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Yorodumi- PDB-2pgt: CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] C... -
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-Basic information
Entry | Database: PDB / ID: 2pgt | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE | ||||||
Components | GLUTATHIONE S-TRANSFERASE | ||||||
Keywords | TRANSFERASE / PI CLASS / HGSTP1-1[V104] / 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 / 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: 1.9 Å | ||||||
Authors | Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase. Authors: Ji, X. / Tordova, M. / O'Donnell, R. / Parsons, J.F. / Hayden, J.B. / Gilliland, G.L. / Zimniak, P. #1: Journal: Biochemistry / Year: 1994 Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9- ...Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene Authors: Ji, X. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L. #2: Journal: Eur.J.Biochem. / Year: 1994 Title: Naturally Occurring Human Glutathione S-Transferase Gstp1-1 Isoforms with Isoleucine and Valine in Position 104 Differ in Enzymic Properties Authors: Zimniak, P. / Nanduri, B. / Pikula, S. / Bandorowicz-Pikula, J. / Singhal, S.S. / Srivastava, S.K. / Awasthi, S. / Awasthi, Y.C. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / 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 | 2pgt.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pgt.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pgt_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2pgt_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2pgt_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 2pgt_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgt ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgt | HTTPS FTP |
-Related structure data
Related structure data | 1pgtSC 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: (0.940109, -0.104945, 0.324317), Vector: |
-Components
#1: Protein | Mass: 23363.742 Da / Num. of mol.: 2 / Mutation: VAL 104 VARIANT Source method: isolated from a genetically manipulated source Details: HGSTP1-1[V104] AND HGSTP1-1[I104] ARE NATURALLY OCCURRING VARIANTS OF HGSTP1-1 OBTAINED BY SITE-DIRECTED MUTAGENESIS Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P09211, glutathione transferase #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM ...Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM SULFATE. THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING BETWEEN 1.9 - 2.0 M AMMONIUM SULFATE IN 0.1 M HEPES BUFFER (PH 7.0)., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 40456 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.61 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.31 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1.45 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 1.77 / % possible all: 77.3 |
Reflection shell | *PLUS % possible obs: 77.3 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1PGT Resolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 3 Details: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK ...Details: X-PLOR IS USED AT EARLY STAGE OF REFINEMENT. GPRLSA IS A MODIFIED VERSION OF PROLSQ BY FUREY, WANG AND SAX (J. APPL. CRYSTALLOGR.,1982,15,160-166). CROSS-VALIDATION INCLUDES GEOMETRY CHECK AND R FACTOR CALCULATION FOR ALL DATA.
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Displacement parameters | Biso mean: 26.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: GPRLSA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(I): 1.5 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |