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- PDB-4bvg: CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bvg | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 | |||||||||
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![]() | HYDROLASE/LIGASE / HYDROLASE-LIGASE COMPLEX / NAD-DEPENDENT DEACETYLASE / NATIVE INTERMEDIATE | |||||||||
Function / homology | ![]() propionate biosynthetic process / propionate-CoA ligase / propionate-CoA ligase activity / acetate biosynthetic process / 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 / propionate-CoA ligase / propionate-CoA ligase activity / acetate biosynthetic process / 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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / 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 / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nguyen, G.T.T. / Gertz, M. / Weyand, M. / Steegborn, C. | |||||||||
![]() | ![]() Title: Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism. Authors: Gertz, M. / Fischer, F. / Nguyen, G.T. / Lakshminarasimhan, M. / Schutkowski, M. / Weyand, M. / Steegborn, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.5 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.5 KB | Display | ![]() |
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Full document | ![]() | 719.8 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4buzC ![]() 4bv2C ![]() 4bv3C ![]() 4bvbC ![]() 4bveC ![]() 4bvfC ![]() 4bvhC ![]() 3gltS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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.) ![]() ![]() ![]() References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1207.494 Da / Num. of mol.: 1 / Fragment: RESIDUES 638-647 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 7 types, 71 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/XYQ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/XYQ.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-ZN / | #8: Chemical | ChemComp-XYQ / ( | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.97 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 0.2 M (NH4)2SO4, 0.1M BISTRIS PH 5.5, 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2012 / 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: 2.5→38.2 Å / Num. obs: 12915 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.8 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GLT Resolution: 2.5→38.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.264 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.366 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.18 Å
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