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- PDB-6zst: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 6zst
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 3-(3-methoxyquinoxalin-2-yl)propanoic acid
ComponentsThioredoxin glutathione reductase
KeywordsPROTEIN BINDING / fragment binding / redox enzyme / inhibitor
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / electron transfer activity
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / 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. / FAD/NAD-linked reductase, dimerisation domain superfamily ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / 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. / FAD/NAD-linked reductase, dimerisation domain superfamily / 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 / TRIETHYLENE GLYCOL / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionJul 16, 2020Deposition 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7228
Polymers65,1081
Non-polymers1,6147
Water8,413467
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,44316
Polymers130,2162
Non-polymers3,22714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area11380 Å2
ΔGint-64 kcal/mol
Surface area49010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.741, 102.677, 58.746
Angle α, β, γ (deg.)90.000, 113.020, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin glutathione reductase


Mass: 65108.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_048430 / Production host: Escherichia coli (E. coli)
References: UniProt: G4V8J4, thioredoxin-disulfide reductase (NADPH)

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Non-polymers , 6 types, 474 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EY7 / 3-(3-methoxyquinoxalin-2-yl)propanoic acid


Mass: 232.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350 20%, potassium iodide 0.2M, Bis-Tris 0.1M, DTT 5mM

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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: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→39.93 Å / Num. obs: 83411 / % possible obs: 97.7 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4363 / CC1/2: 0.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6O

2v6o


Resolution: 1.7→39.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.841 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 4188 5 %RANDOM
Rwork0.1737 ---
obs0.1751 79198 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.25 Å2 / Biso mean: 21.081 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.35 Å2
2---0.23 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.7→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 108 473 5090
Biso mean--32.63 31.47 -
Num. residues----589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174407
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6466372
X-RAY DIFFRACTIONr_angle_other_deg1.481.5810253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9823.614202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1831517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 307 -
Rwork0.222 5796 -
all-6103 -
obs--96.43 %

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