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- PDB-6i7n: Trypanothione Reductase from Leismania infantum in complex with TRL156 -

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Basic information

Entry
Database: PDB / ID: 6i7n
TitleTrypanothione Reductase from Leismania infantum in complex with TRL156
ComponentsTrypanothione reductase
KeywordsFLAVOPROTEIN / Inhibitor / Complex / Dimer / Oxidoreductase
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / 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-H6H / Trypanothione reductase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCarriles, A.A. / Hermoso, J.A.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Pyrrolopyrimidine vs Imidazole-Phenyl-Thiazole Scaffolds in Nonpeptidic Dimerization Inhibitors of Leishmania infantum Trypanothione Reductase.
Authors: Revuelto, A. / Ruiz-Santaquiteria, M. / de Lucio, H. / Gamo, A. / Carriles, A.A. / Gutierrez, K.J. / Sanchez-Murcia, P.A. / Hermoso, J.A. / Gago, F. / Camarasa, M.J. / Jimenez-Ruiz, A. / Velazquez, S.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 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)108,8889
Polymers106,3672
Non-polymers2,5217
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Inhibition of enzyme activity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-111 kcal/mol
Surface area37080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.184, 106.387, 186.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 487 / Label seq-ID: 2 - 488

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trypanothione reductase


Mass: 53183.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: TRYR, LINJ_05_0350 / Production host: Escherichia coli (E. coli)
References: UniProt: A4HSF7, trypanothione-disulfide reductase

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Non-polymers , 5 types, 202 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-H6H / ~{N}-(4-azanylbutyl)-~{N}-(2-azanyl-2-oxidanylidene-ethyl)-7-(3-azanyl-3-oxidanylidene-propyl)-4-(dimethylamino)-2-(2-naphthalen-2-ylethylamino)pyrrolo[2,3-d]pyrimidine-6-carboxamide


Mass: 573.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H39N9O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.2 Å3/Da / Density % sol: 44.11 % / Description: Yello bi-pyramidal crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.2M ammonium sulphate, 0.1M Tris-HCl pH 8-8.5 / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.3→46.68 Å / Num. obs: 23420 / % possible obs: 81.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rpim(I) all: 0.07 / Net I/σ(I): 5.2
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 2.6 % / CC1/2: 0.79 / Rpim(I) all: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JK6

2jk6


Resolution: 3.3→46.68 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU B: 56.74 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.582 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27323 1111 4.8 %RANDOM
Rwork0.23654 ---
obs0.23825 22213 80.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.879 Å2
Baniso -1Baniso -2Baniso -3
1-5.35 Å2-0 Å20 Å2
2---0.58 Å20 Å2
3----4.77 Å2
Refinement stepCycle: 1 / Resolution: 3.3→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7401 0 170 195 7766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177074
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.64910487
X-RAY DIFFRACTIONr_angle_other_deg1.3311.58216426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4385976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9122.784352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.855151261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1361538
X-RAY DIFFRACTIONr_chiral_restr0.0710.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028679
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021559
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_it3.8077.7763913
X-RAY DIFFRACTIONr_mcbond_other3.7947.7713909
X-RAY DIFFRACTIONr_mcangle_it6.38611.6524886
X-RAY DIFFRACTIONr_mcangle_other6.37611.654885
X-RAY DIFFRACTIONr_scbond_it3.7528.293817
X-RAY DIFFRACTIONr_scbond_other3.758.2713810
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.30812.2415590
X-RAY DIFFRACTIONr_long_range_B_refined12.47830503
X-RAY DIFFRACTIONr_long_range_B_other12.44430444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12483 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.25 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 77 -
Rwork0.373 1440 -
obs--72.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2188-0.0898-0.04160.0504-0.01140.23670.01230.0089-0.0036-0.0389-0.0263-0.0009-0.0639-0.00760.0140.3125-0.01660.02070.1535-0.01880.00510.738552.873421.5278
20.4792-0.0186-0.01250.18760.16730.2327-0.0262-0.0398-0.00710.00550.01760.02560.00390.04880.00860.27580.0030.01010.1370.0050.006625.236523.973725.8811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 93
2X-RAY DIFFRACTION1A94 - 191
3X-RAY DIFFRACTION1A192 - 465
4X-RAY DIFFRACTION1A466 - 491
5X-RAY DIFFRACTION2B3 - 27
6X-RAY DIFFRACTION2B38 - 93
7X-RAY DIFFRACTION2B94 - 166
8X-RAY DIFFRACTION2B167 - 262
9X-RAY DIFFRACTION2B263 - 306
10X-RAY DIFFRACTION2B307 - 380
11X-RAY DIFFRACTION2B381 - 490

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