+Open data
-Basic information
Entry | Database: PDB / ID: 7u4l | |||||||||||||||||||||
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Title | Crystal structure of human GPX4-U46C in complex with MAC-5576 | |||||||||||||||||||||
Components | Phospholipid hydroperoxide glutathione peroxidase | |||||||||||||||||||||
Keywords | OXIDOREDUCTASE / GPX4 | |||||||||||||||||||||
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 / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process / 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 / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / cellular response to oxidative stress / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||||||||||||||
Authors | Forouhar, F. / Liu, H. / Lin, A.J. / Wang, Q. / Polychronidou, V. / Soni, R.K. / Xia, X. / Stockwell, B.R. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Cell Chem Biol / Year: 2022 Title: Small-molecule allosteric inhibitors of GPX4. Authors: Liu, H. / Forouhar, F. / Lin, A.J. / Wang, Q. / Polychronidou, V. / Soni, R.K. / Xia, X. / Stockwell, B.R. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u4l.cif.gz | 286.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u4l.ent.gz | 234.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4l ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4l | HTTPS FTP |
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-Related structure data
Related structure data | 7u4iC 7u4jC 7u4kC 7u4mC 7u4nC 7l8kS S: Starting model for refinement 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21888.098 Da / Num. of mol.: 4 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 #2: Chemical | ChemComp-LW1 / #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: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.6 Details: 2 M sodium chloride and 0.1 M sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→91.51 Å / Num. obs: 67235 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.197 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.083 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4076 / CC1/2: 0.34 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7L8K Resolution: 2.25→72.19 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 23.42 / Stereochemistry target values: ML
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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 max: 102.5 Å2 / Biso mean: 34.2225 Å2 / Biso min: 5.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→72.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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Refinement TLS params. | Method: refined / Origin x: 38.6612 Å / Origin y: -6.0321 Å / Origin z: 9.996 Å
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Refinement TLS group |
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