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Open data
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Basic information
Entry | Database: PDB / ID: 6n0m | ||||||
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Title | CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 | ||||||
![]() | Sestrin-2 | ||||||
![]() | SIGNALING PROTEIN / MTOR / LEUCINE / AMINO-ACID / SENSING | ||||||
Function / homology | ![]() regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / cellular oxidant detoxification / L-leucine binding / Atg1/ULK1 kinase complex / cellular response to leucine starvation / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / PH domain binding ...regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / cellular oxidant detoxification / L-leucine binding / Atg1/ULK1 kinase complex / cellular response to leucine starvation / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / PH domain binding / TORC2 complex / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / cellular response to L-leucine / Amino acids regulate mTORC1 / triglyceride homeostasis / GDP-dissociation inhibitor activity / positive regulation of lipophagy / regulation of gluconeogenesis / fatty acid beta-oxidation / glucose import / positive regulation of macroautophagy / DNA damage response, signal transduction by p53 class mediator / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / cellular response to glucose starvation / response to glucose / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / protein sequestering activity / cellular response to amino acid starvation / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / regulation of protein phosphorylation / response to insulin / negative regulation of cell growth / positive regulation of protein localization to nucleus / peroxidase activity / KEAP1-NFE2L2 pathway / glucose homeostasis / cellular response to oxidative stress / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosomal membrane / protein-containing complex binding / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | O'Neill, D. | ||||||
![]() | ![]() Title: Discovery of NV-5138, the first selective Brain mTORC1 activator. Authors: Sengupta, S. / Giaime, E. / Narayan, S. / Hahm, S. / Howell, J. / O'Neill, D. / Vlasuk, G.P. / Saiah, 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 | ![]() | 370.5 KB | Display | ![]() |
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PDB format | ![]() | 301.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 83.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dj4S 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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2 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47458.730 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-K94 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0 / PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→48.4 Å / Num. obs: 82533 / % possible obs: 99.8 % / Redundancy: 23 % / Rmerge(I) obs: 0.53 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.98→3.06 Å / Mean I/σ(I) obs: 0.29 / CC1/2: 0.223 / Rrim(I) all: 0.543 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DJ4 Resolution: 3.3→48.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.599 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 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: 218.53 Å2 / Biso mean: 107.251 Å2 / Biso min: 65.47 Å2
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Refinement step | Cycle: final / Resolution: 3.3→48.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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