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Yorodumi- PDB-8v2n: Human SIRT3 co-crystallized with ligands, including p53-AMC pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8v2n | ||||||
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Title | Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD | ||||||
Components |
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Keywords | HYDROLASE / Activator / Complex / Deacylase | ||||||
Function / homology | Function and homology information positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. ...Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T. | ||||||
Funding support | 1items
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Citation | Journal: biorxiv / Year: 2023 Title: Computationally Driven Discovery and Characterization of SIRT3 Activating Compounds that Fully Recover Catalytic Activity under NAD+ Depletion Authors: Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v2n.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v2n.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 8v2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/8v2n ftp://data.pdbj.org/pub/pdb/validation_reports/v2/8v2n | HTTPS FTP |
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-Related structure data
Related structure data | 8v15C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31340.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9NTG7 |
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#2: Protein/peptide | Mass: 699.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-CNA / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M ...Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→42.04 Å / Num. obs: 25473 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.993 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.74→1.77 Å / Num. unique obs: 1288 / CC1/2: 0.649 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→42.04 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.224 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.339 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→42.04 Å
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Refine LS restraints |
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