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Yorodumi- PDB-4ij9: Bovine PKA C-alpha in complex with 2-[[5-(4-pyridyl)-1H-1,2,4-tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ij9 | ||||||
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Title | Bovine PKA C-alpha in complex with 2-[[5-(4-pyridyl)-1H-1,2,4-triazol-3-yl]sulfanyl]-1-(2-thiophenyl)ethanone | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / 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 / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of protein import into nucleus / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2.55 Å | ||||||
Authors | Dreyer, M.K. / Schiffer, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Accounting for Conformational Variability in Protein-Ligand Docking with NMR-Guided Rescoring Authors: Skjaerven, L. / Codutti, L. / Angelini, A. / Grimaldi, M. / Latek, D. / Monecke, P. / Dreyer, M.K. / Carlomagno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ij9.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ij9.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ij9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ij9 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ij9 | HTTPS FTP |
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-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: 40706.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: UNP residues 6-25 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925 |
#3: Chemical | ChemComp-PTV / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: LiCl, MesBisTris, methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→19.12 Å / Num. all: 243779 / Num. obs: 243558 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.31 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.55→19.12 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.8428 / SU R Cruickshank DPI: 0.549 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.833 / SU Rfree Blow DPI: 0.3 / SU Rfree Cruickshank DPI: 0.293 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.258 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→19.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.75 Å / Total num. of bins used: 7
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