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Yorodumi- PDB-4jg8: Structure of RSK2 T493M CTD mutant bound to 2-cyano-N-(1-hydroxy-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jg8 | ||||||
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Title | Structure of RSK2 T493M CTD mutant bound to 2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-(3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl)acrylamide | ||||||
Components | Ribosomal protein S6 kinase alpha-3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Phosphorylation / Covalent Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / skeletal system development / central nervous system development / positive regulation of cell differentiation / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / positive regulation of cell growth / chemical synaptic transmission / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / synapse / negative regulation of apoptotic process / nucleolus / protein kinase binding / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1002 Å | ||||||
Authors | Miller, R.M. / Paavilainen, V.O. / Krishnan, S. / Serafimova, I.M. / Taunton, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Electrophilic fragment-based design of reversible covalent kinase inhibitors. Authors: Miller, R.M. / Paavilainen, V.O. / Krishnan, S. / Serafimova, I.M. / Taunton, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jg8.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jg8.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 4jg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jg8_validation.pdf.gz | 739.8 KB | Display | wwPDB validaton report |
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Full document | 4jg8_full_validation.pdf.gz | 742.9 KB | Display | |
Data in XML | 4jg8_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4jg8_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jg8 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jg8 | HTTPS FTP |
-Related structure data
Related structure data | 4jg6C 4jg7C 2qr8S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 40097.645 Da / Num. of mol.: 1 / Mutation: T493M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 / Production host: Escherichia coli (E. coli) References: UniProt: P51812, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-1LE / ( |
#3: 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: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, 50 mM Ammonium Sulfate, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 2010 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.76 Å / Num. all: 6465 / Num. obs: 6457 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 3.1→3.29 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QR8 Resolution: 3.1002→45.778 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.79 / σ(F): 0 / Phase error: 25.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.904 Å2 / ksol: 0.427 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1002→45.778 Å
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Refine LS restraints |
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LS refinement shell |
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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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