+Open data
-Basic information
Entry | Database: PDB / ID: 19gs | ||||||
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Title | Glutathione s-transferase p1-1 | ||||||
Components | GLUTATHIONE S-TRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTATHIONE TRANSFERASE / LIGAND / BROMOSULFALEIN / DETOXIFICATION | ||||||
Function / homology | Function and homology information S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / regulation of ERK1 and ERK2 cascade / hepoxilin biosynthetic process / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / negative regulation of canonical NF-kappaB signal transduction / linoleic acid metabolic process / negative regulation of MAP kinase activity / glutathione metabolic process / xenobiotic metabolic process / central nervous system development / fatty acid binding / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Oakley, A.J. / Lo Bello, M. / Parker, M.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The ligandin (non-substrate) binding site of human Pi class glutathione transferase is located in the electrophile binding site (H-site). Authors: Oakley, A.J. / Lo Bello, M. / Nuccetelli, M. / Mazzetti, A.P. / Parker, M.W. #1: Journal: J.Mol.Biol. / Year: 1997 Title: The Structures of Human Glutathione Transferase P1-1 in Complex with Glutathione and Various Inhibitors at High Resolution Authors: Oakley, A.J. / Lo Bello, M. / Battistoni, A. / Ricci, G. / Rossjohn, J. / Villar, H.O. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 19gs.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb19gs.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 19gs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 19gs_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 19gs_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 19gs_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 19gs_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/9g/19gs ftp://data.pdbj.org/pub/pdb/validation_reports/9g/19gs | HTTPS FTP |
-Related structure data
Related structure data | 12gsC 13gsC 18gsC 20gsC 5gssS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.941256, 0.137672, 0.308357), Vector: |
-Components
#1: Protein | Mass: 23246.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Gene: GSTP1 / Gene (production host): GSTP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase #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: 2.57 Å3/Da / Density % sol: 52.06 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: hanging drop / pH: 6 Details: CRYSTALLISATION PERFORMED USING THE HANGING DROP TECHNIQUE. 2 MICROL OF PROTEIN SOLUTION (8MG/ML) IN 10MM PHOSPHATE BUFFER PH7.0, 1MM EDTA AND 2MM BETA-MERCAPTOETHANOL WAS ADDED TO 2 MICROL ...Details: CRYSTALLISATION PERFORMED USING THE HANGING DROP TECHNIQUE. 2 MICROL OF PROTEIN SOLUTION (8MG/ML) IN 10MM PHOSPHATE BUFFER PH7.0, 1MM EDTA AND 2MM BETA-MERCAPTOETHANOL WAS ADDED TO 2 MICROL OF RESERVOIR SOLUTION. THE RESERVOIR CONTAINED 20-25% AMMONIUM SULFATE, 30-60 MM DITHIOTHREITOL AND 100MM MORPHOLINOETHANESULFONIC ACID BUFFER PH5.4. DROPS WERE STREAK SEEDED AFTER 1 DAY USING A CAT'S WHISKER FROM CRYSTALS GROWN UNDER SIMILAR CONDITIONS. AFTER X DAYS, THE CRYSTAL WAS TRANSFERED TO ARTIFICIAL MOTHER LIQUOR WHICH LACKED DITHIOTHREITOL. SOLID BROMOSULFALEIN WAS SEEDED INTO THE DROP. SEVEN WEEKS LATER THE CRYSTALS WERE SUBJECTED TO X-RAY ANALYSIS., pH 6.0, hanging drop PH range: 5.4-7.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Oakley, A.J., (1997) J.Mol.Biol., 274, 84. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 26, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 35002 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 2.42 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.5 / % possible all: 87.4 |
Reflection | *PLUS Num. measured all: 84660 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 87 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5GSS Resolution: 1.9→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.33 |