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- PDB-4yqu: Glutathione S-transferase Omega 1 bound to covalent inhibitor C1-31 -

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Basic information

Entry
Database: PDB / ID: 4yqu
TitleGlutathione S-transferase Omega 1 bound to covalent inhibitor C1-31
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) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / 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) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / 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 / 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 / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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-4GB / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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: Data collection / Database references ...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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9086
Polymers55,7442
Non-polymers1,1644
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-8 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.645, 72.588, 65.310
Angle α, β, γ (deg.)90.000, 112.690, 90.000
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) / Strain (production host): Rosetta2
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-4GB / N-{5-(azepan-1-ylsulfonyl)-2-[(ethylsulfanyl)methoxy]phenyl}acetamide


Mass: 386.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N2O4S2
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The GSTO1-C1-31 complex was concentrated to 23.9 mg/mL prior to crystallization. Crystals formed from drops containing equal volumes of complex and well solution (22.5% PEG 3350, 90 mM MES ...Details: The GSTO1-C1-31 complex was concentrated to 23.9 mg/mL prior to crystallization. Crystals formed from drops containing equal volumes of complex and well solution (22.5% PEG 3350, 90 mM MES pH 6.5 and 4% tert-butanol).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / 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: 1.94→50 Å / Num. obs: 36745 / % possible obs: 93.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.08 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.278 / Net I/av σ(I): 14.527 / Net I/σ(I): 16 / Num. measured all: 114158
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-1.972.90.34319261.50397.5
1.97-2.013.20.25818991.23697.8
2.01-2.053.10.22418821.25298
2.05-2.093.20.18419411.1898.3
2.09-2.143.20.16319151.16598.1
2.14-2.183.20.14719371.26598.2
2.18-2.242.80.13812941.31866.4
2.24-2.32.30.13211731.71260.2
2.3-2.373.20.10619421.28199
2.37-2.443.20.10219531.31799.3
2.44-2.533.20.09319461.29699
2.53-2.633.20.08419371.28799
2.63-2.753.30.07919401.23399.2
2.75-2.93.30.07119521.18499.2
2.9-3.083.30.06619661.19799.3
3.08-3.323.30.06919431.34199.2
3.32-3.652.70.07118121.59391
3.65-4.182.50.06415111.38476.4
4.18-5.263.30.06119691.08598.6
5.26-503.20.06319071.19993.6

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.2refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 1.94→45.22 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9213 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1857 5.06 %RANDOM
Rwork0.203 ---
obs0.2049 36729 91.58 %-
Displacement parametersBiso max: 133.78 Å2 / Biso mean: 34.41 Å2 / Biso min: 8.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.3361 Å20 Å20.0017 Å2
2---2.2423 Å20 Å2
3---2.5784 Å2
Refinement stepCycle: final / Resolution: 1.94→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 68 285 4096
Biso mean--44.6 37.24 -
Num. residues----470
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1846SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes577HARMONIC5
X-RAY DIFFRACTIONt_it3955HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
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_contact4771SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3955HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5355HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion2.95
LS refinement shellResolution: 1.94→2 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2674 102 4.15 %
Rwork0.2423 2353 -
all0.2433 2455 -
obs--91.58 %
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)
11.48450.2398-0.33951.21250.07071.46810.05790.0874-0.1941-0.0436-0.1033-0.0291-0.1244-0.150.0455-0.10490.0368-0.0177-0.0444-0.0092-0.042216.78650.13092.1198
21.1392-0.56760.07091.5292-0.2091.6547-0.084-0.0246-0.01710.1470.0887-0.0206-0.04830.0925-0.0047-0.0899-0.0283-0.0121-0.03790.0046-0.078435.0033-1.051526.1463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|4 - 241}A4 - 241
2X-RAY DIFFRACTION2{B|5 - 241}B5 - 241

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