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- PDB-3km6: Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in... -

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Basic information

Entry
Database: PDB / ID: 3km6
TitleCrystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION / DOUBLE MUTANT / ETHACRYNIC ACID / DIURETIC DRUG / DIMER INTERFACE
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / nitric oxide binding / 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 MAP kinase activity / negative regulation of MAPK cascade / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of protein kinase activity / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
ETHACRYNIC ACID / GLUTATHIONE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Difference Fourier / Resolution: 2.1 Å
AuthorsParker, L.J.
CitationJournal: J.Mol.Recognit.
Title: Diuretic drug binding to human glutathione transferase P1-1: potential role of Cys-101 revealed in the double mutant C47S/Y108V.
Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Wielens, J. / Holien, J.K. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Aguilera, A.M. / Nuccetelli, M. / Mazzetti, A.P. / Lo Bello, M. ...Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Wielens, J. / Holien, J.K. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Aguilera, A.M. / Nuccetelli, M. / Mazzetti, A.P. / Lo Bello, M. / Parker, M.W. / Garcia-Fuentes, L.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Advisory / Non-polymer description
Revision 1.3Dec 21, 2011Group: Advisory / Database references / Non-polymer description
Revision 1.4Mar 21, 2012Group: Non-polymer description
Revision 1.5Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 1, 2023Group: 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

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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)47,79412
Polymers46,3332
Non-polymers1,46110
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-65 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.876, 89.242, 69.206
Angle α, β, γ (deg.)90.000, 89.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23166.463 Da / Num. of mol.: 2 / Mutation: C47S, Y108V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAEES3, GST3, GSTP1 / Plasmid: PSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-EAA / ETHACRYNIC ACID


Mass: 303.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12Cl2O4
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4mg/ml, 267mM calcium acetate, 100mM MES pH 6.0, 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→44.63 Å / Num. obs: 26463 / % possible obs: 98.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / Num. measured all: 22237 / Num. unique all: 3412 / Rsym value: 0.375 / % possible all: 87.5

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: Difference Fourier
Starting model: pdb ID 3HJO

3hjo


Resolution: 2.1→44.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.884 / SU B: 3.827 / SU ML: 0.106 / SU R Cruickshank DPI: 0.205 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1318 5 %RANDOM
Rwork0.153 ---
obs0.155 26463 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.22 Å2 / Biso mean: 13.925 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20.01 Å2
2---0.74 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 84 477 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223406
X-RAY DIFFRACTIONr_angle_refined_deg1.2782.0094621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60724.865148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5531516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022594
X-RAY DIFFRACTIONr_nbd_refined0.1920.21629
X-RAY DIFFRACTIONr_nbtor_refined0.30.22304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2406
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1150.26
X-RAY DIFFRACTIONr_mcbond_it0.6571.52148
X-RAY DIFFRACTIONr_mcangle_it1.02623329
X-RAY DIFFRACTIONr_scbond_it1.72131466
X-RAY DIFFRACTIONr_scangle_it2.5554.51291
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 80 -
Rwork0.164 1507 -
all-1587 -
obs--80.07 %

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