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- PDB-5m6y: Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m6y | ||||||
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Title | Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a methylisoquinoline Fasudil-derivative | ||||||
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![]() | TRANSFERASE / PKA / Kinase / Fasudil-derivative / Inhibition / Cocrystal / 3x-Phosphorylated | ||||||
Function / homology | ![]() negative regulation of cAMP/PKA signal transduction / negative regulation of 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 ...negative regulation of cAMP/PKA signal transduction / negative regulation of 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 / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / 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 / manganese ion binding / cellular response to heat / dendritic spine / regulation of cell cycle / nuclear speck / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wienen-Schmidt, B. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with differently methylated Fasudil-derived ligands Authors: Wienen-Schmidt, B. / Jonker, H. / Gerber, H.-D. / Saxena, K. / Kudlinzki, D. / Sreeramulu, S. / Heine, A. / Schwalbe, H. / 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 | ![]() | 246.4 KB | Display | ![]() |
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PDB format | ![]() | 200.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5m71C ![]() 1q8wS 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
#1: Protein | Mass: 41113.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Phosphorylated at Ser11, Thr198, Ser339 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: UNP Residues 6-25 / Source method: obtained synthetically Details: Amino acids 5-24 from cAMP-dependent protein kinase inhibitor alpha from Sigma (order ID: P7739) Source: (synth.) ![]() |
#3: Chemical | ChemComp-7KB / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: Drop: 10 mg/ml PKA (0.240 mM) 30 mM MBT (MES/Bis-Tris Puffer pH 6.9) 1 mM DTT 0.1 mM EDTA 75 mM LiCl 0.03 mM Mega 8 0.07mM PKI (Sigma: P7739) 1.2 mM ligand solved in DMSO (50 mM Stock) ...Details: Drop: 10 mg/ml PKA (0.240 mM) 30 mM MBT (MES/Bis-Tris Puffer pH 6.9) 1 mM DTT 0.1 mM EDTA 75 mM LiCl 0.03 mM Mega 8 0.07mM PKI (Sigma: P7739) 1.2 mM ligand solved in DMSO (50 mM Stock) Reservoir: 20% Methanol 0.003 mL drop volume, 0.4 mL reservoir volume |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.367→45.774 Å / Num. obs: 98699 / % possible obs: 98.7 % / Redundancy: 3.968 % / Rsym value: 0.033 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.37→1.45 Å / Redundancy: 3.878 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.31 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q8W Resolution: 1.367→45.774 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.367→45.774 Å
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Refine LS restraints |
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LS refinement shell |
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