+Open data
-Basic information
Entry | Database: PDB / ID: 2f1o | ||||||
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Title | Crystal Structure of NQO1 with Dicoumarol | ||||||
Components | NAD(P)H dehydrogenase [quinone] 1 | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / Protein inhibitor / Structural Genomics / Israel Structural Proteomics Center / ISPC / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / 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 / synaptic transmission, cholinergic / response to alkaloid / response to carbohydrate / 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 hormone / response to nutrient / cell redox homeostasis / 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 / dendrite / neuronal cell body / synapse / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Shaul, Y. / Asher, G. / Dym, O. / Tsvetkov, P. / Adler, J. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The crystal structure of NAD(P)H quinone oxidoreductase 1 in complex with its potent inhibitor dicoumarol. Authors: Asher, G. / Dym, O. / Tsvetkov, P. / Adler, J. / Shaul, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f1o.cif.gz | 444.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f1o.ent.gz | 366.3 KB | Display | PDB format |
PDBx/mmJSON format | 2f1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/2f1o ftp://data.pdbj.org/pub/pdb/validation_reports/f1/2f1o | HTTPS FTP |
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-Related structure data
Related structure data | 1dxoS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a dimer which is in the asymmetric unit cell |
-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: NQO1, DIA4, NMOR1 / Production host: Escherichia coli (E. coli) References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-DTC / #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: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 298 K / pH: 8.1 Details: 0.1M NaAcetate, 50mM NaTricine, 11% PEG 3350, 5mM Dicoumarol , pH 8.1, Microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. obs: 63333 / % possible obs: 96.9 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.75→2.8 Å / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DXO Resolution: 2.75→38.66 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.75→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å /
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