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- PDB-6ws0: Rational drug design of phenazopyridine derivatives as novel inhi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ws0 | ||||||
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Title | Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT | ||||||
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![]() | PROTEIN BINDING/Transferase / ![]() | ||||||
Function / homology | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McPherson, K.S. / Korzhnev, D.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Drug Design of Phenazopyridine Derivatives as Inhibitors of Rev1 Interactions in Translesion Synthesis. Authors: McPherson, K.S. / Zaino, A.M. / Dash, R.C. / Rizzo, A.A. / Li, Y. / Hao, B. / Bezsonova, I. / Hadden, M.K. / Korzhnev, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ws5C ![]() 3vu7S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 11011.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9UBZ9, ![]() |
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#2: Protein | Mass: 26101.236 Da / Num. of mol.: 1 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 5632.319 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.86 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 162 mM triammonium citrate and 18% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 280 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.238→29.073 Å / Num. obs: 14749 / % possible obs: 99.4 % / Redundancy: 9 % / CC1/2: 0.997 / Rrim(I) all: 0.107 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.238→2.31 Å / Num. unique obs: 1267 / CC1/2: 0.774 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3vu7 Resolution: 2.24→29.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.367 / ESU R Free: 0.217 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.319 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→29.07 Å
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Refine LS restraints |
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LS refinement shell |
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