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- PDB-9nad: Human GSTO1-1 complexed with C5-1 -

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Basic information

Entry
Database: PDB / ID: 9nad
TitleHuman GSTO1-1 complexed with C5-1
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / 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 / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / cellular response to arsenic-containing substance / Methylation / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / cellular response to arsenic-containing substance / Methylation / Glutathione conjugation / negative regulation of release of sequestered calcium ion into cytosol / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of release of sequestered calcium ion into cytosol / glutathione metabolic process / oxidoreductase activity / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / 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, omega-class / Glutathione S-transferase Omega/Tau-like / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Glutathione transferase family / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsOakley, A.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1156455 Australia
CitationJournal: To Be Published
Title: Human GSTO1-1 complexed with C5-1
Authors: Oakley, A.J.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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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)27,8163
Polymers27,4691
Non-polymers3482
Water3,729207
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6336
Polymers54,9372
Non-polymers6964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2330 Å2
ΔGint-46 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.001, 57.001, 139.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-A1BWU / 1-(4-benzylpiperidin-1-yl)-2-chloroethan-1-one


Mass: 251.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H18ClNO / Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION / References: glutathione transferase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Reservoir volume consisted of 1 ml of 1.9 M (NH4)2SO4, 200 mM potassium sodium tartrate, 3.4 mM ZnSO4, 16.7 mM citric acid, 1.86 mM tri-sodium citrate. Protein (volume 1 uL) at 8.9 mg/ml in ...Details: Reservoir volume consisted of 1 ml of 1.9 M (NH4)2SO4, 200 mM potassium sodium tartrate, 3.4 mM ZnSO4, 16.7 mM citric acid, 1.86 mM tri-sodium citrate. Protein (volume 1 uL) at 8.9 mg/ml in 20 mM Tris pH 8.0, 60 mM NaCl and 1 mM DTT was mixed with 1uL of reservoir solution on a siliconised cover slip.

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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: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→46.568 Å / Num. obs: 18337 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.036 / Rrim(I) all: 0.083 / Net I/σ(I): 10.8
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1254 / CC1/2: 0.915 / Rpim(I) all: 0.346 / Rrim(I) all: 0.578 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSNov 1, 2016data reduction
Aimlessdata scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→46.568 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.47 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.178
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2485 936 5.11 %
Rwork0.184 17380 -
all0.187 --
obs-18316 98.526 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.526 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.205 Å20 Å2
2--0.41 Å20 Å2
3----1.331 Å2
Refinement stepCycle: LAST / Resolution: 1.994→46.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 21 207 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161893
X-RAY DIFFRACTIONr_angle_refined_deg1.691.8692684
X-RAY DIFFRACTIONr_angle_other_deg0.611.7784395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.80459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78210356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1751086
X-RAY DIFFRACTIONr_chiral_restr0.0920.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.2430.2572
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.21985
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21000
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2191
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.234
X-RAY DIFFRACTIONr_nbd_other0.2220.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.230
X-RAY DIFFRACTIONr_mcbond_it1.8322.3951
X-RAY DIFFRACTIONr_mcbond_other1.8322.3951
X-RAY DIFFRACTIONr_mcangle_it2.7364.121187
X-RAY DIFFRACTIONr_mcangle_other2.7354.1221188
X-RAY DIFFRACTIONr_scbond_it2.7372.6771035
X-RAY DIFFRACTIONr_scbond_other2.712.6731032
X-RAY DIFFRACTIONr_scangle_it4.2844.7811497
X-RAY DIFFRACTIONr_scangle_other4.2874.7711492
X-RAY DIFFRACTIONr_lrange_it8.22131.1462589
X-RAY DIFFRACTIONr_lrange_other8.17128.8162521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.994-2.0460.287570.25111960.25313470.9390.95493.02150.22
2.046-2.1020.316730.26912090.27213150.9360.94197.49050.237
2.102-2.1630.244510.19512020.19812660.9620.97298.97310.163
2.163-2.2290.256580.19811520.20112260.9540.97198.69490.17
2.229-2.3020.295560.23211320.23512200.9370.95797.37710.201
2.302-2.3830.226580.18910980.19111670.9650.97799.05740.162
2.383-2.4720.249700.19610770.19911570.9620.97599.13570.169
2.472-2.5730.252520.1879980.1910560.9570.97999.43180.163
2.573-2.6870.245670.1859790.18910560.9650.97899.0530.164
2.687-2.8180.231710.1799220.18310000.9680.9899.30.163
2.818-2.970.204360.1879070.1889470.9740.97799.57760.176
2.97-3.1490.265530.1938650.1979220.9580.97599.56620.189
3.149-3.3650.278420.1878130.1918580.9580.97799.65030.189
3.365-3.6330.192260.1597580.167880.9780.98599.49240.165
3.633-3.9780.236480.1546920.1597540.9610.98698.14320.165
3.978-4.4430.217420.1556410.1586840.9650.98499.85380.173
4.443-5.1230.246290.1595790.1636090.9540.98599.83580.188
5.123-6.2550.288200.195020.1935230.9690.97899.80880.213
6.255-8.7670.34680.1754050.1784130.8840.981000.208
8.767-46.5680.246190.1842530.1882750.960.97798.90910.25
Refinement TLS params.Method: refined / Origin x: 20.486 Å / Origin y: 14.3147 Å / Origin z: 43.1508 Å
111213212223313233
T0.0722 Å2-0.0162 Å20.0031 Å2-0.0255 Å2-0.0072 Å2--0.0311 Å2
L1.4073 °2-0.3794 °2-0.327 °2-1.3452 °20.0564 °2--3.2856 °2
S0.0166 Å °-0.0271 Å °0.0326 Å °0.0646 Å °-0.0359 Å °0.1821 Å °-0.1209 Å °-0.2201 Å °0.0193 Å °
Refinement TLS groupSelection: ALL

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