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- PDB-1gta: CRYSTAL STRUCTURES OF A SCHISTOSOMAL DRUG AND VACCINE TARGET: GLU... -

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Basic information

Entry
Database: PDB / ID: 1gta
TitleCRYSTAL STRUCTURES OF A SCHISTOSOMAL DRUG AND VACCINE TARGET: GLUTATHIONE S-TRANSFERASE FROM SCHISTOSOMA JAPONICA AND ITS COMPLEX WITH THE LEADING ANTISCHISTOSOMAL DRUG PRAZIQUANTEL
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsGLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMctigue, M.A. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Crystal structures of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel.
Authors: McTigue, M.A. / Williams, D.R. / Tainer, J.A.
History
DepositionDec 1, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)25,5351
Polymers25,5351
Non-polymers00
Water2,054114
1
A: GLUTATHIONE S-TRANSFERASE

A: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)51,0692
Polymers51,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3010 Å2
ΔGint-15 kcal/mol
Surface area19350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.200, 125.200, 70.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: CIS PROLINE - PRO 56 / 2: CIS PROLINE - PRO 202
3: HIS 215 - PRO 216 OMEGA = 110.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsTHE SECOND SUBUNIT OF THE GST DIMER IS GENERATED BY THE SYMMETRY OPERATION Y, X, -Z.

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 25534.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: PGEX-3X / References: UniProt: P08515, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / pH: 5.6
Details: McTigue, M.A., (1995) Protein struct. func. gen., 22, 55.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
148-50 %satammonium sulfate1reservoir
20.1 Msodium acetate1reservoir
310-20 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 10832 / Observed criterion σ(F): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→7 Å / Rfactor Rwork: 0.197 / Rfactor obs: 0.197
Refinement stepCycle: LAST / Resolution: 2.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 114 1900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
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_deg4.1
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: 0.197 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 4.1

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