gz | 199.5 KB | Display | PDB format |
PDBx/mmJSON format | 5n1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n1d_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 5n1d_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 5n1d_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5n1d_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n1d ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n1d | HTTPS FTP |
-Related structure data
Related structure data | 5mhiC 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 (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
#1: Protein | Mass: 41113.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Phosphorylation of S11, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Plasmid: pET-16bTEV / 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: 2111.323 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 | ||||
#3: Chemical | #4: Chemical | ChemComp-8FZ / ( | #5: 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: 2.88 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: Jul 18, 2015 / Details: Silicon, active surface |
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: 1.61→50 Å / Num. obs: 61272 / % possible obs: 99.4 % / Redundancy: 4.79 % / CC1/2: 0.99 / Rrim(I) all: 0.07 / Net I/σ(I): 17.23 |
Reflection shell | Resolution: 1.61→1.71 Å / Redundancy: 4.61 % / Num. unique obs: 9718 / CC1/2: 0.82 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WIH Resolution: 1.609→45.815 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.62 / 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: 1.609→45.815 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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