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- PDB-7bia: Crystal structure of human GSTP1 bound to iberin -

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Basic information

Entry
Database: PDB / ID: 7bia
TitleCrystal structure of human GSTP1 bound to iberin
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / Glutathione transferase / ligandin
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
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / 1-isothiocyanato-3-methylsulfinyl-propane / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSchwartz, M. / Neiers, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Food Chem / Year: 2022
Title: Role of human salivary enzymes in bitter taste perception.
Authors: Schwartz, M. / Brignot, H. / Feron, G. / Hummel, T. / Zhu, Y. / von Koskull, D. / Heydel, J.M. / Lirussi, F. / Canon, F. / Neiers, F.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9247
Polymers46,7562
Non-polymers1,1685
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-14 kcal/mol
Surface area17540 Å2
Unit cell
Length a, b, c (Å)77.410, 89.780, 68.854
Angle α, β, γ (deg.)90.000, 98.052, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

21B-502-

HOH

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Components

#1: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23377.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1, FAEES3, GST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TVQ / 1-isothiocyanato-3-methylsulfinyl-propane / iberin


Mass: 163.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NOS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.0, 25% PEG8000, 0.02M CaCl2, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.73→46.84 Å / Num. obs: 48004 / % possible obs: 99 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Net I/σ(I): 15.3
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2189 / CC1/2: 0.957 / Rpim(I) all: 0.154 / % possible all: 82.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
pointlessdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X79

5x79


Resolution: 1.73→44.89 Å / SU ML: 0.1728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 2482 5.17 %
Rwork0.1775 45481 -
obs0.1794 47963 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.73→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 73 406 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693413
X-RAY DIFFRACTIONf_angle_d0.90064624
X-RAY DIFFRACTIONf_chiral_restr0.0522508
X-RAY DIFFRACTIONf_plane_restr0.0051597
X-RAY DIFFRACTIONf_dihedral_angle_d15.54211288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.26451200.20342136X-RAY DIFFRACTION83.99
1.77-1.80.22551210.19932560X-RAY DIFFRACTION99.7
1.8-1.840.2771300.20192515X-RAY DIFFRACTION99.89
1.84-1.880.24781410.20952531X-RAY DIFFRACTION99.81
1.88-1.930.27961540.20442525X-RAY DIFFRACTION99.85
1.93-1.980.21451470.19012546X-RAY DIFFRACTION99.78
1.98-2.040.22921390.19172559X-RAY DIFFRACTION100
2.04-2.110.23051520.18822507X-RAY DIFFRACTION99.85
2.11-2.180.20381400.1862532X-RAY DIFFRACTION99.93
2.18-2.270.2151420.17952553X-RAY DIFFRACTION99.93
2.27-2.370.21071470.18412552X-RAY DIFFRACTION100
2.37-2.50.22221360.18672540X-RAY DIFFRACTION99.96
2.5-2.650.19281420.18262535X-RAY DIFFRACTION99.81
2.65-2.860.25381220.19012576X-RAY DIFFRACTION99.96
2.86-3.150.22641270.18922568X-RAY DIFFRACTION99.96
3.15-3.60.22131490.17062551X-RAY DIFFRACTION100
3.6-4.540.18381410.15022590X-RAY DIFFRACTION99.96
4.54-44.890.18361320.16352605X-RAY DIFFRACTION99.71

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