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- PDB-2x6k: THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x6k | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PI-103 | ||||||
![]() | PHOSPHOTIDYLINOSITOL 3 KINASE 59F | ||||||
![]() | TRANSFERASE / PI103 / PI-103 / AUTOPHAGY / PI3K CLASS III / PHOSPHOINOSITIDE 3-KINASE CLASS III | ||||||
Function / homology | ![]() positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II ...positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / epithelial structure maintenance / dsRNA transport / protein targeting to lysosome / phagophore assembly site / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / regulation of early endosome to late endosome transport / 1-phosphatidylinositol-3-kinase activity / establishment or maintenance of cell polarity / neuron remodeling / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome membrane / autophagosome assembly / cellular response to starvation / regulation of autophagy / autophagy / endocytosis / peroxisome / endosome / early endosome / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L. | ||||||
![]() | ![]() Title: Shaping Development of Autophagy Inhibitors with the Structure of the Lipid Kinase Vps34. Authors: Miller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.3 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 966.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 49.8 KB | Display | |
Data in CIF | ![]() | 67.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x6fC ![]() 2x6hSC ![]() 2x6iC ![]() 2x6jC S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.007605, -0.1132, -0.9935), Vector: |
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Components
#1: Protein | Mass: 78765.469 Da / Num. of mol.: 2 / Fragment: HELICAL DOMAIN, KINASE DOMAIN, RESIDUES 258-949 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9W1M7, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase #2: Chemical | #3: Chemical | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.25 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS ...Details: PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS SOAKED WITH 0.5MM PI-103 IN MOTHER LIQUOR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→77.84 Å / Num. obs: 27069 / % possible obs: 99.7 % / Observed criterion σ(I): 1.3 / Redundancy: 3.56 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.46 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.33 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X6H Resolution: 3.5→61.74 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.875 / SU B: 76.068 / SU ML: 0.536 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.626 / 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: 75.26 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→61.74 Å
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