+Open data
-Basic information
Entry | Database: PDB / ID: 4c78 | ||||||
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Title | Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide | ||||||
Components |
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Keywords | HYDROLASE / SIRTUIN / INHIBITOR / ACTIVATION / RESVERATROL / SIRT1 / METABOLIC SENSOR / METABOLISM / AGING | ||||||
Function / homology | Function and homology information propionate biosynthetic process / acetate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation ...propionate biosynthetic process / acetate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation / peptidyl-lysine deacetylation / acetyl-CoA biosynthetic process / 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 / AMP binding / 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 / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / transferase activity / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nguyen, G.T.T. / Gertz, M. / Weyand, M. / Steegborn, C. | ||||||
Citation | Journal: Chem.Biol. / Year: 2013 Title: Crystal Structures of Sirt3 Complexes with 4'-Bromo-Resveratrol Reveal Binding Sites and Inhibition Mechanism. Authors: Nguyen, G.T.T. / Gertz, M. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c78.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c78.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 4c78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c78 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c78 | HTTPS FTP |
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-Related structure data
Related structure data | 4c7bC 4h8d C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 116-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVFT3S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1248.523 Da / Num. of mol.: 1 / Fragment: RESIDUES 638-647 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NUB1, acetate-CoA ligase |
#3: Chemical | ChemComp-BVB / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE |
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Crystal grow | pH: 6 Details: 250 MM (NH4)2SO4, 100 MM BISTRIS PH 6, 21% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.4 Å / Num. obs: 37699 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.99 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4H8D 4h8d Resolution: 2→37.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.553 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 40.552 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.42 Å
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