+Open data
-Basic information
Entry | Database: PDB / ID: 6mhd | ||||||
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Title | Glutathione S-Transferase Omega 1 bound to covalent inhibitor 44 | ||||||
Components | Glutathione S-transferase omega-1 | ||||||
Keywords | Transferase/Transferase Inhibitor / Transferase / 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: 2.16 Å | ||||||
Authors | Petrunak, E.M. / Stuckey, J.A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2019 Title: Structure-Based Design of N-(5-Phenylthiazol-2-yl)acrylamides as Novel and Potent Glutathione S-Transferase Omega 1 Inhibitors. Authors: Dai, W. / Samanta, S. / Xue, D. / Petrunak, E.M. / Stuckey, J.A. / Han, Y. / Sun, D. / Wu, Y. / Neamati, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mhd.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mhd.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mhd ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mhd | HTTPS FTP |
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-Related structure data
Related structure data | 6mhbC 6mhcC 4yquS 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: 27872.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Production host: Escherichia coli (E. coli) References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 30% PEG-3350, 4% acetone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.1272 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 22575 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.54 Å2 / Rsym value: 0.086 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.1 % / Rsym value: 0.335 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YQU Resolution: 2.16→43.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.226
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Displacement parameters | Biso mean: 27.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.16→43.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.18 Å / Total num. of bins used: 50
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