[English] 日本語
Yorodumi- PDB-1rdq: Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdq | ||||||
---|---|---|---|---|---|---|---|
Title | Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependent protein kinase | ||||||
Components | (cAMP-dependent protein ...) x 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / cAMP-dependent protein kinase / catalytic mechanism / ATP hydrolysis / two nucleotide states / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
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 / 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 / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Yang, J. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of a cAMP-dependent Protein Kinase Mutant at 1.26A: New Insights into the Catalytic Mechanism. Authors: Yang, J. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase Authors: Madhusudan / Akamine, P. / Xuong, N.H. / Taylor, S.S. #2: Journal: Biochemistry / Year: 1993 Title: Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor Authors: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N.H. / Taylor, S.S. / M., Sowadski J. #3: Journal: J.Mol.Biol. / Year: 2003 Title: Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure Authors: Akamine, P. / Madhusudan / Wu, J. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rdq.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rdq.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rdq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rdq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1rdq_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1rdq_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdq ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdq | HTTPS FTP |
-Related structure data
Related structure data | 1apmS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | the biological assembly is a monomer |
-Components
-CAMP-dependent protein ... , 2 types, 2 molecules EI
#1: Protein | Mass: 40565.223 Da / Num. of mol.: 1 / Mutation: Y204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / Keywords: Y204A / References: UniProt: P05132, EC: 2.7.1.37 |
---|---|
#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: residues 5-24 / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Mus musculus (mouse) |
-Non-polymers , 7 types, 446 molecules
#3: Chemical | ChemComp-PO4 / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-ATP / | #7: Chemical | ChemComp-MRD / ( | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, Bicine, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→100 Å / Num. all: 122234 / Num. obs: 114998 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3827 / Rsym value: 0.253 / % possible all: 61 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1APM Resolution: 1.26→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: used cns solve 1.0, then shelxl97 for anisotropic refinement. The R factor values used for refinement shell are isotropic B
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.26→1.34 Å / Rfactor Rfree error: 0.01
|