+Open data
-Basic information
Entry | Database: PDB / ID: 4bn5 | ||||||
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Title | Structure of human SIRT3 in complex with SRT1720 inhibitor | ||||||
Components | NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL | ||||||
Keywords | HYDROLASE / LYSINE DEACETYLASE / ADP RIBOSE | ||||||
Function / homology | Function and homology information positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / 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 / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / 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 / 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 / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Nguyen, G.T.T. / Schaefer, S. / Gertz, M. / Weyand, M. / Steegborn, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and Srt1720: Binding Details and Inhibition Mechanism Authors: Nguyen, G.T.T. / Schaefer, S. / Gertz, M. / Weyand, 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 | 4bn5.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bn5.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 4bn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/4bn5 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bn5 | HTTPS FTP |
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-Related structure data
Related structure data | 4bn4C 3glsS 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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Unit cell |
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-Components
#1: Protein | Mass: 31253.010 Da / Num. of mol.: 12 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 #2: Chemical | ChemComp-CNA / #3: Chemical | ChemComp-SR7 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GOL / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.1 % / Description: NONE |
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Crystal grow | Details: 20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→25 Å / Num. obs: 91158 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.25→3.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.1 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GLS Resolution: 3.25→48.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 55.678 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R: 1.335 / ESU R Free: 0.486 / 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: 97.868 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→48.57 Å
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Refine LS restraints |
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