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

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Basic information

Entry
Database: PDB / ID: 9ifn
TitlePANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z436190540
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 / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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)218,72326
Polymers213,9924
Non-polymers4,73122
Water16,466914
1
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,47014
Polymers106,9962
Non-polymers2,47412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-80 kcal/mol
Surface area37160 Å2
MethodPISA
2
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,25212
Polymers106,9962
Non-polymers2,25710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-63 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.752, 64.007, 170.892
Angle α, β, γ (deg.)90.000, 97.505, 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 , 7 types, 936 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-A1I3V / 1-[(2~{S},3~{a}~{R},6~{a}~{R})-2-methyl-3,3~{a},4,5,6,6~{a}-hexahydro-2~{H}-pyrrolo[3,4-b]pyrrol-1-yl]-2,2-dimethyl-propan-1-one


Mass: 210.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O / 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: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 914 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
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: I04-1 / Wavelength: 0.921237 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921237 Å / Relative weight: 1
ReflectionResolution: 2.11→101.99 Å / Num. obs: 126299 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 35.37 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.5
Reflection shellResolution: 2.11→2.14 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5689 / CC1/2: 0.26 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→69.77 Å / SU ML: 0.3043 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.6212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 6289 4.99 %
Rwork0.1883 119791 -
obs0.1909 126080 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 2.11→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14818 0 294 914 16026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006715463
X-RAY DIFFRACTIONf_angle_d0.861820999
X-RAY DIFFRACTIONf_chiral_restr0.05492369
X-RAY DIFFRACTIONf_plane_restr0.00662675
X-RAY DIFFRACTIONf_dihedral_angle_d15.0385741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.130.3041800.2733446X-RAY DIFFRACTION84.88
2.13-2.160.32312240.28343903X-RAY DIFFRACTION98.29
2.16-2.180.35332120.29073916X-RAY DIFFRACTION98.52
2.18-2.210.33092070.27463975X-RAY DIFFRACTION98.82
2.21-2.240.35042250.27793957X-RAY DIFFRACTION98.42
2.24-2.270.33011970.27783973X-RAY DIFFRACTION99.26
2.27-2.30.31361870.2653983X-RAY DIFFRACTION98.84
2.3-2.340.35332320.26083960X-RAY DIFFRACTION98.54
2.34-2.370.30492100.2514009X-RAY DIFFRACTION99.25
2.37-2.410.27252050.23983913X-RAY DIFFRACTION98.99
2.41-2.450.31612130.24114000X-RAY DIFFRACTION98.78
2.45-2.50.28082020.23683992X-RAY DIFFRACTION99.22
2.5-2.550.28241940.22693979X-RAY DIFFRACTION99.17
2.55-2.60.31982130.22213998X-RAY DIFFRACTION99.15
2.6-2.660.29142040.22044008X-RAY DIFFRACTION99.27
2.66-2.720.29912050.21463990X-RAY DIFFRACTION99.2
2.72-2.790.29792350.20784011X-RAY DIFFRACTION99.3
2.79-2.860.25591950.2063999X-RAY DIFFRACTION99.36
2.86-2.950.27712300.22094021X-RAY DIFFRACTION99.46
2.95-3.040.31132040.21534020X-RAY DIFFRACTION99.53
3.04-3.150.27732340.20723980X-RAY DIFFRACTION99.53
3.15-3.270.26131950.20144040X-RAY DIFFRACTION99.6
3.27-3.420.23912180.18264048X-RAY DIFFRACTION99.53
3.42-3.60.22241990.184030X-RAY DIFFRACTION99.79
3.6-3.830.22832120.16864050X-RAY DIFFRACTION99.67
3.83-4.130.18672310.14434052X-RAY DIFFRACTION99.74
4.13-4.540.15062010.12794078X-RAY DIFFRACTION99.81
4.54-5.20.16982260.13354071X-RAY DIFFRACTION99.81
5.2-6.550.18881860.16224148X-RAY DIFFRACTION99.95
6.55-69.770.17252130.1384241X-RAY DIFFRACTION99.55

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