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Yorodumi- PDB-3jsx: X-ray Crystal structure of NAD(P)H: Quinone Oxidoreductase-1 (NQO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jsx | ||||||
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Title | X-ray Crystal structure of NAD(P)H: Quinone Oxidoreductase-1 (NQO1) bound to the coumarin-based inhibitor AS1 | ||||||
Components | NAD(P)H dehydrogenase [quinone] 1 | ||||||
Keywords | OXIDOREDUCTASE / coumarin-based inhibitors / NQ01 / FAD / Flavoprotein / NAD / NADP | ||||||
Function / homology | Function and homology information response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / removal of superoxide radicals / xenobiotic metabolic process / response to nutrient / cell redox homeostasis / response to hormone / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Dunstan, M.S. / Levy, C. / Leys, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Synthesis and biological evaluation of coumarin-based inhibitors of NAD(P)H: quinone oxidoreductase-1 (NQO1). Authors: Nolan, K.A. / Doncaster, J.R. / Dunstan, M.S. / Scott, K.A. / Frenkel, A.D. / Siegel, D. / Ross, D. / Barnes, J. / Levy, C. / Leys, D. / Whitehead, R.C. / Stratford, I.J. / Bryce, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jsx.cif.gz | 449.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jsx.ent.gz | 372 KB | Display | PDB format |
PDBx/mmJSON format | 3jsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jsx_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 3jsx_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 3jsx_validation.xml.gz | 93 KB | Display | |
Data in CIF | 3jsx_validation.cif.gz | 119.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsx ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsx | HTTPS FTP |
-Related structure data
Related structure data | 2f1oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30776.412 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DIA4, NMOR1, NQO1, NQO1 cDNA / Plasmid: PKK 233-2 / Production host: Escherichia coli (E. coli) References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CC2 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.4M ammonium sulfate, 0.1M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2009 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.954 Å / Num. all: 107399 / Num. obs: 100053 / % possible obs: 93.2 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 1.99 / Redundancy: 4.1 % / Biso Wilson estimate: 53.46 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.079 / Net I/σ(I): 13.98 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6558 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F1O Resolution: 2.45→47.954 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): 2 / Phase error: 33.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.469 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.954 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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