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Yorodumi- PDB-1yds: Structure of CAMP-dependent protein kinase, alpha-catalytic subun... -
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-Basic information
Entry | Database: PDB / ID: 1yds | ||||||
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Title | Structure of CAMP-dependent protein kinase, alpha-catalytic subunit in complex with H8 protein kinase inhibitor [N-(2-methylamino)ethyl]-5-isoquinolinesulfonamide | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHOTRANSFERASE / TRANSFERASE / CAMP / PHOSPHORYLATION / ISOQUINOLINE SULFONAMIDE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitors H7, H8, and H89. Structural implications for selectivity. Authors: Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D. #1: Journal: Embo J. / Year: 1993 Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ ...Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24) Authors: Bossemeyer, D. / Engh, R.A. / Kinzel, V. / Ponstingl, H. / Huber, R. #2: Journal: Biochim.Biophys.Acta / Year: 1992 Title: Cloning of the C Alpha Catalytic Subunit of the Bovine Camp-Dependent Protein Kinase Authors: Wiemann, S. / Kinzel, V. / Pyerin, W. #3: Journal: Biochemistry / Year: 1984 Title: Isoquinolinesulfonamides, Novel and Potent Inhibitors of Cyclic Nucleotide Dependent Protein Kinase and Protein Kinase C Authors: Hidaka, H. / Inagaki, M. / Kawamoto, S. / Sasaki, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yds.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yds.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yds_validation.pdf.gz | 729.4 KB | Display | wwPDB validaton report |
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Full document | 1yds_full_validation.pdf.gz | 738.4 KB | Display | |
Data in XML | 1yds_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1yds_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/1yds ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1yds | HTTPS FTP |
-Related 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: 40681.363 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT Source method: isolated from a genetically manipulated source Details: ALPHA ISOENZYME / Source: (gene. exp.) Bos taurus (cattle) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P04541, UniProt: P63249*PLUS |
#3: Chemical | ChemComp-IQS / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15 % METHANOL, 70 MILLIMOLAR SODIUM SULFATE, 20 MILLIMOLAR MES-BIS-TRIS PH 6.5, 279K USING HANGING DROP DIFFUSION., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.6 / PH range high: 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 17182 / % possible obs: 77 % |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.29 Å / % possible obs: 51 % |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / Rfactor Rwork: 0.199 / Rfactor obs: 0.199 / σ(F): 3 Details: ONLY THE WATER MOLECULES IN THE VICINITY OF THE BOUND H-8 INHIBITOR MOLECULE HAVE BEEN MODELED. THE PEPTIDE CHAIN IN THE REGION OF THE GLYCINE FLAP RESIDUES GLY E 50 TO VAL E 57 ADOPTS OPEN ...Details: ONLY THE WATER MOLECULES IN THE VICINITY OF THE BOUND H-8 INHIBITOR MOLECULE HAVE BEEN MODELED. THE PEPTIDE CHAIN IN THE REGION OF THE GLYCINE FLAP RESIDUES GLY E 50 TO VAL E 57 ADOPTS OPEN AND CLOSED CONFORMATIONS. INCLUDED ARE THE COORDINATES OF THE MODEL REFINED IN THE OPEN CONFORMATION. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Num. reflection obs: 17182 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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