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- PDB-3pkj: Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pkj | ||||||
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Title | Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose | ||||||
![]() | NAD-dependent deacetylase sirtuin-6 | ||||||
![]() | HYDROLASE / ROSSMANN FOLD / ZN-BINDING DOMAIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ADP-RIBOSYLATION / 2'-N-Acetyl ADP ribose | ||||||
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 / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase 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 / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / 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 / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / NAD-dependent histone deacetylase activity / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of fat cell differentiation / regulation of protein localization to plasma membrane / pericentric heterochromatin / negative regulation of gluconeogenesis / response to UV / nucleosome binding / 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 / regulation of circadian rhythm / positive regulation of insulin secretion / 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 | ![]() ![]() | ||||||
![]() | Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Pan, P.W. / Dong, A. / Qiu, W. / Loppnau, P. / Wang, J. / Ravichandran, M. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Min, J. / Edwards, A.M. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.4 KB | Display | ![]() |
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PDB format | ![]() | 271 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 65.7 KB | Display | |
Data in CIF | ![]() | 86.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k35SC ![]() 3pkiC 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
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 39106.707 Da / Num. of mol.: 6 / Mutation: K267E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N6T7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 5 types, 545 molecules ![](data/chem/img/A2N.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-A2N / [( #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 297 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 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 29, 2010 / Details: VariMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. all: 100089 / Num. obs: 100089 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 35.52 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.12→2.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 2.02 / Num. unique all: 5012 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K35 Resolution: 2.12→20.5 Å / Cor.coef. Fo:Fc: 0.8585 / Cor.coef. Fo:Fc free: 0.8263 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.342 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→20.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.17 Å / Total num. of bins used: 20
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