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Yorodumi- PDB-6y1e: Crystal structure of human glutathione transferase P1-1 (hGSTP1-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y1e | ||||||
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Title | Crystal structure of human glutathione transferase P1-1 (hGSTP1-1) that was co-crystallised in the presence of indanyloxyacetic acid-94 (IAA-94) | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | TRANSFERASE / Indanyloxyacetic acid-94 / IAA-94 / chloride ion channel inhibitor / ethacrynic acid / EA / glutathione transferase P1-1 / CLIC1 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.402 Å | ||||||
Authors | Pandian, R. / Worth, R. / Thangaraj, V. / Sayed, Y. / Dirr, H.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The interaction of IAA-94 with the soluble conformation of the CLIC1 protein and its structural homolog hGSTP1-1 Authors: Worth, R. / Pandian, R. / Thangaraj, V. / Sayed, Y. / Dirr, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y1e.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y1e.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y1e_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6y1e_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6y1e_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 6y1e_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/6y1e ftp://data.pdbj.org/pub/pdb/validation_reports/y1/6y1e | HTTPS FTP |
-Related structure data
Related structure data | 1aqxS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23377.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase |
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-Non-polymers , 5 types, 856 molecules
#2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-MES / #4: Chemical | #5: Chemical | #6: 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: 47.61 % / Description: Cubic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 mg/ml hGSTP1-1 (50 mM dipotassium phosphate, 1.5 mM EDTA, 10 mM DTT, 10 mM GSH and 0.02 % (w/v) sodium azide, pH 7.0) with 3.5 mM IAA-94 (5% DMSO (v/v)) was crystallized in 100 mM MES and ...Details: 10 mg/ml hGSTP1-1 (50 mM dipotassium phosphate, 1.5 mM EDTA, 10 mM DTT, 10 mM GSH and 0.02 % (w/v) sodium azide, pH 7.0) with 3.5 mM IAA-94 (5% DMSO (v/v)) was crystallized in 100 mM MES and 16 % (w/v) PEG-6000, pH 6.5. The crystals were harvested and then immersed two to three times in 100% (v/v) Parabar 10312 (Paratone) PH range: 6.5 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.402→68.638 Å / Num. obs: 163749 / % possible obs: 96.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.402→1.427 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.251 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7637 / CC1/2: 0.327 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AQX Resolution: 1.402→55.966 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.24 Å2 / Biso mean: 22.178 Å2 / Biso min: 8.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.402→55.966 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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