[English] 日本語
Yorodumi- PDB-3csi: Crystal Structure of the Glutathione Transferase Pi allelic varia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3csi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Glutathione Transferase Pi allelic variant*C, I104V/A113V, in complex with the Chlorambucil-Glutathione Conjugate | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / DETOXIFICATION / CHLORAMBUCIL / ALLELIC VARIANT | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Parker, L.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The anti-cancer drug chlorambucil as a substrate for the human polymorphic enzyme glutathione transferase P1-1: kinetic properties and crystallographic characterisation of allelic variants. Authors: Parker, L.J. / Ciccone, S. / Italiano, L.C. / Primavera, A. / Oakley, A.J. / Morton, C.J. / Hancock, N.C. / Bello, M.L. / Parker, M.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3csi.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3csi.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 3csi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3csi_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3csi_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3csi_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 3csi_validation.cif.gz | 66.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/3csi ftp://data.pdbj.org/pub/pdb/validation_reports/cs/3csi | HTTPS FTP |
-Related structure data
Related structure data | 3cshC 3csjC 5gssS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23260.598 Da / Num. of mol.: 4 / Mutation: I105V, A114V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Plasmid: pSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P09211, glutathione transferase |
---|
-Non-polymers , 8 types, 922 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-LZ6 / #5: Chemical | ChemComp-GSH / #6: Chemical | ChemComp-CO3 / | #7: Chemical | #8: Chemical | ChemComp-SO4 / | #9: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | WATERS 398A, 414A, 439A, 440A, 385B AND 409B FROM ONE DIMER AND WATERS 330C, 332C, 390C, 410C, ...WATERS 398A, 414A, 439A, 440A, 385B AND 409B FROM ONE DIMER AND WATERS 330C, 332C, 390C, 410C, 576D, 605D AND 576D FROM THE SECOND DIMER FORM A CIRCLE ABOUT CYS101 AT THE DIMER INTERFACE. THEY HAVE BEEN MODELLED AS PARTIAL WATERS BASED ON DIFFERENCE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Resevior solution contained: 100mM MES, 22% PEG 8000, 20mM CaCl2, 10mM DTT and 10mM GSH. Soaking conditions as above, minus DTT, plus 2mM Chlorambucil dissolved in ethanol., pH 6.0, VAPOR ...Details: Resevior solution contained: 100mM MES, 22% PEG 8000, 20mM CaCl2, 10mM DTT and 10mM GSH. Soaking conditions as above, minus DTT, plus 2mM Chlorambucil dissolved in ethanol., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2007 / Details: AXCO |
Radiation | Monochromator: AXCO MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→73.93 Å / Num. all: 70325 / Num. obs: 68745 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2 / Num. unique all: 9830 / Rsym value: 0.638 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 5GSS Resolution: 1.9→25.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.502 / SU ML: 0.103 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
|