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Open data
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Basic information
Entry | Database: PDB / ID: 7cl0 | ||||||
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Title | Crystal structure of human SIRT6 | ||||||
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![]() | TRANSFERASE / deacylase | ||||||
Function / homology | ![]() NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / chromosome, subtelomeric region / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / NAD-dependent histone deacetylase activity / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / TORC2 complex binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / lncRNA binding / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / regulation of protein secretion / positive regulation of stem cell proliferation / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / regulation of lipid metabolic process / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of fat cell differentiation / regulation of protein localization to plasma membrane / nucleosome binding / negative regulation of gluconeogenesis / pericentric heterochromatin / response to UV / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / protein destabilization / base-excision repair / positive regulation of insulin secretion / regulation of circadian rhythm / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / site of double-strand break / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, K. / Zhang, J. | ||||||
![]() | ![]() Title: Reply to: Binding site for MDL-801 on SIRT6. Authors: Huang, Z. / Zhao, J. / Deng, W. / Chen, Y. / Shang, J. / Song, K. / Zhang, L. / Wang, C. / Lu, S. / Yang, X. / He, B. / Min, J. / Hu, H. / Tan, M. / Xu, J. / Zhang, Q. / Zhong, J. / Sun, X. ...Authors: Huang, Z. / Zhao, J. / Deng, W. / Chen, Y. / Shang, J. / Song, K. / Zhang, L. / Wang, C. / Lu, S. / Yang, X. / He, B. / Min, J. / Hu, H. / Tan, M. / Xu, J. / Zhang, Q. / Zhong, J. / Sun, X. / Mao, Z. / Lin, H. / Xiao, M. / Chin, Y.E. / Jiang, H. / Shen, H. / Xu, Y. / Chen, G. / Zhang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cl1C ![]() 5x16S 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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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 39180.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N6T7, protein acetyllysine N-acetyltransferase |
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#2: Protein/peptide | Mass: 906.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 7 types, 254 molecules ![](data/chem/img/AR6.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/G4U.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/G4U.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-AR6 / [( | ||||||||
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#4: Chemical | ChemComp-ZN / | ||||||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-G4U / | #8: Chemical | ChemComp-PEG / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.06 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→114.41 Å / Num. obs: 24693 / % possible obs: 100 % / Redundancy: 22.4 % / CC1/2: 0.995 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.53→2.62 Å / Num. unique obs: 2416 / CC1/2: 0.836 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X16 Resolution: 2.53→114.41 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.868 / SU B: 6.606 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.33 Å2 / Biso mean: 45.614 Å2 / Biso min: 16.61 Å2
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Refinement step | Cycle: final / Resolution: 2.53→114.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.532→2.598 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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