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Yorodumi- PDB-1kbo: Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kbo | ||||||
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Title | Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type 1 with 5-methoxy-1,2-dimethyl-3-(phenoxymethyl)indole-4,7-dione (ES1340) | ||||||
Components | NAD(P)H dehydrogenase [quinone] 1 | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / PRODRUG-ENZYME COMPLEX | ||||||
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 / xenobiotic metabolic process / removal of superoxide radicals / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Faig, M. / Bianchet, M.A. / Amzel, L.M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Characterization of a mechanism-based inhibitor of NAD(P)H:quinone oxidoreductase 1 by biochemical, X-ray crystallographic, and mass spectrometric approaches. Authors: Winski, S.L. / Faig, M. / Bianchet, M.A. / Siegel, D. / Swann, E. / Fung, K. / Duncan, M.W. / Moody, C.J. / Amzel, L.M. / Ross, D. #1: Journal: Structure / Year: 2001 Title: Structure-based Development of Anticancer Drugs: Complexes of NAD(P)H:Quinone Reductase 1 with Chemotherapeutic Quinones Authors: Faig, M. / Bianchet, M.A. / Winski, S. / Hargreaves, R. / Moody, C.J. / Hudnott, A.R. / Ross, D. / Amzel, L.M. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structures of Recombinant Mouse and Human NAD(P)H:Quinone Oxidoreductases: Species Comparison and Structural Changes with Substrate Binding and Release Authors: Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S.L. / Ross, D. / Talalay, P. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kbo.cif.gz | 225.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kbo.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kbo ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kbo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30776.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15559, EC: 1.6.99.2 #2: Chemical | ChemComp-340 / #3: Chemical | ChemComp-FAD / #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: 2.37 Å3/Da / Density % sol: 48.03 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 8.5 / Details: PEG 4K, Na Acetate, pH 8.5, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Faig, M., (2000) Proc.Natl.Acad.Sci.USA, 97, 3177. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1999 / Details: OSMIC MIRRORS |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.5 Å / Num. obs: 47881 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.098 / Net I/σ(I): 13.57 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.221 / % possible all: 94.3 |
Reflection | *PLUS Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 94.3 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→35.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 461040.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.7923 Å2 / ksol: 0.305857 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→35.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.341 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.278 |