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Yorodumi- PDB-1apm: 2.0 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT O... -
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-Basic information
Entry | Database: PDB / ID: 1apm | ||||||
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Title | 2.0 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH A PEPTIDE INHIBITOR AND DETERGENT | ||||||
Components |
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Keywords | TRANSFERASE(PHOSPHOTRANSFERASE) | ||||||
Function / homology | Function and homology information spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / 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 / regulation of G2/M transition of mitotic cell cycle / 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 / sperm midpiece / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / 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 / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / mRNA processing / presynapse / peptidyl-serine phosphorylation / manganese ion binding / cellular response to heat / postsynapse / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of cell population proliferation / ubiquitin protein ligase binding / glutamatergic synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Knighton, D.R. / Bell, S.M. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: 2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent. Authors: Knighton, D.R. / Bell, S.M. / Zheng, J. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. #1: Journal: Biochemistry / Year: 1993 Title: Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mg/ATP and Peptide Inhibitor Authors: Zheng, J. / Knighton, D.R. / Teneyck, L.F. / Karlsson, R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #2: Journal: Science / Year: 1991 Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Ashford, V.A. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #3: Journal: Science / Year: 1991 Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J. / Teneyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #4: Journal: J.Biol.Chem. / Year: 1989 Title: Expression of the Catalytic Subunit of C/AMP-Dependent Protein Kinase in Escherichia Coli Authors: Slice, L.W. / Taylor, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1apm.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apm.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1apm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apm_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 1apm_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1apm_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1apm_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apm ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Atom site foot note | 1: RESIDUES SER E 10, THR E 197, AND SER E 338 ARE PHOSPHORYLATED. 2: ARG E 56 AND ARG I 18 HAVE TWO MODELED SIDE-CHAIN CONFORMATIONS. |
-Components
#1: Protein | Mass: 40721.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P05132, 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 Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P63248 |
#3: Chemical | ChemComp-OCT / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | INHIBITOR RESIDUE NUMBERING CORRESPONDS TO NUMBERS FROM THE SEQUENCE OF THE LARGER NATURALLY ...INHIBITOR RESIDUE NUMBERING CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Zheng, J., (1992) Acta Crystallogr., B48, 241. / PH range low: 8.3 / PH range high: 8 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.95 Å / Num. obs: 30428 / % possible obs: 90 % / Rmerge(I) obs: 0.0561 |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / Rfactor Rwork: 0.186 / σ(F): 0 Details: RESIDUES E 51-E 55, E 319-E 322, AND I 23-I 24 HAVE WEAK BACKBONE ELECTRON DENSITY. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: XPLOR/TNT / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 / Lowest resolution: 30 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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