+Open data
-Basic information
Entry | Database: PDB / ID: 4rlo | ||||||
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Title | Human p70s6k1 with ruthenium-based inhibitor EM5 | ||||||
Components | Ribosomal protein S6 kinase beta-1Ribosome | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / 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: 2.527 Å | ||||||
Authors | Domsic, J.F. / Barber-Rotenberg, J. / Salami, J. / Qin, J. / Marmorstein, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Development of Organometallic S6K1 Inhibitors. Authors: Qin, J. / Rajaratnam, R. / Feng, L. / Salami, J. / Barber-Rotenberg, J.S. / Domsic, J. / Reyes-Uribe, P. / Liu, H. / Dang, W. / Berger, S.L. / Villanueva, J. / Meggers, E. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rlo.cif.gz | 209.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rlo.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/4rlo ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rlo | HTTPS FTP |
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-Related structure data
Related structure data | 4rlpC 3a62S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32691.326 Da / Num. of mol.: 2 / Fragment: UNP residues 85-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1, STK14A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P23443, non-specific serine/threonine protein kinase |
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-Non-polymers , 7 types, 96 molecules
#2: Chemical | ChemComp-3T3 / [( | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-STU / | #7: Chemical | ChemComp-DMS / | #8: 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: 3.27 Å3/Da / Density % sol: 62.34 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, 3.5M Sodium Formate, with staurosporine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2011 |
Radiation | Monochromator: a / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.527→49.03 Å / Num. all: 28523 / Num. obs: 28440 / % possible obs: 99.71 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rsym value: 0.079 |
Reflection shell | Resolution: 2.527→2.618 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2745 / Rsym value: 0.407 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A62 Resolution: 2.527→49.03 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 22.53 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.527→49.03 Å
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Refine LS restraints |
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LS refinement shell |
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