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- PDB-2zzb: Crystal structure of human thioredoxin reductase I and terpyridin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zzb | ||||||
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Title | Crystal structure of human thioredoxin reductase I and terpyridine platinum(II) | ||||||
![]() | Thioredoxin reductase 1, cytoplasmic | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Alternative splicing / Cytoplasm / Electron transport / FAD / Flavoprotein / NADP / Nucleus / Phosphoprotein / Polymorphism / Redox-active center / Selenium / Selenocysteine / Transport | ||||||
Function / homology | ![]() Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / mesoderm formation / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cellular response to oxidative stress / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lo, Y.C. / Ko, T.P. / Wang, A.H.J. | ||||||
![]() | ![]() Title: Terpyridine-platinum(II) complexes are effective inhibitors of mammalian topoisomerases and human thioredoxin reductase 1. Authors: Lo, Y.C. / Ko, T.P. / Su, W.C. / Su, T.L. / Wang, A.H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.3 KB | Display | ![]() |
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PDB format | ![]() | 315.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 87.1 KB | Display | |
Data in CIF | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zz0SC ![]() 2zzcC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 56490.328 Da / Num. of mol.: 4 / Fragment: residues (-13)-499 / Mutation: SeCys498Cys Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16881, thioredoxin-disulfide reductase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SWISSPROT SHOWS SELENOCYST | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, additive: 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 chennel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 46840 / Num. obs: 46746 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4593 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ZZ0 Resolution: 3.2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.0043
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