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Open data
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Basic information
Entry | Database: PDB / ID: 4k7o | ||||||
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Title | HUMAN PEROXIREDOXIN 5 with a fragment | ||||||
![]() | Peroxiredoxin-5, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / enzyme / cytosol | ||||||
Function / homology | ![]() peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species / antioxidant activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / cellular response to reactive oxygen species / peroxidase activity / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guichou, J.F. | ||||||
![]() | ![]() Title: Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5 Authors: Aguirre, C. / Brink, T.T. / Guichou, J.F. / Cala, O. / Krimm, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.6 KB | Display | ![]() |
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PDB format | ![]() | 88.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 463.1 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17835.475 Da / Num. of mol.: 3 / Fragment: UNP residues 54-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 22% PEG3350, 0.1M sodium citrate buffer, 0.2M potassium sodium tartrate, 5mM 1,4-dithio-dl-threitol, 0.02%(w/v) sodium azide, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→65.1 Å / Num. all: 45126 / Num. obs: 45081 / % possible obs: 99.9 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 1.8 / Redundancy: 11.3 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.98→65.1 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 28.256 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→65.1 Å
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