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Yorodumi- PDB-4cet: Crystal structure of the complex of the P187S variant of human NA... -
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-Basic information
Entry | Database: PDB / ID: 4cet | ||||||
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Title | Crystal structure of the complex of the P187S variant of human NAD(P) H:quinone oxidoreductase with dicoumarol at 2.2 A resolution | ||||||
Components | NAD(P)H DEHYDROGENASE [QUINONE] 1 | ||||||
Keywords | OXIDOREDUCTASE / COUMARIN-BASED INHIBITORS / NQ01 / FAD / FLAVOPROTEIN / NAD / NADP / NADPH / OXIDOREDUCTASE-INHIBITOR COMPLEX / SINGLE AMINO ACID EXCHANGE / P187S | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lienhart, W.D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P. | ||||||
Citation | Journal: FEBS J. / Year: 2014 Title: Collapse of the Native Structure by a Single Amino Acid Exchange in Human Nad(P)H:Quinone Oxidoreductase (Nqo1). Authors: Lienhart, W.-D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cet.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cet.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/4cet ftp://data.pdbj.org/pub/pdb/validation_reports/ce/4cet | HTTPS FTP |
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-Related structure data
Related structure data | 4cf6C 1qbgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33068.934 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-DTC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.67 Å3/Da / Density % sol: 26.37 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.005 M CO(II)CL-HEXAHYDRATE, 0.005 M NI(II)CL-HEXAHYDRATE, 0.005 M CDCL-HYDRATE, 0.005 M MGCL-HEAXHYDRATE, 0.1 M HEPES PH 7.5, 12 % PEG-3350 (W/V) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1354 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1354 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.8 Å / Num. obs: 12127 / % possible obs: 99.8 % / Observed criterion σ(I): 3.2 / Redundancy: 11.9 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QBG Resolution: 2.2→33.197 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 2 AND THE LAST 51 RESIDUES (MISSING C-TERMINAL REGION).
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.2 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.197 Å
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Refine LS restraints |
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LS refinement shell |
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