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- PDB-5swp: Crystal Structure of PI3Kalpha in complex with fragments 6 and 24 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5swp | |||||||||
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Title | Crystal Structure of PI3Kalpha in complex with fragments 6 and 24 | |||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / cis-Golgi network / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / RHOF GTPase cycle / kinase activator activity / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gabelli, S.B. / Vogelstein, B. / Miller, M.S. / Amzel, L.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of allosteric binding sites for PI3K alpha oncogenic mutant specific inhibitor design. Authors: Miller, M.S. / Maheshwari, S. / McRobb, F.M. / Kinzler, K.W. / Amzel, L.M. / Vogelstein, B. / Gabelli, S.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289 KB | Display | ![]() |
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PDB format | ![]() | 226.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5sw8C ![]() 5swgC ![]() 5swoC ![]() 5swrC ![]() 5swtC ![]() 5sx8C ![]() 5sx9C ![]() 5sxaC ![]() 5sxbC ![]() 5sxcC ![]() 5sxdC ![]() 5sxeC ![]() 5sxfC ![]() 5sxiC ![]() 5sxjC ![]() 5sxkC ![]() 4ovuS C: citing same article ( S: Starting model for refinement |
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Similar 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: 127982.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P42336, ![]() ![]() | ||||
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#2: Protein | Mass: 33666.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % / Mosaicity: 0.635 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: NaFormate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→50 Å / Num. obs: 27455 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.121 / Χ2: 1.107 / Net I/av σ(I): 17.087 / Net I/σ(I): 6.9 / Num. measured all: 184879 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4OVU Resolution: 3.41→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.866 / SU B: 35.028 / SU ML: 0.532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.668 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 248.27 Å2 / Biso mean: 117.081 Å2 / Biso min: 47.71 Å2
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Refinement step | Cycle: final / Resolution: 3.41→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.409→3.498 Å / Total num. of bins used: 20
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