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- PDB-5uk8: The co-structure of (R)-4-(6-(1-(cyclopropylsulfonyl)cyclopropyl)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uk8 | ||||||
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Title | The co-structure of (R)-4-(6-(1-(cyclopropylsulfonyl)cyclopropyl)-2-(1H-indol-4-yl)pyrimidin-4-yl)-3-methylmorpholine and a rationally designed PI3K-alpha mutant that mimics ATR | ||||||
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![]() | TRANSFERASE/SIGNALING PROTEIN/INHIBITOR / inhibitor / lipid kinase / mutation / ATR / TRANSFERASE-SIGNALING PROTEIN-INHIBITOR complex | ||||||
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 / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / cardiac muscle cell contraction / RHOF GTPase cycle / kinase activator activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / relaxation of cardiac muscle / positive regulation of leukocyte migration / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / phosphatidylinositol 3-kinase / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / negative regulation of macroautophagy / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / response to dexamethasone / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / protein kinase activator activity / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / negative regulation of anoikis / T cell differentiation / RET signaling / intercalated disc / regulation of multicellular organism growth / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Knapp, M.S. / Mamo, M. / Elling, R.A. | ||||||
![]() | ![]() Title: Rationally Designed PI3K alpha Mutants to Mimic ATR and Their Use to Understand Binding Specificity of ATR Inhibitors. Authors: Lu, Y. / Knapp, M. / Crawford, K. / Warne, R. / Elling, R. / Yan, K. / Doyle, M. / Pardee, G. / Zhang, L. / Ma, S. / Mamo, M. / Ornelas, E. / Pan, Y. / Bussiere, D. / Jansen, J. / Zaror, I. ...Authors: Lu, Y. / Knapp, M. / Crawford, K. / Warne, R. / Elling, R. / Yan, K. / Doyle, M. / Pardee, G. / Zhang, L. / Ma, S. / Mamo, M. / Ornelas, E. / Pan, Y. / Bussiere, D. / Jansen, J. / Zaror, I. / Lai, A. / Barsanti, P. / Sim, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 406.3 KB | Display | ![]() |
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PDB format | ![]() | 312.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 850.4 KB | Display | ![]() |
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Full document | ![]() | 857.9 KB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 61.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 125243.844 Da / Num. of mol.: 1 Mutation: M232K,L233K, I800M, F930V, R770E, W780K, E798I, V850W Source method: isolated from a genetically manipulated source Details: Point mutation to the binding pocket of p110 PI3K alpha designed to mimic ATR ligand binding properties. Source: (gene. exp.) ![]() ![]() References: UniProt: P42336, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 35142.750 Da / Num. of mol.: 1 / Mutation: T6Y Source method: isolated from a genetically manipulated source Details: Fragment of wild type p85 / Source: (gene. exp.) ![]() ![]() |
#3: Chemical | ChemComp-8DV / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.42 % / Description: long rectangular rods |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 3 UL OF PROTEIN WAS MIXED WITH 5 UL OF WELL SOLUTION CONTAINING 12% PEG 3350 AND 120 MM POTASSIUM THIOCYANATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 303.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→48.52 Å / Num. obs: 52602 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 67.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.064 / Rrim(I) all: 0.159 / Net I/σ(I): 11.3 / Num. measured all: 320232 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in-house Resolution: 2.5→48.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.472 / SU Rfree Blow DPI: 0.262 / SU Rfree Cruickshank DPI: 0.266
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Displacement parameters | Biso max: 165.55 Å2 / Biso mean: 70.38 Å2 / Biso min: 29.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.52 Å
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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