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- PDB-9lhf: Crystal structure of A13 with hGSTO1 -

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Basic information

Entry
Database: PDB / ID: 9lhf
TitleCrystal structure of A13 with hGSTO1
ComponentsGlutathione S-transferase omega-1
KeywordsOXIDOREDUCTASE / Inhibitor / Complex
Function / homology
Function and homology information


positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / negative regulation of release of sequestered calcium ion into cytosol / glutathione transferase / glutathione transferase activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of release of sequestered calcium ion into cytosol / oxidoreductase activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / 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, omega-class / Glutathione S-transferase Omega/Tau-like / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, Y. / Zhou, L. / Lu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of Potent, Allosteric GSTO1 Covalent Inhibitors with a New Binding Mode
Authors: Sun, Y. / Zhou, L. / Lu, W.
History
DepositionJan 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase omega-1
B: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2143
Polymers55,8582
Non-polymers3551
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.958, 68.277, 62.757
Angle α, β, γ (deg.)90.000, 112.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutathione S-transferase omega-1 / GSTO-1 / Glutathione S-transferase omega 1-1 / GSTO 1-1 / Glutathione-dependent dehydroascorbate ...GSTO-1 / Glutathione S-transferase omega 1-1 / GSTO 1-1 / Glutathione-dependent dehydroascorbate reductase / Monomethylarsonic acid reductase / MMA(V) reductase / S-(Phenacyl)glutathione reductase / SPG-R


Mass: 27929.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Production host: Escherichia coli (E. coli)
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-A1ELW / 1-[(2~{R})-2-[5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl]pyrrolidin-1-yl]propan-1-one


Mass: 355.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16F3N3OS
Details: The ligand SMILES string that interacts with Cys32 in chain A is: C=CC(N1CCC[C@@H]1c2sc(c3ccc(C(F)(F)F)cc3)nn2)=O, featuring a double bond between C8 and C9. However, as the coordinates ...Details: The ligand SMILES string that interacts with Cys32 in chain A is: C=CC(N1CCC[C@@H]1c2sc(c3ccc(C(F)(F)F)cc3)nn2)=O, featuring a double bond between C8 and C9. However, as the coordinates represent the product state (with a single bond between C8 and C9), we created A1ELW based on the product state configuration.
Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH6.6, PEG3350-26%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.3→42.56 Å / Num. obs: 20036 / % possible obs: 97.49 % / Redundancy: 2 % / Biso Wilson estimate: 35.29 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.47
Reflection shellResolution: 2.302→2.384 Å / Mean I/σ(I) obs: 2.61 / Num. unique obs: 1719 / CC1/2: 0.361

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPXdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.56 Å / SU ML: 0.2968 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.3274
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 1003 5.01 %
Rwork0.2037 19020 -
obs0.2058 20023 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 0 135 3902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023876
X-RAY DIFFRACTIONf_angle_d0.51245251
X-RAY DIFFRACTIONf_chiral_restr0.0406561
X-RAY DIFFRACTIONf_plane_restr0.0039676
X-RAY DIFFRACTIONf_dihedral_angle_d12.061472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.29891270.25972401X-RAY DIFFRACTION86.63
2.42-2.570.3031450.23572752X-RAY DIFFRACTION99.66
2.58-2.770.28421450.2322757X-RAY DIFFRACTION99.9
2.77-3.050.26681450.22812753X-RAY DIFFRACTION99.01
3.05-3.490.25621460.21342775X-RAY DIFFRACTION99.29
3.49-4.40.21461460.17952772X-RAY DIFFRACTION99.76
4.4-42.560.22951490.18282810X-RAY DIFFRACTION98.44
Refinement TLS params.Method: refined / Origin x: -4.63840305214 Å / Origin y: -0.121751644807 Å / Origin z: 13.3569015628 Å
111213212223313233
T0.226439277115 Å20.00657601177083 Å20.0358837144431 Å2-0.248382596114 Å20.0247166214376 Å2--0.290393042915 Å2
L1.00692662732 °20.163918333226 °20.144050737375 °2-0.582755972475 °20.215985023164 °2--1.26156629173 °2
S0.00498848840599 Å °0.016579354731 Å °-0.028482213112 Å °0.0226620152491 Å °-0.00801127916329 Å °-0.0569384674824 Å °0.0188294774023 Å °0.073449493674 Å °-0.0140010996009 Å °
Refinement TLS groupSelection details: all

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