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- PDB-6pnm: Human GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(morpholinosu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pnm | |||||||||
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Title | Human GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(morpholinosulfonyl)phenyl)acetamide | |||||||||
![]() | Glutathione S-transferase omega-1 | |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / glutathione transferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / glutathione metabolic process / oxidoreductase activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Oakley, A.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of Benzenesulfonamide Derivatives as Potent Glutathione Transferase Omega-1 Inhibitors. Authors: Xie, Y. / Tummala, P. / Oakley, A.J. / Deora, G.S. / Nakano, Y. / Rooke, M. / Cuellar, M.E. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Casarotto, M.G. / Board, P.G. / Baell, J.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.7 KB | Display | ![]() |
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PDB format | ![]() | 93.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414 KB | Display | ![]() |
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Full document | ![]() | 418.7 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pnnC ![]() 6pnoC ![]() 1eemS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27468.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase | ||||||
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#2: Chemical | ChemComp-XX0 / | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-TLA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.7-2.2 M ammonium sulfate, 100 mM sodium citrate, 0.1 M sodium potassium tartrate, 0.75 mM zinc sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→47 Å / Num. obs: 29406 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.034 / Rrim(I) all: 0.153 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 20.7 % / Mean I/σ(I) obs: 6.8 / Num. unique obs: 1424 / CC1/2: 0.98 / Rpim(I) all: 0.1 / Rrim(I) all: 0.459 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1EEM Resolution: 1.82→40.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.761 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.122 / 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: 28.088 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→40.48 Å
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Refine LS restraints |
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