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- PDB-5j41: Glutathione S-transferase bound with hydrolyzed Piperlongumine -

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Basic information

Entry
Database: PDB / ID: 5j41
TitleGlutathione S-transferase bound with hydrolyzed Piperlongumine
ComponentsGlutathione S-transferase P
Keywordstransferase/transferase inhibitor / GSTP1 / Piperlongumine / glutathione / 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 / negative regulation of nitric-oxide synthase 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 / Paracetamol ADME / glutathione peroxidase activity / 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
3-(3,4,5-trimethoxyphenyl)propanoic acid / GLUTATHIONE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19035345576 Å
AuthorsHarshbarger, W. / Gondi, S. / Ficarro, S. / Hunter, J. / Udayakumar, D. / Gurbani, D. / Marto, J. / Westover, K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine.
Authors: Harshbarger, W. / Gondi, S. / Ficarro, S.B. / Hunter, J. / Udayakumar, D. / Gurbani, D. / Singer, W.D. / Liu, Y. / Li, L. / Marto, J.A. / Westover, K.D.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)47,9798
Polymers46,4932
Non-polymers1,4866
Water13,115728
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-14 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.495, 89.458, 69.001
Angle α, β, γ (deg.)90.000, 98.235, 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-557-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (0.929928541027, 0.145568034247, 0.337702318601), (0.147084827962, -0.988895778486, 0.0212412964925), (0.337044451024, 0.0299179995768, -0.941013257789)Vector: -30. ...NCS oper: (Code: given
Matrix: (0.929928541027, 0.145568034247, 0.337702318601), (0.147084827962, -0.988895778486, 0.0212412964925), (0.337044451024, 0.0299179995768, -0.941013257789)
Vector: -30.0972316704, 22.2286367967, 162.479144875)

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Components

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


Mass: 23246.570 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-3LF / 3-(3,4,5-trimethoxyphenyl)propanoic acid


Mass: 240.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16O5
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M ammonium sulfate, 100mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 152714 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.69108304655 Å2 / Net I/σ(I): 24.16

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GUS

3gus


Resolution: 1.19035345576→22.4017586458 Å / SU ML: 0.102037305567 / Cross valid method: FREE R-VALUE / σ(F): 1.35952612655 / Phase error: 16.8028892625
RfactorNum. reflection% reflection
Rfree0.185671458122 1998 1.33953712891 %
Rwork0.16339530549 --
obs0.1636933887 149156 99.2586677314 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.8567376399 Å2
Refinement stepCycle: LAST / Resolution: 1.19035345576→22.4017586458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 98 728 4095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008660908448243463
X-RAY DIFFRACTIONf_angle_d1.085435870394699
X-RAY DIFFRACTIONf_chiral_restr0.0795922585336518
X-RAY DIFFRACTIONf_plane_restr0.00629484025119606
X-RAY DIFFRACTIONf_dihedral_angle_d18.9568539231309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1904-1.22010.2101221429091300.2233323992129537X-RAY DIFFRACTION90.9321794751
1.2201-1.25310.2401649811951420.20167306369610464X-RAY DIFFRACTION99.0474411655
1.2531-1.290.1891158132121430.18458640825610558X-RAY DIFFRACTION99.962634283
1.29-1.33160.2015601782081440.17472807289810565X-RAY DIFFRACTION100
1.3316-1.37920.1944064649281450.16964950393110622X-RAY DIFFRACTION100
1.3792-1.43440.1836355733211420.1674797480910501X-RAY DIFFRACTION100
1.4344-1.49970.1638336052771440.15660899609410563X-RAY DIFFRACTION100
1.4997-1.57870.155105129371440.15131458206910586X-RAY DIFFRACTION100
1.5787-1.67760.1617163730891420.15185055863310558X-RAY DIFFRACTION99.9719704756
1.6776-1.80710.1729242644171450.15544683173810647X-RAY DIFFRACTION99.9814711877
1.8071-1.98880.1689344781691440.16225229269210605X-RAY DIFFRACTION99.9813970793
1.9888-2.27640.1661258173351440.16145797519110578X-RAY DIFFRACTION99.9906742516
2.2764-2.86710.2025569139321440.17045219581110654X-RAY DIFFRACTION100
2.8671-22.40570.1983493558041450.15376615352210720X-RAY DIFFRACTION99.6697550683

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