[English] 日本語
![](img/lk-miru.gif)
- PDB-3qfa: Crystal structure of the human thioredoxin reductase-thioredoxin ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3qfa | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human thioredoxin reductase-thioredoxin complex | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE / Protein-Protein Complex / Rossmann Fold / Thioredoxin fold / homodimeric pyridine nucleotide disulfide oxidoreductase / electron transport | ||||||
Function / homology | ![]() Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Protein repair / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / mesoderm formation / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / PPARA activates gene expression / fibrillar center / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / Oxidative Stress Induced Senescence / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K. | ||||||
![]() | ![]() Title: Crystal structure of the human thioredoxin reductase-thioredoxin complex Authors: Fritz-Wolf, K. / Kehr, S. / Stumpf, M. / Rahlfs, S. / Becker, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 257.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 203.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 989.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 53.7 KB | Display | |
Data in CIF | ![]() | 72.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qfbC ![]() 1aiuS ![]() 2j3nS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS ensembles :
| ||||||||
Details | THIOREDOXIN REDUCTASE DIMER (A, B) WITH EACH SUBUNIT COMPLEXED WITH ONE MOLECULE THIOREDOXIN (C or D) |
-
Components
#1: Protein | Mass: 56925.805 Da / Num. of mol.: 2 / Mutation: C497S, U498C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16881, thioredoxin-disulfide reductase #2: Protein | Mass: 12992.681 Da / Num. of mol.: 2 / Mutation: C35S, C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF ENTITY 1 BASED ON ISOFORM 5 OF DATABASE Q16881 (TRXR1_HUMAN). RESIDUE 498 IS ...THE SEQUENCE OF ENTITY 1 BASED ON ISOFORM 5 OF DATABASE Q16881 (TRXR1_HUMAN). RESIDUE 498 IS SELENOCYST | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.21 % |
---|---|
Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.15 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0068 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 84458 / Num. obs: 70734 / % possible obs: 83.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.096 / Net I/σ(I): 6.73 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2j3n and 1aiu Resolution: 2.2→24.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3192308.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.8778 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.91 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NUMBER OF NCS GROUPS : 1. NCS GROUP : 1. NCS OPERATOR : 1. REFERENCE SELECTION: CHAIN A AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID ...NCS model details: NUMBER OF NCS GROUPS : 1. NCS GROUP : 1. NCS OPERATOR : 1. REFERENCE SELECTION: CHAIN A AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID 279:335 OR RESID 342:410 OR RESID 412:428 OR RESID 434:490). SELECTION : CHAIN B AND (RESID 15:50 OR RESID 54:81 OR RESID 100:106 OR RESID 135:220 OR RESID 227:240 OR RESID 279:335 OR RESID 342:410 OR RESID 412:428 OR RESID 434:490) Type: medium positional / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|