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- PDB-4yqm: Glutathione S-transferase Omega 1 bound to covalent inhibitor C1-27 -

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Basic information

Entry
Database: PDB / ID: 4yqm
TitleGlutathione S-transferase Omega 1 bound to covalent inhibitor C1-27
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) 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / 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 / 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 / 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 / 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-4G9 / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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
Revision 1.3Oct 16, 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
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1369
Polymers83,6163
Non-polymers1,5196
Water2,180121
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7576
Polymers55,7442
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2900 Å2
ΔGint-8 kcal/mol
Surface area20610 Å2
MethodPISA
2
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7576
Polymers55,7442
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-7 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.838, 71.247, 61.852
Angle α, β, γ (deg.)90.00, 104.08, 90.00
Int Tables number5
Space group name H-MC121

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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-4G9 / 2-chloro-N-[4-chloro-3-(dimethylsulfamoyl)phenyl]acetamide


Mass: 311.185 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12Cl2N2O3S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 3350 and 100 mM MES pH 6.5 with a drop configuration of 2 uL of complex, 1.8 uL well and 0.2 uL 40% tert-butanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 30716 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 54.36 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.245 / % possible all: 100

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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: 2.38→40.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.407 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1547 5.04 %RANDOM
Rwork0.205 ---
obs0.207 30710 98.7 %-
Displacement parametersBiso mean: 56.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.4752 Å20 Å23.8343 Å2
2---0.3418 Å20 Å2
3---3.817 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.38→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 85 121 5790
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095866HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2674SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes865HARMONIC5
X-RAY DIFFRACTIONt_it5866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion2.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion734SEMIHARMONIC5
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_contact6738SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.248 159 5.66 %
Rwork0.23 2648 -
all0.231 2807 -
obs--92.01 %
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)
12.6605-1.0119-0.4274.13421.41812.13890.3940.2770.1438-0.3168-0.2036-0.48890.10650.1253-0.1904-0.1220.0613-0.0045-0.19180.0483-0.18076.2681-11.35725.0458
23.628-0.0663-0.01852.9835-0.24651.7381-0.28490.18-0.32150.09020.1010.2520.276-0.22060.1839-0.124-0.06860.0921-0.165-0.0565-0.213619.172522.562-3.905
30.8946-0.39010.38151.5478-0.48253.34030.00860.17530.1578-0.0969-0.1442-0.31570.47850.26890.1356-0.09420.0430.0369-0.12420.0879-0.110446.204123.2008-15.6867
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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