+Open data
-Basic information
Entry | Database: PDB / ID: 20gs | ||||||
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Title | GLUTATHIONE S-TRANSFERASE P1-1 COMPLEXED WITH CIBACRON BLUE | ||||||
Components | GLUTATHIONE S-TRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTATHIONE TRANSFERASE / LIGAND / CIBACRON BLUE / DETOXIFICATION | ||||||
Function / homology | Function and homology information nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / response to reactive oxygen species / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Oakley, A.J. / Lo Bello, M. / Nuccetelli, M. / Mazzetti, A.P. / 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 | 20gs.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb20gs.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 20gs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/0g/20gs ftp://data.pdbj.org/pub/pdb/validation_reports/0g/20gs | HTTPS FTP |
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-Related structure data
Related structure data | 12gsC 13gsC 18gsC 19gsC 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: (0.943003, 0.116095, 0.311878), 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) / Tissue: UBIQUITOUS / Cell: UBIQUITOUS / Cellular location: CYTOSOL / Gene: GSTP1 / Organ: UBIQUITOUS / Gene (production host): GSTP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | NOT ALL OF THE LIGAND CIBACRON BLUE WAS SEEN IN DENSITY. THEREFORE, ONLY A PORTION OF THE MOLECULE ...NOT ALL OF THE LIGAND CIBACRON BLUE WAS SEEN IN DENSITY. THEREFORE, ONLY A PORTION OF THE MOLECULE IS INCLUDED IN THIS ENTRY. | |
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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: 2.6 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Method: vapor diffusion - hanging drop - streak seeding / 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. SOLID CIBACRON BLUE WAS SEEDED INTO THE DROP. SIX WEEKS LATER THE CRYSTALS WERE SUBJECTED TO X-RAY ANALYSIS., pH 6.0, vapor diffusion - hanging drop - streak seeding PH range: 5.4-7.0 |
-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: May 31, 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: 2.45→15 Å / Num. obs: 16729 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.97 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.7 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5GSS Resolution: 2.45→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / 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: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.54 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
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Xplor file |
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