+Open data
-Basic information
Entry | Database: PDB / ID: 5h5r | ||||||
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Title | Crystal structure of human GPX4 in complex with GXpep-2 | ||||||
Components |
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Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE 4 / SELENOCYSTEINE / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / negative regulation of ferroptosis / protein polymerization / lipoxygenase pathway / phospholipid metabolic process / arachidonate metabolic process / nuclear envelope / chromatin organization / response to estradiol / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T7 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Sogabe, S. / Kadotani, A. / Lane, W. / Snell, G. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Discovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis Authors: Sakamoto, K. / Sogabe, S. / Kamada, Y. / Matsumoto, S.I. / Kadotani, A. / Sakamoto, J.I. / Tani, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h5r.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h5r.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 5h5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h5r_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 5h5r_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 5h5r_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5h5r_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/5h5r ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h5r | HTTPS FTP |
-Related structure data
Related structure data | 5h5qC 5h5sC 2obiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19419.070 Da / Num. of mol.: 1 / Mutation: C29S, C37A, C64S, U73C, C93R, C102S, C134E, C175V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Production host: Escherichia coli (E. coli) References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase |
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#2: Protein/peptide | Mass: 1730.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus) |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 0.2M sodium acetate, 25% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 51699 / % possible obs: 93.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 5.7 / % possible all: 55.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OBI Resolution: 1.2→35.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.895 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.569 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→35.72 Å
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