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- PDB-4yqv: Glutathione S-transferase Omega 1 bound to covalent inhibitor C4-10 -

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Basic information

Entry
Database: PDB / ID: 4yqv
TitleGlutathione S-transferase Omega 1 bound to covalent inhibitor C4-10
ComponentsGlutathione S-transferase omega-1
KeywordsTransferase/Transferase Inhibitor / Covalent Inhibitor / Thioltransferase / chloroacetamide / 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-4GG / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsStuckey, J.A.
CitationJournal: Nat Commun / Year: 2016
Title: Mechanistic evaluation and transcriptional signature of a glutathione S-transferase omega 1 inhibitor.
Authors: Ramkumar, K. / Samanta, S. / Kyani, A. / Yang, S. / Tamura, S. / Ziemke, E. / Stuckey, J.A. / Li, S. / Chinnaswamy, K. / Otake, H. / Debnath, B. / Yarovenko, V. / Sebolt-Leopold, J.S. / ...Authors: Ramkumar, K. / Samanta, S. / Kyani, A. / Yang, S. / Tamura, S. / Ziemke, E. / Stuckey, J.A. / Li, S. / Chinnaswamy, K. / Otake, H. / Debnath, B. / Yarovenko, V. / Sebolt-Leopold, J.S. / Ljungman, M. / Neamati, N.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4856
Polymers83,6163
Non-polymers8683
Water7,296405
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3234
Polymers55,7442
Non-polymers5792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1830 Å2
ΔGint-17 kcal/mol
Surface area21170 Å2
MethodPISA
2
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3234
Polymers55,7442
Non-polymers5792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.320, 71.373, 61.968
Angle α, β, γ (deg.)90.00, 105.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

21A-659-

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: 27872.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-4GG / 2-(ethylsulfanyl)-N-methyl-N-[(1-phenyl-1H-pyrazol-4-yl)methyl]acetamide


Mass: 289.396 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H19N3OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Complex was concentrated to 26.2 mg/mL. Crystals of the complex grew from sitting drops containing equal volumes of protein complex and well solution (22.5% PEG 3350, 90 mM MES pH 6.5 and 10 mM BaCl2).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 46437 / % possible obs: 98 % / Redundancy: 5 % / Biso Wilson estimate: 34.91 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.2
Reflection shellResolution: 2.06→2.14 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.316 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 2.06→44.96 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2345 5.05 %RANDOM
Rwork0.195 ---
obs0.196 46430 95.4 %-
Displacement parametersBiso mean: 40.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.8892 Å20 Å27.6456 Å2
2--2.3325 Å20 Å2
3----1.4433 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.06→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 51 405 6060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095812HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.927875HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2650SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes137HARMONIC2
X-RAY DIFFRACTIONt_gen_planes873HARMONIC5
X-RAY DIFFRACTIONt_it5812HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion2.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
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_contact7058SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 107 4.78 %
Rwork0.213 2131 -
all0.216 2238 -
obs--62.11 %
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)
11.4884-0.3698-0.27691.56090.28812.0926-0.01710.05890.07470.01390.0213-0.14710.21740.2242-0.0042-0.07170.0119-0.0306-0.10260.0117-0.08945.637-11.214424.766
22.0595-0.20070.17792.0531-0.22281.3351-0.07370.1047-0.2371-0.041-0.0290.17850.1875-0.13070.1028-0.0751-0.00330.0104-0.098-0.0641-0.101320.085222.5042-3.7386
30.987-0.43030.31161.37250.14222.0275-0.0390.14650.08210.0038-0.0621-0.13930.1040.16960.1011-0.09530.00650.0094-0.04860.071-0.057447.443523.5553-15.2433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|5 - 241}
2X-RAY DIFFRACTION2{B|5 - 241}
3X-RAY DIFFRACTION3{C|5 - 241}

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