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

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Basic information

Entry
Database: PDB / ID: 9ifg
TitlePANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z2204875953
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 / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / (3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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)219,24228
Polymers213,9924
Non-polymers5,25024
Water16,484915
1
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,61314
Polymers106,9962
Non-polymers2,61712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-64 kcal/mol
Surface area36570 Å2
MethodPISA
2
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,62914
Polymers106,9962
Non-polymers2,63312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-60 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.888, 63.545, 169.583
Angle α, β, γ (deg.)90.000, 97.707, 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 , 6 types, 939 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.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-Q7L / (3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole


Mass: 188.183 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
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: 1.86→92.29 Å / Num. obs: 179220 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.9
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7711 / CC1/2: 0.25 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→81.84 Å / SU ML: 0.3096 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 8923 4.99 %
Rwork0.1923 169871 -
obs0.1942 178794 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.72 Å2
Refinement stepCycle: LAST / Resolution: 1.86→81.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14818 0 334 915 16067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006615766
X-RAY DIFFRACTIONf_angle_d0.847721434
X-RAY DIFFRACTIONf_chiral_restr0.05512389
X-RAY DIFFRACTIONf_plane_restr0.00682810
X-RAY DIFFRACTIONf_dihedral_angle_d15.44195932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.41652130.37554482X-RAY DIFFRACTION78.78
1.88-1.910.41953060.37645662X-RAY DIFFRACTION99.47
1.91-1.930.34213210.32895662X-RAY DIFFRACTION99.62
1.93-1.950.35452680.3245576X-RAY DIFFRACTION99.39
1.95-1.980.34563160.3035667X-RAY DIFFRACTION99.35
1.98-2.010.31172880.28375609X-RAY DIFFRACTION98.76
2.01-2.030.28193080.25795685X-RAY DIFFRACTION99.68
2.03-2.060.32272860.2615637X-RAY DIFFRACTION99.56
2.06-2.10.28953080.25245612X-RAY DIFFRACTION99.1
2.1-2.130.28013010.23735672X-RAY DIFFRACTION99.9
2.13-2.170.33190.23465670X-RAY DIFFRACTION99.97
2.17-2.210.28233220.22975706X-RAY DIFFRACTION99.97
2.21-2.250.29332810.22325651X-RAY DIFFRACTION99.9
2.25-2.30.29192880.22625728X-RAY DIFFRACTION99.92
2.3-2.350.26753060.22245689X-RAY DIFFRACTION99.98
2.35-2.40.26423030.21755695X-RAY DIFFRACTION100
2.4-2.460.27232820.20915679X-RAY DIFFRACTION99.98
2.46-2.530.25672910.20315695X-RAY DIFFRACTION100
2.53-2.60.27313080.20865702X-RAY DIFFRACTION100
2.6-2.690.26232830.20345732X-RAY DIFFRACTION99.97
2.69-2.780.27093220.20195697X-RAY DIFFRACTION100
2.78-2.890.26313020.20765708X-RAY DIFFRACTION99.98
2.89-3.020.27083040.21115747X-RAY DIFFRACTION100
3.02-3.180.25353150.20095725X-RAY DIFFRACTION100
3.18-3.380.20462960.18485685X-RAY DIFFRACTION99.98
3.38-3.640.21362830.17695790X-RAY DIFFRACTION100
3.64-4.010.17743300.15925735X-RAY DIFFRACTION99.98
4.01-4.590.1582940.13465773X-RAY DIFFRACTION100
4.59-5.780.16522980.14285844X-RAY DIFFRACTION100
5.78-81.840.16462810.15125956X-RAY DIFFRACTION99.52

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