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- PDB-6mhb: Glutathione S-Transferase Omega 1 bound to covalent inhibitor 18 -

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Basic information

Entry
Database: PDB / ID: 6mhb
TitleGlutathione S-Transferase Omega 1 bound to covalent inhibitor 18
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
Chem-JR7 / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase omega-1
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
D: Glutathione S-transferase omega-1
E: Glutathione S-transferase omega-1
F: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,61416
Polymers167,2336
Non-polymers2,38110
Water1,29772
1
A: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6686
Polymers55,7442
Non-polymers9244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-9 kcal/mol
Surface area19990 Å2
MethodPISA
2
B: Glutathione S-transferase omega-1
F: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4735
Polymers55,7442
Non-polymers7293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area20420 Å2
MethodPISA
3
D: Glutathione S-transferase omega-1
E: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4735
Polymers55,7442
Non-polymers7293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.386, 68.825, 93.645
Angle α, β, γ (deg.)106.58, 100.35, 96.16
Int Tables number1
Space group name H-MP1

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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.: 6
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-JR7 / N-[4-(4-chlorophenyl)-1,3-thiazol-2-yl]propanamide


Mass: 266.747 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H11ClN2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 25% PEG-3350, 3% methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 35454 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 53.9 Å2 / Rsym value: 0.058 / Net I/σ(I): 10
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.399 / % possible all: 98.6

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Processing

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

4yqu


Resolution: 2.75→45.81 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.371
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1653 4.88 %RANDOM
Rwork0.209 ---
obs0.211 33855 94 %-
Displacement parametersBiso mean: 49.63 Å2
Baniso -1Baniso -2Baniso -3
1--6.5611 Å2-1.6816 Å2-2.7567 Å2
2--6.8223 Å22.6495 Å2
3----0.2612 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.75→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10455 0 142 72 10669
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110982HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0115058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4813SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1914HARMONIC5
X-RAY DIFFRACTIONt_it10982HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1427SEMIHARMONIC5
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_contact12939SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.78 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2966 -3.69 %
Rwork0.2291 653 -
all0.2316 678 -
obs--51.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31850.21121.0042.2184-0.32072.73870.13320.42190.1848-0.1874-0.1374-0.0206-0.08220.3620.0042-0.18720.06040.01780.00920.045-0.12450.0151-0.11860.8101
23.991.49752.61471.77560.38444.56140.19340.3055-0.2486-0.06950.16370.09930.07470.4864-0.3571-0.24070.05470.0062-0.088-0.0569-0.0093-15.703933.6869-27.865
33.503-0.21421.76142.70480.79253.41540.0561-0.18160.32470.1787-0.16060.28270.0311-0.44890.1044-0.1923-0.07280.0508-0.09440.0714-0.0704-15.1497-2.050125.7727
41.45510.43970.61212.113-0.71424.2650.06040.511-0.244-0.18380.0969-0.30190.12110.6531-0.1573-0.29250.0916-0.0020.0592-0.1382-0.040916.5444-31.972429.944
56.75181.72783.43733.91921.2034.39080.207-0.65060.10430.4672-0.3977-0.13380.0552-0.48110.1907-0.2171-0.0975-0.0772-0.1190.0968-0.201-0.004-33.410452.8945
62.75980.10492.29021.5662.38928.59560.3927-0.7487-0.12590.1888-0.37270.09460.3124-1.9332-0.02-0.344-0.2333-0.01160.28790.2115-0.1805-32.981631.727-4.4238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|6 - 241}
2X-RAY DIFFRACTION2{B|6 - 241}
3X-RAY DIFFRACTION3{C|6 - 240}
4X-RAY DIFFRACTION4{D|6 - 241}
5X-RAY DIFFRACTION5{E|6 - 240}
6X-RAY DIFFRACTION6{F|6 - 241}

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