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- PDB-5m0b: 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: 5m0b | ||||||
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Title | Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a short-chained N-(2-aminoethyl)isoquinoline-5-sulfonamide) Fasudil-derivative (Ligand 03) | ||||||
![]() | (cAMP-dependent protein kinase ...) x 2 | ||||||
![]() | TRANSFERASE / PKA / Kinase / Fasudil-derivative / Inhibition / Cocrystal / 3x-Phosphorylated / Ligand 03 | ||||||
Function / homology | ![]() 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 ...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 / 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 | ![]() ![]() ![]() | ||||||
![]() | 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 different Fasudil-derivatives Authors: Wienen-Schmidt, B. / Jonker, H.R.A. / 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 | ![]() | 242.3 KB | Display | ![]() |
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PDB format | ![]() | 194 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 710.3 KB | Display | ![]() |
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Full document | ![]() | 711.6 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lcqC ![]() 5lcrC ![]() 5lctC ![]() 5lcuC ![]() 5m0cC ![]() 5m0lC ![]() 5m6vC ![]() 1q8wS C: citing same article ( S: Starting model for refinement |
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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 Details: Phosphorylated at Ser11, Thr198, Ser339 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Amino acids 5-24 from cAMP-dependent protein kinase inhibitor alpha from Sigma (order ID: P7739); the last amino acid is not well defined in the crystal structure Source: (synth.) ![]() |
-Non-polymers , 4 types, 509 molecules ![](data/chem/img/IQU.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IQU / | ||
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#4: Chemical | ChemComp-MPD / ( | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 53.33 % |
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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: 18% 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.506→45.08 Å / Num. obs: 73047 / % possible obs: 99.9 % / Redundancy: 7.32 % / Rsym value: 0.054 / Net I/σ(I): 26.28 |
Reflection shell | Resolution: 1.506→1.6 Å / Redundancy: 7.26 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.89 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q8W Resolution: 1.506→39.876 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.506→39.876 Å
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Refine LS restraints |
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LS refinement shell |
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