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- PDB-5dak: Crystal Structure of human Glutathione Transferase Pi complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dak | ||||||
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Title | Crystal Structure of human Glutathione Transferase Pi complexed with a metalloid in the absence of Glutathione | ||||||
![]() | (Glutathione S-transferase P) x 2 | ||||||
![]() | TRANSFERASE / Metalloid / Anti-cancer | ||||||
Function / homology | ![]() 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 / response to reactive oxygen species / fatty acid binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parker, L.J. / Parker, M.W. / Morton, C.J. | ||||||
![]() | ![]() Title: Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-based Therapeutics Authors: Parker, L.J. / Parker, M.W. / Morton, C.J. / Bocedi, A. / Ascher, D.B. / Aitken, J.B. / Harris, H.H. / Lo Bello, M. / Ricci, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 124.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.7 KB | Display | ![]() |
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Full document | ![]() | 457.7 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dalC ![]() 5dcgC ![]() 5ddlC ![]() 5gssS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23377.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 23393.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100MM MES, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2 10MM DTT. Soaked in 2mM PAO dissolved in DMSO PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.11→47.75 Å / Num. obs: 50403 / % possible obs: 94.5 % / Redundancy: 11.6 % / Biso Wilson estimate: 22.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Net I/σ(I): 11 / Num. measured all: 297531 / Scaling rejects: 432 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5GSS Resolution: 2.11→46.902 Å / FOM work R set: 0.8514 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 22.02 / 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: 97.21 Å2 / Biso mean: 25.7 Å2 / Biso min: 7.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→46.902 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: 18
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