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- PDB-1gg5: CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE OXIDOREDU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gg5 | ||||||
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Title | CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AND A CHEMOTHERAPEUTIC DRUG (E09) AT 2.5 A RESOLUTION | ||||||
![]() | NAD(P)H DEHYDROGENASE [QUINONE] 1 | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD | ||||||
Function / homology | ![]() 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) / negative regulation of ferroptosis / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to nutrient / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to hormone / cell redox homeostasis / response to ischemia / negative regulation of protein catabolic process / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Faig, M. / Bianchet, M.A. / Winski, S. / Hargreaves, R. / Moody, C.J. / Hudnott, A.R. / Ross, D. / Amzel, L.M. | ||||||
![]() | ![]() Title: Structure-based development of anticancer drugs: complexes of NAD(P)H:quinone oxidoreductase 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. #1: ![]() Title: Structures of Recombinant Human and Mouse Nad(P)H:Quinone Oxidoreductases: Species Comparison and Structural Changes with Substrate Binding and Release Authors: Faig, M. / Bianchet, M.A. / Talalay, P. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M. #2: ![]() Title: Structure and Mechanism of Cytosolic Quinone Reductases Authors: Bianchet, M.A. / Foster, C. / Faig, M. / Talalay, P. / Amzel, L.M. #3: ![]() Title: Crystal Structure of Human Quinone Reductase Type 2, a Metalloprotein Authors: Foster, C. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M. #4: ![]() Title: The Three-Dimensional Structure of Nad(P)H:Quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.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 | ![]() | 227.8 KB | Display | ![]() |
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PDB format | ![]() | 185.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 891.9 KB | Display | ![]() |
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Full document | ![]() | 942.7 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-E09 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.74 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8.5 Details: 30 % PEG 3350, 200 MM NAACETATE, 12-24 MICROM FAD, 100MM NA-TRICINE PH 8.5, pH 8.50, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.44 Å / Num. obs: 46509 / % possible obs: 81.7 % / Observed criterion σ(I): -3 / Redundancy: 1.68 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 4.79 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.39 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.169 / % possible all: 23.3 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 38859 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 81.3 % |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.5→32.23 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 402404.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.81 Å2 / ksol: 0.297 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→32.23 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.351 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.281 |