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Yorodumi- PDB-3km6: Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3km6 | ||||||
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Title | Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / DETOXIFICATION / DOUBLE MUTANT / ETHACRYNIC ACID / DIURETIC DRUG / DIMER INTERFACE | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Difference Fourier / Resolution: 2.1 Å | ||||||
Authors | Parker, L.J. | ||||||
Citation | Journal: J.Mol.Recognit. Title: Diuretic drug binding to human glutathione transferase P1-1: potential role of Cys-101 revealed in the double mutant C47S/Y108V. Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Wielens, J. / Holien, J.K. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Aguilera, A.M. / Nuccetelli, M. / Mazzetti, A.P. / Lo Bello, M. ...Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Wielens, J. / Holien, J.K. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Aguilera, A.M. / Nuccetelli, M. / Mazzetti, A.P. / Lo Bello, M. / Parker, M.W. / Garcia-Fuentes, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3km6.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3km6.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 3km6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3km6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3km6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3km6_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 3km6_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/3km6 ftp://data.pdbj.org/pub/pdb/validation_reports/km/3km6 | HTTPS FTP |
-Related structure data
Related structure data | 3hjoS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 23166.463 Da / Num. of mol.: 2 / Mutation: C47S, Y108V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAEES3, GST3, GSTP1 / Plasmid: PSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #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: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 4mg/ml, 267mM calcium acetate, 100mM MES pH 6.0, 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.63 Å / Num. obs: 26463 / % possible obs: 98.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / Num. measured all: 22237 / Num. unique all: 3412 / Rsym value: 0.375 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier Starting model: pdb ID 3HJO Resolution: 2.1→44.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.884 / SU B: 3.827 / SU ML: 0.106 / SU R Cruickshank DPI: 0.205 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.22 Å2 / Biso mean: 13.925 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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