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- PDB-3gst: STRUCTURE OF THE XENOBIOTIC SUBSTRATE BINDING SITE OF A GLUTATHIO... -

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Basic information

Entry
Database: PDB / ID: 3gst
TitleSTRUCTURE OF THE XENOBIOTIC SUBSTRATE BINDING SITE OF A GLUTATHIONE S-TRANSFERASE AS REVEALED BY X-RAY CRYSTALLOGRAPHIC ANALYSIS OF PRODUCT COMPLEXES WITH THE DIASTEREOMERS OF 9-(S-GLUTATHIONYL)-10-HYDROXY-9, 10-DIHYDROPHENANTHRENE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase ...Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity / response to axon injury / response to amino acid / xenobiotic catabolic process / steroid binding / glutathione metabolic process / response to lead ion / sensory perception of smell / cellular response to xenobiotic stimulus / response to ethanol / response to xenobiotic stimulus / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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
Chem-GPR / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJi, X. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1994
Title: Structure and function of the xenobiotic substrate binding site of a glutathione S-transferase as revealed by X-ray crystallographic analysis of product complexes with the diastereomers of 9- ...Title: Structure and function of the xenobiotic substrate binding site of a glutathione S-transferase as revealed by X-ray crystallographic analysis of product complexes with the diastereomers of 9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene.
Authors: Ji, X. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Tyrosine 115 Participates Both in Chemical and Physical Steps of the Catalytic Mechanism of a Glutathione S-Transferase
Authors: Johnson, W.W. / Liu, S. / Ji, X. / Gilliland, G.L. / Armstrong, R.N.
#2: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2 Angstroms Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
#3: Journal: J.Biol.Chem. / Year: 1992
Title: Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
Authors: Liu, S. / Zhang, P. / Ji, X. / Johnson, W.W. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionJun 7, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX H5A, H5B, H6A, AND H6B OF THE HELIX MAY BE CONSIDERED AS A SINGLE LONG HELIX WHICH BENDS BY ...HELIX H5A, H5B, H6A, AND H6B OF THE HELIX MAY BE CONSIDERED AS A SINGLE LONG HELIX WHICH BENDS BY ABOUT 35 DEGREES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,31311
Polymers51,6382
Non-polymers1,6769
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-94 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.240, 69.440, 81.280
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 38, 60, AND 206 OF BOTH CHAINS ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

21B-287-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8179, -0.1067, 0.5654), (-0.1041, -0.9939, -0.0369), (0.5659, -0.0288, -0.824)
Vector: -6.3371, 31.8033, 26.4302)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*, WHICH CORRESPONDS TO A ROTATION OF 179.755 DEGREES AROUND THE DIRECTION 0.9534 -0.0553 0.2967.

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 25818.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P04905, glutathione transferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GPR / (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE


Mass: 501.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.9 / Method: vapor diffusion, hanging drop
Details: referred to 'Sesay, M. A.', (1987) J.Mol.Biol., 197, 377-378
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111.3 mg/mlprotein1drop
23.5 mM(9R,-10R)-9,10-dihydro-9-(S-glutathionyl)-10-hydroxyphenanthrene1drop
30.4 %(w/v)beta-octylglucopyranoside1drop
440 %(w/v)satammonium sulfate1drop
510 mM1dropKH2PO4
660-74 %(w/v)satammonium sulfate1reservoir
70.46 %(w/v)beta-octylglucopyranoside1reservoir
810 mM1reservoirKH2PO4

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 94783 / Num. obs: 34613 / Rmerge(I) obs: 0.0837

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Processing

SoftwareName: GPRLSA / Classification: refinement
RefinementRfactor obs: 0.159 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 105 437 4178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 28714 / σ(I): 2 / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_planar_d0.034
X-RAY DIFFRACTIONp_chiral_restr0.2
X-RAY DIFFRACTIONp_mcbond_it0.742
X-RAY DIFFRACTIONp_scbond_it1.408
X-RAY DIFFRACTIONp_mcangle_it1.208
X-RAY DIFFRACTIONp_scangle_it2.14

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