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Yorodumi- PDB-3qaq: Crystal structure of PI3K-gamma in complex with triazine-benzimid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qaq | ||||||
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Title | Crystal structure of PI3K-gamma in complex with triazine-benzimidazole 1 | ||||||
Components | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / p110 / kinase / transferase / ATP binding / p84 / p101 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of triglyceride catabolic process / secretory granule localization / natural killer cell chemotaxis / phosphatidylinositol-4-phosphate 3-kinase / neutrophil extravasation / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis ...negative regulation of triglyceride catabolic process / secretory granule localization / natural killer cell chemotaxis / phosphatidylinositol-4-phosphate 3-kinase / neutrophil extravasation / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / dendritic cell chemotaxis / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / mast cell degranulation / 1-phosphatidylinositol-3-kinase activity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / phosphorylation / neutrophil chemotaxis / ephrin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / T cell activation / platelet aggregation / positive regulation of cytokine production / positive regulation of MAP kinase activity / endocytosis / G beta:gamma signalling through PI3Kgamma / kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / angiogenesis / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / inflammatory response / immune response / G protein-coupled receptor signaling pathway / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Whittington, D.A. / Tang, J. / Yakowec, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Discovery of triazine-benzimidazoles as selective inhibitors of mTOR. Authors: Peterson, E.A. / Andrews, P.S. / Be, X. / Boezio, A.A. / Bush, T.L. / Cheng, A.C. / Coats, J.R. / Colletti, A.E. / Copeland, K.W. / Dupont, M. / Graceffa, R. / Grubinska, B. / Harmange, J.C. ...Authors: Peterson, E.A. / Andrews, P.S. / Be, X. / Boezio, A.A. / Bush, T.L. / Cheng, A.C. / Coats, J.R. / Colletti, A.E. / Copeland, K.W. / Dupont, M. / Graceffa, R. / Grubinska, B. / Harmange, J.C. / Kim, J.L. / Mullady, E.L. / Olivieri, P. / Schenkel, L.B. / Stanton, M.K. / Teffera, Y. / Whittington, D.A. / Cai, T. / La, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qaq.cif.gz | 357.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qaq.ent.gz | 291.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qaq_validation.pdf.gz | 692.5 KB | Display | wwPDB validaton report |
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Full document | 3qaq_full_validation.pdf.gz | 702.3 KB | Display | |
Data in XML | 3qaq_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 3qaq_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/3qaq ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qaq | HTTPS FTP |
-Related structure data
Related structure data | 3qarC 1e8yS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 109824.055 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 144-1102) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CG / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P48736, phosphatidylinositol-4,5-bisphosphate 3-kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-QAQ / [( | #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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.3 Details: 21% PEG 3350, 0.1 M Tris pH 7.3, 245 mM ammonium sulfate, 5 mM EDTA, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. all: 23416 / Num. obs: 23346 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E8Y Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 41.009 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.731 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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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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