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- PDB-2glr: MOLECULAR STRUCTURE AT 1.8 ANGSTROMS OF MOUSE LIVER CLASS PI GLUT... -

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Basic information

Entry
Database: PDB / ID: 2glr
TitleMOLECULAR STRUCTURE AT 1.8 ANGSTROMS OF MOUSE LIVER CLASS PI GLUTATHIONE S-TRANSFERASE COMPLEXED WITH S-(P-NITROBENZYL)GLUTATHIONE AND OTHER INHIBITORS
ComponentsGLUTATHIONE S-TRANSFERASE YFYF
KeywordsTRANSFERASE(GLUTATHIONE)
Function / homology
Function and homology information


negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / cellular response to cell-matrix adhesion / negative regulation of leukocyte proliferation / kinase regulator activity / response to L-ascorbic acid / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process ...negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / cellular response to cell-matrix adhesion / negative regulation of leukocyte proliferation / kinase regulator activity / response to L-ascorbic acid / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / oligodendrocyte development / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / negative regulation of stress-activated MAPK cascade / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / prostaglandin metabolic process / regulation of stress-activated MAPK cascade / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / response to amino acid / animal organ regeneration / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / Neutrophil degranulation / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / positive regulation of superoxide anion generation / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / response to toxic substance / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / inflammatory response / negative regulation of apoptotic process / protein-containing complex / mitochondrion / nucleus / cytosol
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-HEXYLGLUTATHIONE / Glutathione S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsParraga, A. / Garcia-Saez, I. / Coll, M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Molecular structure at 1.8 A of mouse liver class pi glutathione S-transferase complexed with S-(p-nitrobenzyl)glutathione and other inhibitors.
Authors: Garcia-Saez, I. / Parraga, A. / Phillips, M.F. / Mantle, T.J. / Coll, M.
#1: Journal: Embo J. / Year: 1991
Title: The Three-Dimensional Structure of Class Pi Glutathione S-Transferase in Complex with Glutathione Sulfonate at 2.3 Angstroms Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Schaffer, J. / Gallay, O. / Huber, R.
History
DepositionMay 4, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE YFYF
B: GLUTATHIONE S-TRANSFERASE YFYF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7934
Polymers47,0082
Non-polymers7852
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-22 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.950, 77.640, 57.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 2 / 2: CIS PROLINE - PRO A 53 / 3: CIS PROLINE - PRO B 2 / 4: CIS PROLINE - PRO B 53

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE YFYF


Mass: 23503.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P19157, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenzyme1drop
210 mMMES1drop
318 mMglutathione sulphonic acid1drop
450 mMMES1drop
50.02 %1dropNaN3
620 %PEG60001drop
750 mMimidazole1drop
80.3 Msodium/phosphate phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 22084 / % possible obs: 91 % / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.2 Å / % possible obs: 85 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.169 -
obs0.169 22084
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 52 185 3545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.563
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.563

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