[English] 日本語
Yorodumi- PDB-3oog: human cAMP-dependent protein kinase in complex with a small fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oog | ||||||
---|---|---|---|---|---|---|---|
Title | human cAMP-dependent protein kinase in complex with a small fragment | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / ATP Binding / Phosphorylation | ||||||
Function / homology | Function and homology information PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / 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 / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / Factors involved in megakaryocyte development and platelet production / cellular response to heat / manganese ion binding / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Koester, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Fragment based drug design on human PKA Authors: Koester, H. / Craan, T. / Brass, S. / Heine, A. / Klebe, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3oog.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3oog.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oog_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3oog_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 3oog_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3oog_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/3oog ftp://data.pdbj.org/pub/pdb/validation_reports/oo/3oog | HTTPS FTP |
-Related structure data
Related structure data | 3n47 |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40808.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKACA, PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase |
---|---|
#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: residues 5-24 / Source method: obtained synthetically / References: UniProt: P61925 |
#3: Chemical | ChemComp-YTP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 5 mM MES, 5mM BisTris-propane, 75mM LiCl, 1mM DTT, 0.1 mM EDTA equilibrated against water/ethanol, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2009 / Details: mirrors |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 30200 / Num. obs: 30200 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.06 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1492 / Rsym value: 0.446 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Num. parameters: 11803 / Num. restraintsaints: 11679 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2936 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|