[English] 日本語
![](img/lk-miru.gif)
- PDB-4c7b: Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4c7b | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide | ||||||
![]() |
| ||||||
![]() | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / HYDROLASE / SIRTUIN / INHIBITOR / ACTIVATION / RESVERATROL / SIRT1 / METABOLIC SENSOR / METABOLISM / AGING | ||||||
Function / homology | ![]() 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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / protein deacetylation / NAD-dependent histone deacetylase activity / 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 / 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 / nucleus Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, G.T.T. / Gertz, M. / Weyand, M. / Steegborn, C. | ||||||
![]() | ![]() Title: Crystal Structures of Sirt3 Complexes with 4'-Bromo-Resveratrol Reveal Binding Sites and Inhibition Mechanism. Authors: Nguyen, G.T.T. / Gertz, M. / Steegborn, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 124.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 700.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 704.2 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c78C ![]() 4h8d C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 31427.162 Da / Num. of mol.: 1 / Fragment: RESIDUES 117-399 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 |
---|---|
#2: Protein/peptide | Mass: 769.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 142 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BVB.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BVB.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#4: Chemical | ChemComp-BVB / | ||
#5: Chemical | ChemComp-IPA / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 200 MM NACL,100 MM HEPES PH 7, 10% (V/V) ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92039 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.1 Å / Num. obs: 35487 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4H8D ![]() 4h8d Resolution: 2.1→46.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.863 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 39.286 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|