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Open data
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Basic information
Entry | Database: PDB / ID: 5fbw | ||||||
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Title | PI4KB in complex with Rab11 and the MI369 Inhibitor | ||||||
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![]() | TRANSFERASE / Inhibitor / Complex / Kinase / Lipid | ||||||
Function / homology | ![]() regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / melanosome transport / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / phosphatidylinositol-mediated signaling / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / inner ear development / centriolar satellite / mitotic spindle assembly / vesicle-mediated transport / transport vesicle / 14-3-3 protein binding / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / small monomeric GTPase / receptor-mediated endocytosis / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
![]() | ![]() Title: PI4KB in complex with Rab11 and the MI369 Inhibitor Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 897.2 KB | Display | ![]() |
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Full document | ![]() | 923.1 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d0lS 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: 65264.766 Da / Num. of mol.: 1 Fragment: UNP Residues 128-422, 523-729,UNP Residues 128-422, 523-729 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase |
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#2: Protein | Mass: 24813.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-5W8 / ~{ |
#4: Chemical | ChemComp-GSP / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulfate, 0.1M MES pH=6.5, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.48→47.47 Å / Num. obs: 12696 / % possible obs: 98.32 % / Redundancy: 4.27 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.77 / Num. measured all: 54212 |
Reflection shell | Resolution: 3.48→3.61 Å / Mean I/σ(I) obs: 0.87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D0L Resolution: 3.487→47.469 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.487→47.469 Å
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Refine LS restraints |
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LS refinement shell |
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