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- PDB-3dk9: Catalytic cycle of human glutathione reductase near 1 A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dk9 | ||||||
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Title | Catalytic cycle of human glutathione reductase near 1 A resolution | ||||||
![]() | Glutathione reductase | ||||||
![]() | OXIDOREDUCTASE / flavoenzyme / glutathione / nicotinamide / Alternative initiation / FAD / Flavoprotein / Mitochondrion / NADP / Phosphoprotein / Redox-active center / Transit peptide | ||||||
Function / homology | ![]() glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding / flavin adenine dinucleotide binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Berkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A. | ||||||
![]() | ![]() Title: Catalytic cycle of human glutathione reductase near 1 A resolution. Authors: Berkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244 KB | Display | ![]() |
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PDB format | ![]() | 193.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 713.1 KB | Display | ![]() |
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Full document | ![]() | 722 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3djgC ![]() 3djjC ![]() 3dk4C ![]() 3dk8C ![]() 3grsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 51636.242 Da / Num. of mol.: 1 / Fragment: UNP residues 45 to 522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00390, glutathione-disulfide reductase | ||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 3% ammonium sulfate, 0.1 M potassium phosphate and 0.1% beta-octyl glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 290866 / % possible obs: 88 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 0.95→0.96 Å / Rmerge(I) obs: 0.347 / % possible all: 45.2 |
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Processing
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Refinement | Starting model: PDB ENTRY 3GRS Resolution: 0.95→50 Å / Occupancy max: 1 / Occupancy min: 0.16 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 17.916 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→50 Å
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Refine LS restraints |
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