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- PDB-6ggd: p53 cancer mutant Y220C in complex with small-molecule stabilizer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ggd | ||||||
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Title | p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9324 | ||||||
![]() | Cellular tumor antigen p53![]() | ||||||
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Function / homology | ![]() 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 ...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 | ![]() ![]() ![]() | ||||||
![]() | Joerger, A.C. / Bauer, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A structure-guided molecular chaperone approach for restoring the transcriptional activity of the p53 cancer mutant Y220C. Authors: Bauer, M.R. / Jones, R.N. / Tareque, R.K. / Springett, B. / Dingler, F.A. / Verduci, L. / Patel, K.J. / Fersht, A.R. / Joerger, A.C. / Spencer, J. #1: ![]() Title: Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Authors: Joerger, A.C. / Ang, H.C. / Fersht, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.6 KB | Display | ![]() |
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PDB format | ![]() | 140.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ggaC ![]() 6ggbC ![]() 6ggcC ![]() 6ggeC ![]() 6ggfC ![]() 2j1xS 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
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 24530.811 Da / Num. of mol.: 2 / Mutation: M133L, V203A, Y220C, N239Y, N268D, Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking ...Details: Protein solution: 6 mg/ml protein in 25 mM sodium phosphate, ph 7.2, 150 mm KCl, 5 mm DTT. Reservoir buffer: 100 mm HEPES, pH 7.2, 19% (w/v) polyethylene glycol 4000, 5 mm DTT. Soaking buffer: Saturated solution of compound in 100 mm HEPES, ph 7.2, 10 mM sodium phosphate, ph 7.2, 19% (w/v) polyethylene glycol 4000, 20 % (v/v) glycerol, 150 mm KCl. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→29.53 Å / Num. obs: 96032 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.4503105329 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2J1X Resolution: 1.4000088608→29.5285963691 Å / SU ML: 0.131019184989 / Cross valid method: THROUGHOUT / σ(F): 1.33646014145 / Phase error: 16.3921221783
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7235365305 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4000088608→29.5285963691 Å
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Refine LS restraints |
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LS refinement shell |
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