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Yorodumi- PDB-1l3r: Crystal Structure of a Transition State Mimic of the Catalytic Su... -
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-Basic information
Entry | Database: PDB / ID: 1l3r | ||||||
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Title | Crystal Structure of a Transition State Mimic of the Catalytic Subunit of cAMP-dependent Protein Kinase | ||||||
Components | (CAMP-DEPENDENT PROTEIN ...) x 2 | ||||||
Keywords | TRANSFERASE / protein kinase / protein-ALF3 complex / transition state mimic | ||||||
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 / negative regulation of catalytic activity / negative regulation of cAMP-dependent protein kinase activity / 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 / negative regulation of protein kinase activity / 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 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Madhusudan / Akamine, P. / Xuong, N.-H. / Taylor, S.S. | ||||||
Citation | 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. #1: 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. / Taylor, S.S. / Sowadski, J.M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: 2.2 A Refined Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with MnATP and a Peptide Inhibitor Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M. #3: Journal: Protein Sci. / Year: 1994 Title: cAMP-dependent Protein Kinase: Crystallografic Insights into Substrate Recognition and Phosphotransfer Authors: Madhusudan / Trafny, E.A. / Xuong, N.H. / Adams, J.A. / Ten Eyck, L.F. / Taylor, S.S. / Sowadski, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l3r.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l3r.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l3r_validation.pdf.gz | 772.8 KB | Display | wwPDB validaton report |
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Full document | 1l3r_full_validation.pdf.gz | 775.1 KB | Display | |
Data in XML | 1l3r_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1l3r_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/1l3r ftp://data.pdbj.org/pub/pdb/validation_reports/l3/1l3r | HTTPS FTP |
-Related structure data
Related structure data | 1jbpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-CAMP-DEPENDENT PROTEIN ... , 2 types, 2 molecules EI
#1: Protein | Mass: 40817.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 2199.386 Da / Num. of mol.: 1 / Fragment: Residues 5-24 / Mutation: N20A, A21S / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P27776, UniProt: P63249*PLUS |
-Non-polymers , 5 types, 238 molecules
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-AF3 / | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, bicine, methanol, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal grow | *PLUS Details: Zheng, J.H., (1993) Acta Cryst., D49, 362. |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2000 |
Radiation | Monochromator: 58 cm long, Pt-coated, fused silica, vertical focusmirror, Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. all: 30685 / Num. obs: 30443 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.068 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.409 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. measured all: 139545 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 95.8 % / Rmerge(I) obs: 0.408 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JBP Resolution: 2→35 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å /
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Xplor file |
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Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.29 |