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- PDB-5v3q: Human GSTO1-1 complexed with ML175 -

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Basic information

Entry
Database: PDB / ID: 5v3q
TitleHuman GSTO1-1 complexed with ML175
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / glutathione transferase / inhibitor / ML175 / 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) 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, 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 / 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 / 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
Chem-MLX / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOakley, A.J.
CitationJournal: Sci Rep / Year: 2017
Title: GSTO1-1 plays a pro-inflammatory role in models of inflammation, colitis and obesity.
Authors: Menon, D. / Innes, A. / Oakley, A.J. / Dahlstrom, J.E. / Jensen, L.M. / Brustle, A. / Tummala, P. / Rooke, M. / Casarotto, M.G. / Baell, J.B. / Nguyen, N. / Xie, Y. / Cuellar, M. / Strasser, ...Authors: Menon, D. / Innes, A. / Oakley, A.J. / Dahlstrom, J.E. / Jensen, L.M. / Brustle, A. / Tummala, P. / Rooke, M. / Casarotto, M.G. / Baell, J.B. / Nguyen, N. / Xie, Y. / Cuellar, M. / Strasser, J. / Dahlin, J.L. / Walters, M.A. / Burgio, G. / O'Neill, L.A.J. / Board, P.G.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Apr 13, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1604
Polymers27,6001
Non-polymers5603
Water2,648147
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3198
Polymers55,2002
Non-polymers1,1206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2740 Å2
ΔGint-77 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.103, 57.103, 139.613
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1011-

HOH

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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: 27599.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pGEX2T / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-MLX / N-{3-[(2-chloro-acetyl)-(4-nitro-phenyl)-amino]-propyl}-2,2,2-trifluoro-acetamide


Mass: 367.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13ClF3N3O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.0-1.2 M ammonium sulfate, 50 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 12, 2016
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 12979 / % possible obs: 98.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.027 / Χ2: 1.029 / Net I/σ(I): 57.84
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.51 / Num. unique obs: 1229 / CC1/2: 0.991 / Χ2: 1.016 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EEM

1eem


Resolution: 2.25→49.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.226 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23266 686 5.3 %RANDOM
Rwork0.16988 ---
obs0.17314 12277 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.25→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 33 147 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022014
X-RAY DIFFRACTIONr_bond_other_d0.0020.021876
X-RAY DIFFRACTIONr_angle_refined_deg2.2911.9932723
X-RAY DIFFRACTIONr_angle_other_deg1.192.9974386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35424.65988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99415.041367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.111159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212182
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02399
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4452.28957
X-RAY DIFFRACTIONr_mcbond_other1.4382.277956
X-RAY DIFFRACTIONr_mcangle_it2.2773.4071195
X-RAY DIFFRACTIONr_mcangle_other2.2773.411196
X-RAY DIFFRACTIONr_scbond_it1.9842.5431057
X-RAY DIFFRACTIONr_scbond_other1.962.5371049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0613.7091515
X-RAY DIFFRACTIONr_long_range_B_refined5.65928.432434
X-RAY DIFFRACTIONr_long_range_B_other5.6127.962397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.249→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 61 -
Rwork0.193 852 -
obs--97.23 %
Refinement TLS params.Method: refined / Origin x: 22.7571 Å / Origin y: -10.5563 Å / Origin z: 19.8695 Å
111213212223313233
T0.0398 Å2-0.0132 Å2-0.0012 Å2-0.066 Å2-0.007 Å2--0.045 Å2
L1.0267 °20.0312 °20.0166 °2-1.8074 °20.0661 °2--3.9503 °2
S-0.0022 Å °-0.0802 Å °0.206 Å °0.0147 Å °-0.0005 Å °0.0716 Å °-0.3856 Å °0.0274 Å °0.0027 Å °

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