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Open data
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Basic information
Entry | Database: PDB / ID: 20gs | ||||||
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Title | GLUTATHIONE S-TRANSFERASE P1-1 COMPLEXED WITH CIBACRON BLUE | ||||||
![]() | GLUTATHIONE S-TRANSFERASE | ||||||
![]() | TRANSFERASE / GLUTATHIONE TRANSFERASE / LIGAND / CIBACRON BLUE / DETOXIFICATION | ||||||
Function / homology | ![]() 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 / hepoxilin 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 / hepoxilin biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / 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 / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / xenobiotic metabolic process / glutathione metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Oakley, A.J. / Lo Bello, M. / Nuccetelli, M. / Mazzetti, A.P. / Parker, M.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12gsC ![]() 13gsC ![]() 18gsC ![]() 19gsC ![]() 5gssS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.943003, 0.116095, 0.311878), Vector: |
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Components
#1: Protein | Mass: 23246.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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