+Open data
-Basic information
Entry | Database: PDB / ID: 8c5d | ||||||
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Title | Glutathione transferase P1-1 from Mus musculus | ||||||
Components | Glutathione S-transferase P 1 | ||||||
Keywords | TRANSFERASE / multidrug resistance / pesticide / enzyme inhibition / drug design | ||||||
Function / homology | Function and homology information cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / kinase regulator activity / response to L-ascorbic acid / negative regulation of leukocyte proliferation ...cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / kinase regulator activity / response to L-ascorbic acid / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / organic cyclic compound binding / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / oligodendrocyte development / negative regulation of JUN kinase activity / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / cellular response to glucocorticoid stimulus / 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 vascular associated smooth muscle cell proliferation / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / toxic substance binding / response to amino acid / animal organ regeneration / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / glutathione metabolic process / cellular response to epidermal growth factor stimulus / Neutrophil degranulation / xenobiotic metabolic process / response to nutrient levels / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / response to ethanol / cellular response to lipopolysaccharide / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Papageorgiou, A.C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Biomolecules / Year: 2023 Title: Inhibition Analysis and High-Resolution Crystal Structure of Mus musculus Glutathione Transferase P1-1. Authors: Kupreienko, O. / Pouliou, F. / Konstandinidis, K. / Axarli, I. / Douni, E. / Papageorgiou, A.C. / Labrou, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5d.cif.gz | 321.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5d.ent.gz | 220.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5d ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5d | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23635.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gstp1, Gstpib / Production host: Escherichia coli (E. coli) / References: UniProt: P19157, glutathione transferase |
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-Non-polymers , 6 types, 622 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.35 Å3/Da / Density % sol: 47.66 % / Description: Rectangular rods |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 6000 20% (w/v), 0.2 M calcium chloride dihydrate, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→56.62 Å / Num. obs: 114851 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.059 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 6.3 % / Num. unique obs: 5532 / CC1/2: 0.35 / Rrim(I) all: 2.485 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→38.68 Å / SU ML: 0.1516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8494 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→38.68 Å
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Refine LS restraints |
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LS refinement shell |
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