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- PDB-6pno: Human GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(N-isopropyls... -

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Basic information

Entry
Database: PDB / ID: 6pno
TitleHuman GSTO1-1 complexed with 2-chloro-N-(4-chloro-3-(N-isopropylsulfamoyl)phenyl)acetamide
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / glutathione 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-ORM / L(+)-TARTARIC ACID / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsOakley, A.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1124673 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1156455 Australia
CitationJournal: J.Med.Chem. / Year: 2020
Title: Development of Benzenesulfonamide Derivatives as Potent Glutathione Transferase Omega-1 Inhibitors.
Authors: Xie, Y. / Tummala, P. / Oakley, A.J. / Deora, G.S. / Nakano, Y. / Rooke, M. / Cuellar, M.E. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Casarotto, M.G. / Board, P.G. / Baell, J.B.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2326
Polymers27,4691
Non-polymers7635
Water4,522251
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,46412
Polymers54,9372
Non-polymers1,52710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3720 Å2
ΔGint-105 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.260, 57.260, 139.991
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-1125-

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: 27468.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-ORM / 2-chloro-N-{4-chloro-3-[(propan-2-yl)sulfamoyl]phenyl}acetamide


Mass: 325.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.7-2.2 M ammonium sulfate, 100 mM sodium citrate, 0.1 M sodium potassium tartrate, 0.75 mM zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 24901 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0021 / Rrim(I) all: 0.067 / Net I/σ(I): 25.5
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1469 / CC1/2: 0.956 / Rpim(I) all: 0.137 / Rrim(I) all: 0.427 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
MOSFLMdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EEM

1eem


Resolution: 1.82→40.5 Å / SU B: 5.844 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23839 1246 5 %RANDOM
Rwork0.19381 ---
obs0.19381 23575 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 43 251 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132129
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171983
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.6632893
X-RAY DIFFRACTIONr_angle_other_deg1.4851.5884635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.9375.336268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29622.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9837915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3071510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
X-RAY DIFFRACTIONr_mcbond_it0.9290.821002
X-RAY DIFFRACTIONr_mcbond_other0.9280.8191001
X-RAY DIFFRACTIONr_mcangle_it1.6381.2251256
X-RAY DIFFRACTIONr_mcangle_other1.6381.2271257
X-RAY DIFFRACTIONr_scbond_it1.3841.0381127
X-RAY DIFFRACTIONr_scbond_other1.17911112
X-RAY DIFFRACTIONr_scangle_it2.0541.4941630
X-RAY DIFFRACTIONr_scangle_other1.9731.4441611
X-RAY DIFFRACTIONr_lrange_it8.26912.7692640
X-RAY DIFFRACTIONr_lrange_other8.07411.3872555
LS refinement shellResolution: 1.82→1.862 Å
RfactorNum. reflection% reflection
Rfree0.276 83 -
Rwork0.218 --
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 22.6665 Å / Origin y: -10.3404 Å / Origin z: 19.6701 Å
111213212223313233
T0.1198 Å2-0.0216 Å2-0.0018 Å2-0.1481 Å2-0.0041 Å2--0.162 Å2
L0.7874 °20.1616 °2-0.1151 °2-1.2428 °20.2384 °2--1.7817 °2
S-0.0052 Å °-0.0421 Å °0.1085 Å °-0.0277 Å °-0.038 Å °0.04 Å °-0.245 Å °0.0221 Å °0.0433 Å °

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