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Yorodumi- PDB-5djm: Structure of WT Human Glutathione Transferase in complex with cis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5djm | ||||||
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Title | Structure of WT Human Glutathione Transferase in complex with cisplatin in the absence of glutathione. | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | transferase/transferase inhibitor / Anticancer Cisplatin / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 | 5djm.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5djm.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 5djm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5djm_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 5djm_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 5djm_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5djm_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5djm ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5djm | HTTPS FTP |
-Related structure data
Related structure data | 5djlC 5gssS C: citing same article (ref.) 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
#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 #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: 2.55 Å3/Da / Density % sol: 51.79 % |
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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. Soaked in 0.1MM Cisplatin for 24hrs |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2004 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→46.88 Å / Num. obs: 36278 / % possible obs: 98.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.03 / Net I/σ(I): 18.1 / Num. measured all: 268519 | |||||||||||||||||||||||||||
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: 1.9→27.978 Å / FOM work R set: 0.7931 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.66 / 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: 137.35 Å2 / Biso mean: 32.79 Å2 / Biso min: 3.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→27.978 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: 13
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