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Yorodumi- PDB-3wf5: Crystal structure of S6K1 kinase domain in complex with a pyrazol... -
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-Basic information
Entry | Database: PDB / ID: 3wf5 | ||||||
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Title | Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine | ||||||
Components | Ribosomal protein S6 kinase beta-1Ribosome | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE PROTEIN KINASE DOMAIN / TRANSFERASE / PHOSPHORYLATION / ATP-BINDING / ZINC-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon / response to testosterone / positive regulation of smooth muscle cell migration / TOR signaling / mTORC1-mediated signalling / germ cell development / positive regulation of translational initiation / skeletal muscle contraction / long-term memory / behavioral fear response / response to tumor necrosis factor / response to glucose / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / response to nutrient levels / positive regulation of translation / protein phosphatase 2A binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / PDZ domain binding / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / response to toxic substance / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / cell migration / postsynapse / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Niwa, H. / Shirouzu, M. / Yokoyama, S. | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2014 Title: Crystal structures of the S6K1 kinase domain in complexes with inhibitors Authors: Niwa, H. / Mikuni, J. / Sasaki, S. / Tomabechi, Y. / Honda, K. / Ikeda, M. / Ohsawa, N. / Wakiyama, M. / Handa, N. / Shirouzu, M. / Honma, T. / Tanaka, A. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wf5.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wf5.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/3wf5 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/3wf5 | 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: 37178.816 Da / Num. of mol.: 1 / Fragment: UNP residues 78-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P23443, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FZ8 / |
#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: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 2.9-3.3M sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 25, 2011 |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. all: 20923 / Num. obs: 20923 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rsym value: 0.08 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.099→2.14 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 994 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→40.404 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 21.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.67 Å2 / Biso mean: 49.7192 Å2 / Biso min: 21.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→40.404 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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