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- PDB-4bvf: CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bvf | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 | ||||||
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![]() | HYDROLASE/LIGASE / HYDROLASE-LIGASE COMPLEX / THIO-INTERMEDIATE / HYDROLASE-HYDROLASE | ||||||
Function / homology | ![]() propionate biosynthetic process / acetate biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gertz, M. / Weyand, M. / Steegborn, C. | ||||||
![]() | ![]() Title: Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Authors: Gertz, M. / Fischer, F. / Nguyen, G.T.T. / Lakshminarasimhan, M. / Schutkowski, M. / Weyand, M. / Steegborn, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4buzC ![]() 4bv2C ![]() 4bv3C ![]() 4bvbC ![]() 4bveC ![]() 4bvgC ![]() 4bvhC ![]() 3gltS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 116-399' Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9NTG7, ![]() |
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#2: Protein/peptide | Mass: 1805.889 Da / Num. of mol.: 1 / Fragment: RESIDUES 638-647 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-EDO / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Sequence details | CONSTRUCT COVERS RESIDUES 116-399 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.21 % / Description: NONE |
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Crystal grow![]() | pH: 5.6 / Details: 25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2012 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→33.7 Å / Num. obs: 11091 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3GLT Resolution: 2.7→33.73 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.289 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.629 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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 mean: 33.823 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→33.73 Å
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Refine LS restraints |
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