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- PDB-3gss: HUMAN GLUTATHIONE S-TRANSFERASE P1-1 IN COMPLEX WITH ETHACRYNIC A... -

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Basic information

Entry
Database: PDB / ID: 3gss
TitleHUMAN GLUTATHIONE S-TRANSFERASE P1-1 IN COMPLEX WITH ETHACRYNIC ACID-GLUTATHIONE CONJUGATE
ComponentsGLUTATHIONE S-TRANSFERASE P1-1
KeywordsTRANSFERASE / GLUTATHIONE / PI / DETOXIFICATION / ETHACRYNIC ACID
Function / homology
Function and homology information


nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / 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 / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / xenobiotic metabolic process / response to reactive oxygen species / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / 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 / secretory granule lumen / cellular response to lipopolysaccharide / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
ETHACRYNIC ACID / GLUTATHIONE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOakley, A.J. / Rossjohn, J. / Parker, M.W.
Citation
Journal: Biochemistry / Year: 1997
Title: The three-dimensional structure of the human Pi class glutathione transferase P1-1 in complex with the inhibitor ethacrynic acid and its glutathione conjugate.
Authors: Oakley, A.J. / Rossjohn, J. / Lo Bello, M. / Caccuri, A.M. / Federici, G. / Parker, M.W.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W.
History
DepositionOct 29, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 P1-1
B: GLUTATHIONE S-TRANSFERASE P1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2019
Polymers46,4932
Non-polymers1,7077
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-40 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.657, 89.347, 68.596
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.938073, 0.148235, 0.313123), (0.14981, -0.988529, 0.019167), (0.312373, 0.028929, -0.949519)
Vector: -5.9887, 20.864, 27.0091)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUTATHIONE S-TRANSFERASE P1-1 / GST


Mass: 23246.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ETHACRYNIC ACID-GLUTATHIONE CONJUGATE
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: GSTP1 / Organ: UBIQUITOUS / Plasmid: PGST-1 / Cellular location (production host): CYTOPLASM / Gene (production host): GSTP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BMH 71/18 / References: UniProt: P09211, glutathione transferase

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Non-polymers , 5 types, 371 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-EAA / ETHACRYNIC ACID / Etacrynic acid


Mass: 303.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12Cl2O4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growpH: 5.2 / Details: pH 5.2
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
25 Mphosphate1drop
30.5 mMEDTA1drop
41 mMmercaptoethanol1drop
511.5-13.5 %(w/v)ammonium sulfate1drop
627.5-32.5 mMDTT1drop
70.05 MMES1drop
823-27 %(w/v)ammonium sulfate1reservoir
955-65 mMDTT1reservoir
100.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 33121 / % possible obs: 90.7 % / Observed criterion σ(I): -1 / Redundancy: 1.8 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.6 / % possible all: 87.3
Reflection
*PLUS
Num. measured all: 61022
Reflection shell
*PLUS
% possible obs: 87.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSS

1gss


Resolution: 1.9→15 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 -4.5048 %RANDOM
Rwork0.206 ---
obs0.206 33120 90.7 %-
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 107 364 3733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.297
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.264
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.7
X-RAY DIFFRACTIONx_mcangle_it2.2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1 Å2 / Rms dev position: 500 Å
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2831 179 3.962 %
Rwork0.2604 3777 -
obs--90.69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.932
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.264
LS refinement shell
*PLUS
% reflection Rfree: 3.9628 %

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