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- PDB-8c5d: Glutathione transferase P1-1 from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 8c5d
TitleGlutathione transferase P1-1 from Mus musculus
ComponentsGlutathione S-transferase P 1
KeywordsTRANSFERASE / multidrug resistance / pesticide / enzyme inhibition / drug design
Function / homology
Function and homology information


cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / S-nitrosoglutathione binding / kinase regulator activity / response to L-ascorbic acid ...cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / S-nitrosoglutathione binding / kinase regulator activity / response to L-ascorbic acid / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / organic cyclic compound binding / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / oligodendrocyte development / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / negative regulation of leukocyte proliferation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / cellular response to glucocorticoid stimulus / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / toxic substance binding / response to amino acid / animal organ regeneration / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / cellular response to epidermal growth factor stimulus / xenobiotic metabolic process / Neutrophil degranulation / response to nutrient levels / regulation of ERK1 and ERK2 cascade / response to reactive oxygen species / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / response to ethanol / cellular response to lipopolysaccharide / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleus / plasma membrane / cytosol / cytoplasm
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 / 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
S-(P-NITROBENZYL)GLUTATHIONE / Glutathione S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsPapageorgiou, A.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT653706European Union
CitationJournal: Biomolecules / Year: 2023
Title: Inhibition Analysis and High-Resolution Crystal Structure of Mus musculus Glutathione Transferase P1-1.
Authors: Kupreienko, O. / Pouliou, F. / Konstandinidis, K. / Axarli, I. / Douni, E. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionJan 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase P 1
B: Glutathione S-transferase P 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,78822
Polymers47,2702
Non-polymers1,51820
Water10,845602
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-190 kcal/mol
Surface area17370 Å2
Unit cell
Length a, b, c (Å)56.617, 77.366, 101.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase P 1 / Gst P1 / GST YF-YF / GST class-pi / GST-piB / Preadipocyte growth factor


Mass: 23635.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gstp1, Gstpib / Production host: Escherichia coli (E. coli) / References: UniProt: P19157, glutathione transferase

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Non-polymers , 6 types, 622 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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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Details

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: 2.35 Å3/Da / Density % sol: 47.66 % / Description: Rectangular rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000 20% (w/v), 0.2 M calcium chloride dihydrate, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.28→56.62 Å / Num. obs: 114851 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.059 / Net I/σ(I): 12.7
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 6.3 % / Num. unique obs: 5532 / CC1/2: 0.35 / Rrim(I) all: 2.485 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→38.68 Å / SU ML: 0.1516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1856 1.62 %
Rwork0.1752 112889 -
obs0.1756 114745 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.22 Å2
Refinement stepCycle: LAST / Resolution: 1.28→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 88 602 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573489
X-RAY DIFFRACTIONf_angle_d0.92444731
X-RAY DIFFRACTIONf_chiral_restr0.0688509
X-RAY DIFFRACTIONf_plane_restr0.0086620
X-RAY DIFFRACTIONf_dihedral_angle_d6.8003492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.37241390.33058482X-RAY DIFFRACTION98.26
1.31-1.350.32591410.29578565X-RAY DIFFRACTION99.32
1.35-1.40.3121400.26498556X-RAY DIFFRACTION99.66
1.4-1.450.28081420.24548637X-RAY DIFFRACTION99.77
1.45-1.50.20931430.20928632X-RAY DIFFRACTION99.91
1.5-1.570.27181420.18648675X-RAY DIFFRACTION99.82
1.57-1.660.20291420.17458633X-RAY DIFFRACTION99.8
1.66-1.760.20641430.16838659X-RAY DIFFRACTION99.83
1.76-1.90.21041420.16618697X-RAY DIFFRACTION99.9
1.9-2.090.24631430.16968714X-RAY DIFFRACTION99.73
2.09-2.390.17661440.15668736X-RAY DIFFRACTION99.83
2.39-3.010.17711460.16848807X-RAY DIFFRACTION99.62
3.01-38.680.18121490.16819096X-RAY DIFFRACTION99.44

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