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- PDB-6zp3: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 6zp3
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 2-Methylindole-3-acetic 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / FLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-(2-methyl-1~{H}-indol-3-yl)ethanoic acid / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 8, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.3Nov 20, 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)66,84510
Polymers65,1081
Non-polymers1,7379
Water6,233346
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,69020
Polymers130,2162
Non-polymers3,47418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14320 Å2
ΔGint-70 kcal/mol
Surface area45670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.849, 102.186, 58.572
Angle α, β, γ (deg.)90.000, 112.940, 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 , 10 types, 355 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-QN5 / 2-(2-methyl-1~{H}-indol-3-yl)ethanoic acid / 2-Methylindole-3-acetic acid


Mass: 189.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 7.2
Details: PEG 3350 20%, potassium iodide 0.2, BisTris 0.1M, DTT 5mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.684 Å / Num. obs: 70295 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4221 / CC1/2: 0.769 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6O

2v6o


Resolution: 1.8→39.684 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 3637 5.17 %
Rwork0.172 66654 -
obs0.1737 70291 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.09 Å2 / Biso mean: 34.4444 Å2 / Biso min: 11.8 Å2
Refinement stepCycle: final / Resolution: 1.8→39.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 210 346 5059
Biso mean--43.21 34.12 -
Num. residues----588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82370.28191460.22852598100
1.8237-1.84870.25221320.21652582100
1.8487-1.87510.25991310.19962566100
1.8751-1.90310.24251360.1892603100
1.9031-1.93280.24551440.18222574100
1.9328-1.96450.17941500.17042582100
1.9645-1.99840.22751310.16612557100
1.9984-2.03470.20231310.16212617100
2.0347-2.07380.19821560.16672561100
2.0738-2.11620.22581270.1615254999
2.1162-2.16220.18611180.1627261599
2.1622-2.21250.20081120.1612254598
2.2125-2.26780.18961550.1566250298
2.2678-2.32910.18671430.1613250897
2.3291-2.39760.21561230.1642251197
2.3976-2.4750.20351280.1709245395
2.475-2.56340.22441380.1784240892
2.5634-2.66610.21281620.1743252498
2.6661-2.78740.1981480.17762587100
2.7874-2.93430.24181540.17782577100
2.9343-3.11810.23381500.18222586100
3.1181-3.35870.19921270.17982605100
3.3587-3.69650.19151510.16132614100
3.6965-4.23080.1811270.15272611100
4.2308-5.32840.17171570.15882596100
5.3284-39.6840.22241600.1992262399
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)
10.8243-0.050.0950.75490.19030.4569-0.10240.13320.1572-0.37570.1289-0.2762-0.0910.07120.00220.2527-0.08220.05960.2118-0.02130.264234.513922.62420.7888
20.1432-0.00760.2080.14240.20610.3003-0.0137-0.0962-0.1584-0.07830.0307-0.0475-0.0589-0.0182-0.00040.1845-0.0036-0.00620.160.00330.189810.3612-11.04654.7579
30.01410.0448-0.18550.5553-0.27410.4747-0.0354-0.1779-0.04690.06390.0316-0.0685-0.02540.0439-0.00040.15050.0171-0.01190.18210.0020.138315.4932-2.336224.3638
40.460.04370.16440.1490.01750.3865-0.0523-0.08370.0572-0.00790.02790.0204-0.0904-0.07200.15910.019-0.00320.1255-0.02250.14280.428414.13769.7611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 158 )A6 - 158
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 218 )A159 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 415 )A219 - 415
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 593 )A416 - 593

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