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Yorodumi- PDB-5djl: Structure of WT Human Glutathione Transferase in complex with cis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5djl | ||||||
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Title | Structure of WT Human Glutathione Transferase in complex with cisplatin in the presence of glutathione. | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | transferase/transferase inhibitor / Anticancer Cisplatin Glutathione / transferase-transferase inhibitor complex | ||||||
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 / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Parker, L.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: A structure-based mechanism of cisplatin resistance mediated by Glutathione Transferase P1-1 Authors: Parker, L.J. / Italiano, L.C. / Hancock, N.C. / Aitken, J. / Harris, H.H. / Hansen, G. / Ascher, D.B. / Morton, C.J. / Parker, M.W. / Lo Bello, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5djl.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5djl.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 5djl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5djl_validation.pdf.gz | 931.7 KB | Display | wwPDB validaton report |
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Full document | 5djl_full_validation.pdf.gz | 934 KB | Display | |
Data in XML | 5djl_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5djl_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5djl ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5djl | HTTPS FTP |
-Related structure data
Related structure data | 5djmC 5gssS 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23377.770 Da / Num. of mol.: 2 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 , 7 types, 539 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CO3 / | #7: Chemical | ChemComp-SO4 / | #8: 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: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100MM MES, PH 5.5, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2 10MM DTT, 10MM GSH. Soaked in 0.1MM Cisplatin for 24hrs. |
-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: Nov 9, 2005 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.8→31.58 Å / Num. obs: 43040 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.041 / Net I/σ(I): 9.6 / Num. measured all: 175670 / Scaling rejects: 149 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GSS Resolution: 1.8→29.178 Å / FOM work R set: 0.9053 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.07 Å2 / Biso mean: 20.66 Å2 / Biso min: 7.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→29.178 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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