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- PDB-3dgq: Crystal structure of the glutathione transferase PI enzyme in com... -

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Basic information

Entry
Database: PDB / ID: 3dgq
TitleCrystal structure of the glutathione transferase PI enzyme in complex with the bifunctional inhibitor, etharapta
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION / ETHARAPTA / RUTHENIUM / 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 canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / 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 S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsParker, L.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Rational design of an organometallic glutathione transferase inhibitor
Authors: Ang, W.H. / Parker, L.J. / De Luca, A. / Juillerat-Jeanneret, L. / Morton, C.J. / Lo Bello, M. / Parker, M.W. / Dyson, P.J.
History
DepositionJun 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_seq_id / _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 P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6569
Polymers46,7562
Non-polymers9017
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-58 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.930, 90.330, 68.960
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23377.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1 / Plasmid: PSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P09211, glutathione transferase

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Non-polymers , 6 types, 513 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EAA / ETHACRYNIC ACID / Etacrynic acid


Mass: 303.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12Cl2O4
#4: 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
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEAA A 211 AND CL A 210, HOH A 417, 418 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM MES BUFFER PH 5.5, 22%(W/V) PEG 8000, 20mM CACL2, 10mM DTT, Small amounts of solid compound were streaked through the drops containing preformed crystals. These were soaked for 48hours. ...Details: 100mM MES BUFFER PH 5.5, 22%(W/V) PEG 8000, 20mM CACL2, 10mM DTT, Small amounts of solid compound were streaked through the drops containing preformed crystals. These were soaked for 48hours., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2006 / Details: ACXO
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→19.53 Å / Num. all: 62097 / Num. obs: 61004 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.56 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.50.5541.33055086430.55496.1
1.69-1.793.60.3382.12949882980.33897
1.79-1.913.60.2113.32816378660.21197.7
1.91-2.073.60.1265.62650673680.12698.5
2.07-2.263.60.0769.42464268040.07699.1
2.26-2.533.60.05213.62268962240.05299.6
2.53-2.923.70.03619.22018855060.03699.9
2.92-3.583.70.02328.21732546850.023100
3.58-5.063.70.01833.31351536240.018100
5.06-19.533.60.02219719819860.02298.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementStarting model: 5GSS

5gss


Resolution: 1.6→19.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.85 / SU B: 1.854 / SU ML: 0.066 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3095 5.1 %RANDOM
Rwork0.195 ---
obs0.196 61004 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.68 Å2 / Biso mean: 18.15 Å2 / Biso min: 5.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0.37 Å2
2---0.51 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 51 506 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223411
X-RAY DIFFRACTIONr_angle_refined_deg1.5392.0024634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94724.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14515572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3231516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022588
X-RAY DIFFRACTIONr_nbd_refined0.2030.21776
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2420
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.218
X-RAY DIFFRACTIONr_mcbond_it0.9791.52145
X-RAY DIFFRACTIONr_mcangle_it1.38523356
X-RAY DIFFRACTIONr_scbond_it2.20631451
X-RAY DIFFRACTIONr_scangle_it3.2314.51277
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.61 216 -
Rwork0.48 4125 -
all-4341 -
obs--95.72 %

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