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- PDB-6mhd: Glutathione S-Transferase Omega 1 bound to covalent inhibitor 44 -

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Basic information

Entry
Database: PDB / ID: 6mhd
TitleGlutathione S-Transferase Omega 1 bound to covalent inhibitor 44
ComponentsGlutathione S-transferase omega-1
KeywordsTransferase/Transferase Inhibitor / Transferase / Transferase inhibitor / Transferase-Transferase 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) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / 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) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / glutathione metabolic process / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 ...Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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
ACETONE / Chem-JRD / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPetrunak, E.M. / Stuckey, J.A.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Structure-Based Design of N-(5-Phenylthiazol-2-yl)acrylamides as Novel and Potent Glutathione S-Transferase Omega 1 Inhibitors.
Authors: Dai, W. / Samanta, S. / Xue, D. / Petrunak, E.M. / Stuckey, J.A. / Han, Y. / Sun, D. / Wu, Y. / Neamati, N.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,9068
Polymers55,7442
Non-polymers1,1616
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-1 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.159, 71.060, 60.443
Angle α, β, γ (deg.)90.00, 114.73, 90.00
Int Tables number4
Space group name H-MP1211

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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: 27872.105 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-JRD / N-[(3-methyl-1,2-oxazol-5-yl)methyl]-N-(4-phenyl-1,3-thiazol-2-yl)propanamide


Mass: 327.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N3O2S
#3: 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
#4: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 30% PEG-3350, 4% acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 22575 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.54 Å2 / Rsym value: 0.086 / Net I/σ(I): 10
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.1 % / Rsym value: 0.335 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YQU

4yqu


Resolution: 2.16→43.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1109 4.97 %RANDOM
Rwork0.193 ---
obs0.195 22325 89.1 %-
Displacement parametersBiso mean: 27.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.8139 Å20 Å21.342 Å2
2--1.5839 Å20 Å2
3----0.7699 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.16→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 78 150 3969
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013991HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015492HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes703HARMONIC5
X-RAY DIFFRACTIONt_it3991HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion17.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion500SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4749SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.18 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2518 -5.15 %
Rwork0.2031 424 -
all0.2056 447 -
obs--51.31 %

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