+Open data
-Basic information
Entry | Database: PDB / ID: 6ap9 | ||||||
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Title | Crystal Structure of hGSTP1-1 with S-nitrosation of Cys101 | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | TRANSFERASE | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Kumari, V. / Ji, X. | ||||||
Citation | Journal: to be published Title: Cysteine S-nitrosylation of hGSTP1-1 by nitric oxide (NO)-releasing prodrugs Authors: Kumari, V. / Dyba, M.A. / Ji, X. #1: Journal: Biochemistry / Year: 1999 Title: Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1 Authors: Ji, X. / Blaszczyk, J. / Xiao, B. / O'Donnell, R. / Hu, X. / Herzog, C. / Singh, S.V. / Zimniak, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ap9.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ap9.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ap9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ap9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6ap9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6ap9_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 6ap9_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6ap9 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6ap9 | HTTPS FTP |
-Related structure data
Related structure data | 3pgtS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23406.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09211, glutathione transferase |
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-Non-polymers , 6 types, 761 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / #7: 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: 51.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, MES, Ca(OAc)2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2013 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 68229 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.46 Å2 / Rmerge(I) obs: 0.88 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 0.888 / Net I/av σ(I): 18.166 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / CC1/2: 0.872 / Rpim(I) all: 0.243 / Rrim(I) all: 0.469 / Χ2: 0.658 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PGT Resolution: 1.55→29.318 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→29.318 Å
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Refine LS restraints |
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LS refinement shell |
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