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- PDB-3wf5: Crystal structure of S6K1 kinase domain in complex with a pyrazol... -
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Open data
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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 | ||||||
![]() | Ribosomal protein S6 kinase beta-1![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niwa, H. / Shirouzu, M. / Yokoyama, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P23443, ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FZ8 / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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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