[English] 日本語
Yorodumi- PDB-3gss: HUMAN GLUTATHIONE S-TRANSFERASE P1-1 IN COMPLEX WITH ETHACRYNIC A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gss | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN GLUTATHIONE S-TRANSFERASE P1-1 IN COMPLEX WITH ETHACRYNIC ACID-GLUTATHIONE CONJUGATE | ||||||
Components | GLUTATHIONE S-TRANSFERASE P1-1 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / PI / DETOXIFICATION / ETHACRYNIC ACID | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Oakley, A.J. / Rossjohn, J. / Parker, M.W. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: The three-dimensional structure of the human Pi class glutathione transferase P1-1 in complex with the inhibitor ethacrynic acid and its glutathione conjugate. Authors: Oakley, A.J. / Rossjohn, J. / Lo Bello, M. / Caccuri, A.M. / Federici, G. / Parker, M.W. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gss.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gss.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gss_validation.pdf.gz | 499.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gss_full_validation.pdf.gz | 507.5 KB | Display | |
Data in XML | 3gss_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3gss_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gss ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gss | HTTPS FTP |
-Related structure data
Related structure data | 2gssC 1gssS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.938073, 0.148235, 0.313123), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23246.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH ETHACRYNIC ACID-GLUTATHIONE CONJUGATE Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: GSTP1 / Organ: UBIQUITOUS / Plasmid: PGST-1 / Cellular location (production host): CYTOPLASM / Gene (production host): GSTP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BMH 71/18 / References: UniProt: P09211, glutathione transferase |
---|
-Non-polymers , 5 types, 371 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.2 / Details: pH 5.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 33121 / % possible obs: 90.7 % / Observed criterion σ(I): -1 / Redundancy: 1.8 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.6 / % possible all: 87.3 |
Reflection | *PLUS Num. measured all: 61022 |
Reflection shell | *PLUS % possible obs: 87.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSS Resolution: 1.9→15 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 1 Å2 / Rms dev position: 500 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 3.9628 % |