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Yorodumi- PDB-8x71: Crystal structure of Peroxiredoxin I in complex with compound 19-064 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8x71 | ||||||
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Title | Crystal structure of Peroxiredoxin I in complex with compound 19-064 | ||||||
Components | Peroxiredoxin-1 | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / natural killer cell mediated cytotoxicity / NFE2L2 regulating anti-oxidant/detoxification enzymes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of stress-activated MAPK cascade ...leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / natural killer cell mediated cytotoxicity / NFE2L2 regulating anti-oxidant/detoxification enzymes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / skeletal system development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / melanosome / fibroblast proliferation / response to oxidative stress / cell population proliferation / cadherin binding / RNA binding / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Zhang, H. / Luo, C. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Discovery of a Novel Orally Bioavailable FLT3-PROTAC Degrader for Efficient Treatment of Acute Myeloid Leukemia and Overcoming Resistance of FLT3 Inhibitors. Authors: Wang, J. / Rong, Q. / Ye, L. / Fang, B. / Zhao, Y. / Sun, Y. / Zhou, H. / Wang, D. / He, J. / Cui, Z. / Zhang, Q. / Kang, D. / Hu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x71.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x71.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 8x71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x71_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8x71_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8x71_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 8x71_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/8x71 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/8x71 | HTTPS FTP |
-Related structure data
Related structure data | 8x73C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19337.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q06830, thioredoxin-dependent peroxiredoxin #2: Chemical | Mass: 578.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H46N2O6 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 8% Tacsimate pH 8.0 (v/v), 20% PEG3350 (v/v), 22% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.575→35.77 Å / Num. obs: 54935 / % possible obs: 99.12 % / Redundancy: 13.3 % / Biso Wilson estimate: 16.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 30.86 |
Reflection shell | Resolution: 1.575→1.631 Å / Num. unique obs: 5310 / CC1/2: 0.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→35.77 Å / SU ML: 0.1352 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.3502 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→35.77 Å
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Refine LS restraints |
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LS refinement shell |
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