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- PDB-4bv2: CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bv2 | ||||||
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Title | CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE | ||||||
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Function / homology | ![]() protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria ...protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 211.9 KB | Display | ![]() |
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PDB format | ![]() | 173 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 ![]() 4bv3C ![]() 4bvbC ![]() 4bveC ![]() 4bvfC ![]() 4bvgC ![]() 4bvhC ![]() 1yc5S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 27569.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9WYW0, ![]() #2: Protein/peptide | ![]() Mass: 1597.900 Da / Num. of mol.: 2 / Fragment: RESIDUES 380-384 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % / Description: NONE |
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Crystal grow![]() | pH: 5.9 / Details: 20% PEG 6000, 0.1 M BIS-TRIS PH5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 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: 3.3→60.47 Å / Num. obs: 31261 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.54 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1YC5 Resolution: 3.3→60.47 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.845 / SU B: 108.33 / SU ML: 0.846 / Cross valid method: THROUGHOUT / ESU R Free: 0.787 / 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 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: 114.439 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→60.47 Å
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Refine LS restraints |
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