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Yorodumi- PDB-6pnn: Human GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(N-(2-methoxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pnn | |||||||||
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Title | Human GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(N-(2-methoxyethyl)-N-methylsulfamoyl)phenyl)acetamide | |||||||||
Components | Glutathione S-transferase omega-1 | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / glutathione transferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) / 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 / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) / 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 / negative regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase 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 / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / oxidoreductase activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Oakley, A.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pnn.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnn.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 6pnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnn ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnn | HTTPS FTP |
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-Related structure data
Related structure data | 6pnmC 6pnoC 1eemS S: Starting model for refinement C: citing same article (ref.) |
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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 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.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-OR7 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.97 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
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: 2.1→47 Å / Num. obs: 16146 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 9.5 / Num. unique obs: 1298 / CC1/2: 0.989 / Rpim(I) all: 0.074 / Rrim(I) all: 0.242 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EEM Resolution: 2.1→40.42 Å / SU B: 7.595 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.169 / 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: 12.151 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å
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Refinement TLS params. | Method: refined / Origin x: 22.7378 Å / Origin y: -10.6215 Å / Origin z: 19.839 Å
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