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- PDB-6rb5: Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-... -

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Basic information

Entry
Database: PDB / ID: 6rb5
TitleTrypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide
ComponentsTrypanothione reductase
KeywordsOXIDOREDUCTASE / TRYPANOTHIONE METABOLISM / ANTIOXIDANT / TRYPANOSOMA BRUCEI
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / 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. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / 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, C-terminal dimerisation domain / 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 / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-JWZ / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.977 Å
AuthorsIlari, A. / Fiorillo, A. / Battista, T. / Mocci, S.
CitationJournal: Plos Negl Trop Dis / Year: 2020
Title: Spiro-containing derivatives show antiparasitic activity against Trypanosoma brucei through inhibition of the trypanothione reductase enzyme.
Authors: Turcano, L. / Battista, T. / De Haro, E.T. / Missineo, A. / Alli, C. / Paonessa, G. / Colotti, G. / Harper, S. / Fiorillo, A. / Ilari, A. / Bresciani, A.
History
DepositionApr 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,29024
Polymers110,7742
Non-polymers5,51622
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-182 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.073, 132.622, 161.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trypanothione reductase


Mass: 55387.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 5 types, 509 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-JWZ / 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide


Mass: 607.873 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H57N7O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: SEEDING IN 0,1 M Hepes pH 6.8; 2.1 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.977→102.378 Å / Num. obs: 94907 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Net I/σ(I): 13.276
Reflection shellResolution: 1.977→2.012 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4693 / CC1/2: 0.788 / Rrim(I) all: 0.871 / % possible all: 99.9

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Processing

Software
NameVersionClassification
autoPROCdata collection
XDSJan 26, 2018 (BUILT 20180126)data reduction
Aimless0.7.1data scaling
pointless1.11.12data scaling
STARANISO1.10.15data scaling
Cootmodel building
MOLREPphasing
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBA

2wba


Resolution: 1.977→102.378 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.67 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20659 4839 5.1 %RANDOM
Rwork0.18309 ---
obs0.18427 90068 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0 Å2
2---0.51 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.977→102.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 368 487 8295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028117
X-RAY DIFFRACTIONr_bond_other_d0.0060.027759
X-RAY DIFFRACTIONr_angle_refined_deg1.372.01111079
X-RAY DIFFRACTIONr_angle_other_deg1.2853.01217934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77251011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82424.608319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.391151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6411536
X-RAY DIFFRACTIONr_chiral_restr0.070.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021745
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1783.4763966
X-RAY DIFFRACTIONr_mcbond_other1.1763.4753965
X-RAY DIFFRACTIONr_mcangle_it1.9465.2054967
X-RAY DIFFRACTIONr_mcangle_other1.9465.2064968
X-RAY DIFFRACTIONr_scbond_it1.4033.9954151
X-RAY DIFFRACTIONr_scbond_other1.4033.9954151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3585.8886093
X-RAY DIFFRACTIONr_long_range_B_refined4.29441.9348953
X-RAY DIFFRACTIONr_long_range_B_other4.241.7038849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.977→2.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 365 -
Rwork0.281 6571 -
obs--99.77 %

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