+Open data
-Basic information
Entry | Database: PDB / ID: 3k35 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human SIRT6 | ||||||
Components | NAD-dependent deacetylase sirtuin-6 | ||||||
Keywords | HYDROLASE / Rossmann fold / Zn-binding domain / Structural Genomics / Structural Genomics Consortium / SGC / ADP-ribosylation / Metal-binding / NAD / NADP / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information 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 / positive regulation of fat cell differentiation / 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 / nucleosome binding / regulation of protein localization to plasma membrane / 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 / regulation of circadian rhythm / circadian regulation of gene expression / protein destabilization / base-excision repair / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / transcription corepressor activity / double-strand break repair / glucose homeostasis / Processing of DNA double-strand break ends / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of cold-induced thermogenesis / site of double-strand break / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Min, J. / Edwards, A.M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure and biochemical functions of SIRT6. Authors: Pan, P.W. / Feldman, J.L. / Devries, M.K. / Dong, A. / Edwards, A.M. / Denu, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3k35.cif.gz | 355.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3k35.ent.gz | 283.8 KB | Display | PDB format |
PDBx/mmJSON format | 3k35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k35_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3k35_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3k35_validation.xml.gz | 71 KB | Display | |
Data in CIF | 3k35_validation.cif.gz | 97.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/3k35 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/3k35 | HTTPS FTP |
-Related structure data
Related structure data | 3pkiC 3pkjC 1yc5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 35147.238 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L6, SIRT6 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon(+) pRARE References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
---|
-Non-polymers , 5 types, 1004 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-APR / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 30, 2009 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 120514 / Num. obs: 120514 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 9.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YC5 Resolution: 2→19.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.661 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.84 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.002→2.053 Å / Total num. of bins used: 20
|