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Open data
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Basic information
Entry | Database: PDB / ID: 4pom | ||||||
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Title | Crystal structures of thioredoxin with mesna at 1.85A resolution | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) 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 ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) 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 / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sridhar, V. / Chie-Leon, B. / Badger, J. / Nienaber, V.L. / Hausheer, F.H. | ||||||
![]() | ![]() Title: BNP7787 Forms Novel Covalent Adducts on Human Thioredoxin and Modulates Thioredoxin Activity Authors: Parker, A.R. / Nienaber, V.L. / Petluru, P.N. / Sridhar, V. / Leverett, B.D. / Ayala, P.Y. / Zhao, M. / Chie-Leon, B. / Jair, K. / Kochat, H. / Badger, J. / Hausheer, F.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
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Full document | ![]() | 468 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pokSC ![]() 4polC 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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Unit cell |
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Components
#1: Protein | Mass: 12051.055 Da / Num. of mol.: 4 / Mutation: E13K, D16K, E95K, E103K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 37414 / Num. obs: 37414 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3733 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4POK Resolution: 1.85→36.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.83 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.139 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→36.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.855→1.903 Å / Total num. of bins used: 20 /
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