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- PDB-7b02: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 7b02
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid
ComponentsThioredoxin glutathione reductase
KeywordsPROTEIN BINDING / fragment binding / redox enzyme / inhibitor / flavoreductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / 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
FLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / Chem-SJN / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionNov 18, 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,65111
Polymers65,0611
Non-polymers1,59010
Water12,052669
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,30222
Polymers130,1222
Non-polymers3,18020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15020 Å2
ΔGint-98 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.834, 102.439, 58.924
Angle α, β, γ (deg.)90.000, 112.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1363-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin glutathione reductase


Mass: 65061.145 Da / Num. of mol.: 1
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 , 8 types, 679 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SJN / 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid / 7-methyl-4-oxidanylidene-3~{H}-1,8-naphthyridine-3-carboxylic acid / 1,4-Dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid / 1,4-Dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid / 7-methyl-4-oxo-1H-1,8-naphthyridine-3-carboxylic acid / 3-Carboxy-4-hydroxy-7-methyl-1,8-naphthyridine


Mass: 204.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0,2M potassium iodide, 0,1M Bis-TRIS, 5mM DTT

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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: 1.45→39.93 Å / Num. obs: 135935 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.2
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5849 / CC1/2: 0.63 / % possible all: 86.1

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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: 1.45→39.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.974 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1734 6752 5 %RANDOM
Rwork0.1388 ---
obs0.1405 129182 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.34 Å2 / Biso mean: 19.252 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.06 Å2
2---0.27 Å20 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.45→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 103 671 5304
Biso mean--25.45 30.67 -
Num. residues----593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134797
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174569
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.6466513
X-RAY DIFFRACTIONr_angle_other_deg1.5811.58310577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9125614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8623.558208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4541518
X-RAY DIFFRACTIONr_chiral_restr0.1180.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021014
X-RAY DIFFRACTIONr_rigid_bond_restr4.16939364
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 449 -
Rwork0.21 8543 -
all-8992 -
obs--87.98 %

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