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- PDB-5x79: Human GST Pi conjugated with novel inhibitor, GS-ESF -

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Basic information

Entry
Database: PDB / ID: 5x79
TitleHuman GST Pi conjugated with novel inhibitor, GS-ESF
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GSTP / covalent inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / hepoxilin biosynthetic process / glutathione derivative 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 / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / : / linoleic acid metabolic process / negative regulation of JUN kinase activity / nitric oxide binding / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / prostaglandin metabolic process / regulation of stress-activated MAPK cascade / 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 MAPK cascade / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / negative regulation of MAP kinase activity / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / response to reactive oxygen species / central nervous system development / fatty acid binding / 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 / cytosol / cytoplasm
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 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, Pi 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 / 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-GF5 / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTomoike, F. / Shishido, Y. / Fukui, K. / Kimura, Y. / Abe, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI Grant Number15K12751 Japan
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP1-1).
Authors: Shishido, Y. / Tomoike, F. / Kimura, Y. / Kuwata, K. / Yano, T. / Fukui, K. / Fujikawa, H. / Sekido, Y. / Murakami-Tonami, Y. / Kameda, T. / Shuto, S. / Abe, H.
History
DepositionFeb 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)47,9816
Polymers46,7562
Non-polymers1,2254
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.041, 89.430, 68.967
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

21B-451-

HOH

31B-641-

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-GF5 / (2S)-2-azanyl-5-[[(2R)-3-(2-fluorosulfonylethylsulfanyl)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid


Mass: 417.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20FN3O8S2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 22% PEG8000, 20 mM calcium chloride, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.132 Å / Num. obs: 36851 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.93 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data collection
MOLREPmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A2R

2a2r


Resolution: 1.9→42.13 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.41
RfactorNum. reflection% reflection
Rfree0.242 1878 5.1 %
Rwork0.198 --
obs0.2 36842 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 74 703 4069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233420
X-RAY DIFFRACTIONf_angle_d1.4144642
X-RAY DIFFRACTIONf_dihedral_angle_d18.3971292
X-RAY DIFFRACTIONf_chiral_restr0.059512
X-RAY DIFFRACTIONf_plane_restr0.024596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.95150.35651280.29492627X-RAY DIFFRACTION98
1.9515-2.00890.33941550.26182656X-RAY DIFFRACTION100
2.0089-2.07380.30041430.24912687X-RAY DIFFRACTION100
2.0738-2.14790.27131410.22882679X-RAY DIFFRACTION100
2.1479-2.23390.2521530.21322702X-RAY DIFFRACTION100
2.2339-2.33550.28111300.19952704X-RAY DIFFRACTION100
2.3355-2.45870.22431650.1972671X-RAY DIFFRACTION100
2.4587-2.61270.22811570.18762661X-RAY DIFFRACTION100
2.6127-2.81440.22721470.18922702X-RAY DIFFRACTION100
2.8144-3.09750.23881360.19482717X-RAY DIFFRACTION100
3.0975-3.54550.22941490.17462690X-RAY DIFFRACTION100
3.5455-4.46620.20831330.16362717X-RAY DIFFRACTION100
4.4662-42.14230.21421410.19672751X-RAY DIFFRACTION100

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