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

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Basic information

Entry
Database: PDB / ID: 9ifi
TitlePANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z32399802
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: 1.67 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)219,00027
Polymers213,9924
Non-polymers5,00823
Water16,880937
1
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,40713
Polymers106,9962
Non-polymers2,41111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-66 kcal/mol
Surface area37230 Å2
MethodPISA
2
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,59314
Polymers106,9962
Non-polymers2,59712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-61 kcal/mol
Surface area37380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.224, 63.976, 171.119
Angle α, β, γ (deg.)90.000, 97.745, 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, 960 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-A1I3U / 1-ethanoylpiperidine-4-carboxamide


Mass: 170.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
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 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921237 Å / Relative weight: 1
ReflectionResolution: 1.67→170.44 Å / Num. obs: 253692 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.97 Å2 / CC1/2: 1 / Net I/σ(I): 10.4
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 12366 / CC1/2: 0.34 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→92.63 Å / SU ML: 0.2787 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 12555 4.98 %
Rwork0.2009 239419 -
obs0.2023 251974 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.38 Å2
Refinement stepCycle: LAST / Resolution: 1.67→92.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14825 0 314 937 16076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006715470
X-RAY DIFFRACTIONf_angle_d0.835821003
X-RAY DIFFRACTIONf_chiral_restr0.05772367
X-RAY DIFFRACTIONf_plane_restr0.00682678
X-RAY DIFFRACTIONf_dihedral_angle_d15.03375747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.38593380.36857062X-RAY DIFFRACTION87.73
1.69-1.710.36683930.35157488X-RAY DIFFRACTION94.11
1.71-1.730.33674190.34137843X-RAY DIFFRACTION97.33
1.73-1.750.34663900.32987903X-RAY DIFFRACTION99.34
1.75-1.780.34394280.33477993X-RAY DIFFRACTION99.56
1.78-1.80.40014290.37057977X-RAY DIFFRACTION99.7
1.8-1.830.38364000.34288035X-RAY DIFFRACTION99.94
1.83-1.850.33514320.31897909X-RAY DIFFRACTION99.88
1.85-1.880.32784330.30828062X-RAY DIFFRACTION99.92
1.88-1.910.30474110.26817916X-RAY DIFFRACTION99.9
1.91-1.950.26944220.23598056X-RAY DIFFRACTION99.99
1.95-1.980.26284330.22947949X-RAY DIFFRACTION99.96
1.98-2.020.25534140.21558009X-RAY DIFFRACTION100
2.02-2.060.2414280.20958041X-RAY DIFFRACTION99.96
2.06-2.10.26594260.22027953X-RAY DIFFRACTION99.95
2.1-2.150.25364360.22678032X-RAY DIFFRACTION99.99
2.15-2.210.27694290.2248011X-RAY DIFFRACTION99.99
2.21-2.270.2594310.21648002X-RAY DIFFRACTION99.96
2.27-2.330.25174160.20468006X-RAY DIFFRACTION100
2.33-2.410.23834320.20768064X-RAY DIFFRACTION99.99
2.41-2.50.25414110.20728028X-RAY DIFFRACTION100
2.5-2.60.2614100.21248065X-RAY DIFFRACTION99.98
2.6-2.710.24964070.21198037X-RAY DIFFRACTION99.99
2.71-2.860.24754410.21088083X-RAY DIFFRACTION100
2.86-3.040.24774300.21228054X-RAY DIFFRACTION100
3.04-3.270.23354300.19968063X-RAY DIFFRACTION100
3.27-3.60.20524120.18288115X-RAY DIFFRACTION100
3.6-4.120.17944460.15988111X-RAY DIFFRACTION100
4.12-5.190.15074280.13798169X-RAY DIFFRACTION100
5.19-92.630.16274000.15348383X-RAY DIFFRACTION99.68

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