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- PDB-1bay: GLUTATHIONE S-TRANSFERASE YFYF CYS 47-CARBOXYMETHYLATED CLASS PI,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bay | ||||||
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Title | GLUTATHIONE S-TRANSFERASE YFYF CYS 47-CARBOXYMETHYLATED CLASS PI, FREE ENZYME | ||||||
![]() | GLUTATHIONE S-TRANSFERASE CLASS PI | ||||||
![]() | TRANSFERASE / MULTIGENE FAMILY | ||||||
Function / homology | ![]() negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid ...negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / oligodendrocyte development / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / negative regulation of interleukin-1 beta production / cellular response to glucocorticoid stimulus / regulation of stress-activated MAPK cascade / negative regulation of acute inflammatory response / glutathione transferase / glutathione transferase activity / negative regulation of tumor necrosis factor production / protein serine/threonine kinase inhibitor activity / animal organ regeneration / response to amino acid / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / negative regulation of canonical NF-kappaB signal transduction / Neutrophil degranulation / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / inflammatory response / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vega, M.C. / Coll, M. | ||||||
![]() | ![]() Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a ...Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a loss of electron density in the alphaB-310B region. Authors: Vega, M.C. / Walsh, S.B. / Mantle, T.J. / Coll, M. #1: ![]() Title: Molecular Structure at 1.8 A of Mouse Liver Class Pi Glutathione S-Transferase Complexed with S-(P-Nitrobenzyl)Glutathione and Other Inhibitors Authors: Garcia-Saez, I. / Parraga, A. / Phillips, M.F. / Mantle, T.J. / Coll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gtiC ![]() 1glqS 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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Unit cell |
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Components
#1: Protein | Mass: 23503.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHEMICAL MODIFICATION ON CYS 47 WITH IODOACETIC ACID, CYS 47 CARBOXYMETHYLATED Source: (natural) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 60.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Detector: IMAGE PLATE / Date: Jul 22, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 28194 / % possible obs: 75 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 2→2.5 Å / % possible all: 56.6 |
Reflection | *PLUS Num. obs: 31316 / % possible obs: 78.7 % / Observed criterion σ(I): 3 |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 56.8 % |
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Processing
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Refinement | Method to determine structure: MOLECULAR REEMPLACEMENT Starting model: PDB ENTRY 1GLQ Resolution: 2→8 Å / Data cutoff high absF: 50 / Data cutoff low absF: 2 / Cross valid method: BRUNGER'S METHOD / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |