+Open data
-Basic information
Entry | Database: PDB / ID: 5gss | ||||||
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Title | HUMAN GLUTATHIONE S-TRANSFERASE P1-1, COMPLEX WITH GLUTATHIONE | ||||||
Components | GLUTATHIONE S-TRANSFERASE P1-1 | ||||||
Keywords | TRANSFERASE / DETOXIFYING ENZYME | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Oakley, A. / Parker, M. | ||||||
Citation | 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. / Bello, M.L. / Battistoni, A. / Ricci, G. / Rossjohn, J. / Villar, H.O. / Parker, M.W. #1: 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 | 5gss.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gss.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gss_validation.pdf.gz | 908.9 KB | Display | wwPDB validaton report |
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Full document | 5gss_full_validation.pdf.gz | 938.6 KB | Display | |
Data in XML | 5gss_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5gss_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/5gss ftp://data.pdbj.org/pub/pdb/validation_reports/gs/5gss | HTTPS FTP |
-Related structure data
Related structure data | 10gsC 6gssC 7gssC 8gssC 9gssC 1gssS 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: (0.944872, 0.144443, 0.29386), Vector: |
-Components
#1: Protein | Mass: 23246.570 Da / Num. of mol.: 2 / Fragment: TWO INTACT MONOMERS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Oct 24, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 29652 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rsym value: 0.033 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 6.7 / Rsym value: 0.109 / % possible all: 77 |
Reflection | *PLUS % possible obs: 88 % / Num. measured all: 63592 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 77 % / Rmerge(I) obs: 0.109 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSS Resolution: 1.95→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.04 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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