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- PDB-9ife: PANDDA analysis - Crystal structure of Trypanosoma brucei trypano... -

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Basic information

Entry
Database: PDB / ID: 9ife
TitlePANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z943693514
ComponentsTrypanothione reductase
KeywordsOXIDOREDUCTASE / trypanothione reductase
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / kinetoplast / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / nuclear lumen / cell redox homeostasis / flavin adenine dinucleotide binding / nucleoplasm ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / kinetoplast / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / nuclear lumen / cell redox homeostasis / flavin adenine dinucleotide binding / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
Trypanothione reductase / : / 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
Similarity search - Domain/homology
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / ~{N}-(4-hydroxyphenyl)-2-methoxy-ethanamide / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsExertier, C. / Antonelli, L. / Ilari, A. / Fiorillo, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery22027European Union
CitationJournal: Front Chem Biol / Year: 2025
Title: Expanding the molecular landscape of fragments binding to trypanothione reductase, a legitimate target for drug design against human African trypanosomiasis
Authors: Exertier, C. / Antonelli, L. / Brufani, V. / Colotti, G. / Ilari, A. / Fiorillo, A.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypanothione reductase
B: Trypanothione reductase
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,25532
Polymers213,9924
Non-polymers5,26328
Water17,511972
1
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,54016
Polymers106,9962
Non-polymers2,54414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-66 kcal/mol
Surface area36470 Å2
MethodPISA
2
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,71516
Polymers106,9962
Non-polymers2,71914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-48 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.262, 63.529, 169.441
Angle α, β, γ (deg.)90.000, 97.834, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Trypanothione reductase / N(1) / N(8)-bis(glutathionyl)spermidine reductase


Mass: 53497.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The electronic density is not well enough defined to unambiguously reconstruct the N-terminal and the C-terminal extremities of the protein.
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.406.0520 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q389T8, trypanothione-disulfide reductase

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Non-polymers , 8 types, 1000 molecules

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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GT4 / ~{N}-(4-hydroxyphenyl)-2-methoxy-ethanamide


Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12-14% PEG3350, 22-24% MPD, 40 mM imidazole pH 8.0, 50 mM NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.68→49.96 Å / Num. obs: 243002 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 1 / Net I/σ(I): 10.4
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 12068 / CC1/2: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→49.96 Å / SU ML: 0.268 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 12087 5 %
Rwork0.1964 229851 -
obs0.198 241938 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.45 Å2
Refinement stepCycle: LAST / Resolution: 1.68→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14825 0 333 972 16130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006515744
X-RAY DIFFRACTIONf_angle_d0.866621392
X-RAY DIFFRACTIONf_chiral_restr0.05752391
X-RAY DIFFRACTIONf_plane_restr0.00672749
X-RAY DIFFRACTIONf_dihedral_angle_d16.1235885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.39383560.37157095X-RAY DIFFRACTION93.03
1.7-1.720.35683920.3567464X-RAY DIFFRACTION97.22
1.72-1.740.3653940.34327566X-RAY DIFFRACTION99.09
1.74-1.760.33823980.32217674X-RAY DIFFRACTION99.45
1.76-1.790.33854260.31917564X-RAY DIFFRACTION99.7
1.79-1.810.34563830.29827744X-RAY DIFFRACTION99.91
1.81-1.840.32344110.29037527X-RAY DIFFRACTION99.85
1.84-1.860.34134160.30597706X-RAY DIFFRACTION99.95
1.86-1.890.32243900.29417614X-RAY DIFFRACTION99.88
1.89-1.920.30524280.26517659X-RAY DIFFRACTION99.83
1.92-1.960.28013730.24577637X-RAY DIFFRACTION99.91
1.96-1.990.27324150.23727693X-RAY DIFFRACTION100
1.99-2.030.25494170.2197636X-RAY DIFFRACTION99.98
2.03-2.070.28014030.2177611X-RAY DIFFRACTION99.89
2.07-2.120.24624010.21087715X-RAY DIFFRACTION99.94
2.12-2.170.26154190.21167623X-RAY DIFFRACTION99.98
2.17-2.220.25594260.20487651X-RAY DIFFRACTION100
2.22-2.280.26173730.20577704X-RAY DIFFRACTION99.91
2.28-2.350.24544250.19987705X-RAY DIFFRACTION99.98
2.35-2.420.25763980.20327655X-RAY DIFFRACTION100
2.42-2.510.24473930.1977693X-RAY DIFFRACTION100
2.51-2.610.27943900.20777716X-RAY DIFFRACTION99.98
2.61-2.730.23554200.19887706X-RAY DIFFRACTION100
2.73-2.870.25254100.20247701X-RAY DIFFRACTION99.96
2.87-3.050.23654180.20147709X-RAY DIFFRACTION100
3.05-3.290.2233890.19417719X-RAY DIFFRACTION100
3.29-3.620.20594060.17717788X-RAY DIFFRACTION100
3.62-4.140.18214230.15977740X-RAY DIFFRACTION100
4.14-5.220.15614140.13887820X-RAY DIFFRACTION100
5.22-49.960.16973800.16318016X-RAY DIFFRACTION99.64

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