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- PDB-1k3y: Crystal Structure Analysis of human Glutathione S-transferase wit... -

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Basic information

Entry
Database: PDB / ID: 1k3y
TitleCrystal Structure Analysis of human Glutathione S-transferase with S-hexyl glutatione and glycerol at 1.3 Angstrom
ComponentsGLUTATHIONE S-TRANSFERASE A1
KeywordsTRANSFERASE / glutathione S-transferase / S-hexyl glutatione / water structure
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, alpha class / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsLe Trong, I. / Stenkamp, R.E. / Ibarra, C. / Atkins, W.M. / Adman, E.T.
CitationJournal: Proteins / Year: 2002
Title: 1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site.
Authors: Le Trong, I. / Stenkamp, R.E. / Ibarra, C. / Atkins, W.M. / Adman, E.T.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE A1
B: GLUTATHIONE S-TRANSFERASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1397
Polymers51,0782
Non-polymers1,0615
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-32 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.380, 93.770, 51.627
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-6099-

HOH

21A-6465-

HOH

31B-6041-

HOH

41B-6150-

HOH

51B-6438-

HOH

61B-6557-

HOH

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE A1 / / GSTA1-1


Mass: 25538.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG2000, 0.1M Tris-Cl 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 116089 / Num. obs: 109989 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.03
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.364 / % possible all: 68.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementStarting model: PDB ENTRY 1GSE [NO LIGAND OR WATER]

1gse


Resolution: 1.3→10 Å / Num. parameters: 38824 / Num. restraintsaints: 46589 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5491 5 %RANDOM
Rwork0.1365 ---
all0.137 109838 --
obs0.137 109838 94.8 %-
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 3721 / Occupancy sum non hydrogen: 4255.5
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 70 602 4264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.097

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