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- PDB-7npx: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 7npx
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 3-(3-Methoxyquinoxalin-2-yl)propanoic acid at 24 hours of soaking
ComponentsThioredoxin glutathione reductase
KeywordsPROTEIN BINDING / fragment binding / redox enzyme / inhibitor / flavoreductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
3-(3-methoxyquinoxalin-2-yl)propanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFata, F. / Silvestri, I. / Williams, D.L. / Angelucci, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33AI127635 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments.
Authors: Fata, F. / Silvestri, I. / Ardini, M. / Ippoliti, R. / Di Leandro, L. / Demitri, N. / Polentarutti, M. / Di Matteo, A. / Lyu, H. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, F.
History
DepositionFeb 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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: Thioredoxin glutathione reductase
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,97418
Polymers130,2162
Non-polymers2,75816
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-100 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.269, 87.933, 185.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin glutathione reductase


Mass: 65108.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The structure is relative to the Sec597Cys mutant / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TGR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q962Y6, EC: 1.6.4.5

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Non-polymers , 6 types, 147 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EY7 / 3-(3-methoxyquinoxalin-2-yl)propanoic acid


Mass: 232.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Bis-tris 0.1M PH = 7.0; Peg 3350 20%; KI 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→39.76 Å / Num. obs: 38527 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 2.7→2.82 Å / Num. unique obs: 4577 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6O

2v6o


Resolution: 2.7→39.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 30.208 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 2005 5.2 %RANDOM
Rwork0.211 ---
obs0.2136 36460 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.41 Å2 / Biso mean: 63.477 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--2.47 Å2-0 Å2
3----1.89 Å2
Refinement stepCycle: final / Resolution: 2.7→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 176 131 9329
Biso mean--57.6 41.73 -
Num. residues----1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139455
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179001
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.64612834
X-RAY DIFFRACTIONr_angle_other_deg1.2611.58520822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48851201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05323.544412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.739151625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5681536
X-RAY DIFFRACTIONr_chiral_restr0.0720.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021998
LS refinement shellResolution: 2.702→2.772 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 118 -
Rwork0.322 2608 -
all-2726 -
obs--97.32 %
Refinement TLS params.Method: refined / Origin x: -16.808 Å / Origin y: -14.9778 Å / Origin z: 29.8622 Å
111213212223313233
T0.0342 Å20.0222 Å2-0.0126 Å2-0.1382 Å2-0.0056 Å2--0.1455 Å2
L1.2613 °20.0959 °2-0.0907 °2-1.1693 °2-0.0997 °2--2.4806 °2
S-0.0021 Å °-0.0915 Å °0.0313 Å °0.0732 Å °0.0577 Å °0.0479 Å °-0.2315 Å °-0.3903 Å °-0.0556 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 593
2X-RAY DIFFRACTION1B6 - 594

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