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Open data
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Basic information
Entry | Database: PDB / ID: 7u4k | ||||||||||||||||||||||||
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Title | Crystal structure of human GPX4-U46C-R152H in complex with ML162 | ||||||||||||||||||||||||
![]() | Phospholipid hydroperoxide glutathione peroxidase | ||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / GPX4 | ||||||||||||||||||||||||
Function / homology | ![]() 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 / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins ...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 / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / arachidonic acid metabolic process / 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 / chromatin organization / nuclear envelope / 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 | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Forouhar, F. / Liu, H. / Lin, A.J. / Wang, Q. / Xia, X. / Soni, R.K. / Stockwell, B.R. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.3 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.2 KB | Display | ![]() |
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Full document | ![]() | 767.3 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u4iC ![]() 7u4jC ![]() 7u4lC ![]() 7u4mC ![]() 7u4nC ![]() 7l8lS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 21869.051 Da / Num. of mol.: 1 / Mutation: U46C, R152H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase | ||||
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#2: Chemical | ChemComp-L9C / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6 / Details: 8% Tacsimate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 28, 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: 1.59→52.55 Å / Num. obs: 23878 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1 / Num. unique obs: 1007 / CC1/2: 0.635 / % possible all: 84.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7L8L Resolution: 1.69→52.55 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.9 / 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: 121.54 Å2 / Biso mean: 35.2649 Å2 / Biso min: 16.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→52.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 16.2804 Å / Origin y: -0.5052 Å / Origin z: 7.8531 Å
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Refinement TLS group |
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