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- PDB-7nvp: Trypanothione reductase from Trypanosoma brucei in complex with N... -

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Basic information

Entry
Database: PDB / ID: 7nvp
TitleTrypanothione reductase from Trypanosoma brucei in complex with N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide
ComponentsN(1),N(8)-bis(glutathionyl)spermidine reductase
KeywordsOXIDOREDUCTASE / Trypanothione / neglected tropical diseases / inhibition / redox equilibrium
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. / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-UT2 / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsBattista, T. / Fiorillo, A. / Colotti, G. / Ilari, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationFISR2019_03796 PROLEISH Italy
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Optimization of Potent and Specific Trypanothione Reductase Inhibitors: A Structure-Based Drug Discovery Approach.
Authors: Battista, T. / Federico, S. / Brogi, S. / Pozzetti, L. / Khan, T. / Butini, S. / Ramunno, A. / Fiorentino, E. / Orsini, S. / Di Muccio, T. / Fiorillo, A. / Exertier, C. / Di Risola, D. / ...Authors: Battista, T. / Federico, S. / Brogi, S. / Pozzetti, L. / Khan, T. / Butini, S. / Ramunno, A. / Fiorentino, E. / Orsini, S. / Di Muccio, T. / Fiorillo, A. / Exertier, C. / Di Risola, D. / Colotti, G. / Gemma, S. / Ilari, A. / Campiani, G.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: N(1),N(8)-bis(glutathionyl)spermidine reductase
BBB: N(1),N(8)-bis(glutathionyl)spermidine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97014
Polymers106,7082
Non-polymers3,26312
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-159 kcal/mol
Surface area37280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.096, 133.334, 158.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 489 / Label seq-ID: 6 - 490

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein N(1),N(8)-bis(glutathionyl)spermidine reductase / Trypanothione reductase


Mass: 53353.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Histidine tag is present at the N-term
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / 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, 185 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-UT2 / N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide / ~{N}-[4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl]-5-nitro-thiophene-2-carboxamide / N-[4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl]-5-nitro-thiophene-2-carboxamide


Mass: 463.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17N3O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: TbTR (10 mg/ml) in 20 mM HEPES pH 7.4; cocrystallisation with 2 mM A1/7 (incubation O/N, 283.15 K). Hanging drop vapor diffusion method + seeding, Crystallisation conditions: 100 mM Hepes pH ...Details: TbTR (10 mg/ml) in 20 mM HEPES pH 7.4; cocrystallisation with 2 mM A1/7 (incubation O/N, 283.15 K). Hanging drop vapor diffusion method + seeding, Crystallisation conditions: 100 mM Hepes pH 7-8 + 2.2-2.3 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.153→158.912 Å / Num. obs: 76940 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1439 / Rpim(I) all: 0.04142 / Rrim(I) all: 0.1499 / Net I/σ(I): 12.14
Reflection shellResolution: 2.153→2.23 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.595 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 7477 / CC1/2: 0.635 / Rpim(I) all: 0.4854 / % possible all: 98.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBA

2wba


Resolution: 2.153→102.143 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.17 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.229 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2777 3832 5 %
Rwork0.2399 72803 -
all0.242 --
obs-76635 99.71 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.472 Å2-0 Å20 Å2
2--0.552 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.153→102.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7438 0 209 175 7822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137869
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177422
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.64210712
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57817135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97723.11344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.816151288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7071534
X-RAY DIFFRACTIONr_chiral_restr0.0650.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028867
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021695
X-RAY DIFFRACTIONr_nbd_refined0.2130.21661
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.27194
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23742
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1090.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.216
X-RAY DIFFRACTIONr_nbd_other0.3380.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.360.22
X-RAY DIFFRACTIONr_mcbond_it4.6185.2063931
X-RAY DIFFRACTIONr_mcbond_other4.6175.2043930
X-RAY DIFFRACTIONr_mcangle_it6.6077.7974915
X-RAY DIFFRACTIONr_mcangle_other6.6077.7984916
X-RAY DIFFRACTIONr_scbond_it4.6965.6843938
X-RAY DIFFRACTIONr_scbond_other4.6665.6653911
X-RAY DIFFRACTIONr_scangle_it7.0148.3585791
X-RAY DIFFRACTIONr_scangle_other6.9918.3295750
X-RAY DIFFRACTIONr_lrange_it10.33460.8478688
X-RAY DIFFRACTIONr_lrange_other10.31960.8578664
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 11.4405 Å2 / Rms dev position: 0.05048 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-IDAuth asym-ID
1AAA
2BBB
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.2090.3612720.3025281X-RAY DIFFRACTION98.8078
2.209-2.2690.3092780.2715143X-RAY DIFFRACTION99.3585
2.269-2.3350.3232640.2735024X-RAY DIFFRACTION99.5669
2.335-2.4070.3252710.2684888X-RAY DIFFRACTION99.6138
2.407-2.4860.3712680.3024725X-RAY DIFFRACTION99.6408
2.486-2.5730.3342190.2744619X-RAY DIFFRACTION99.7731
2.573-2.670.3232540.2774447X-RAY DIFFRACTION99.8301
2.67-2.7790.3472210.2874301X-RAY DIFFRACTION99.8675
2.779-2.9030.3472080.2864136X-RAY DIFFRACTION99.8391
2.903-3.0440.3172150.2813940X-RAY DIFFRACTION99.9759
3.044-3.2090.311960.273756X-RAY DIFFRACTION99.9747
3.209-3.4030.3331990.2663572X-RAY DIFFRACTION99.9205
3.403-3.6380.2921770.2523365X-RAY DIFFRACTION99.9436
3.638-3.9290.2481690.2353155X-RAY DIFFRACTION99.9699
3.929-4.3030.2341680.2022887X-RAY DIFFRACTION99.9673
4.303-4.810.1891360.1922654X-RAY DIFFRACTION99.9642
4.81-5.5520.2261190.2022346X-RAY DIFFRACTION99.9189
5.552-6.7950.244860.2172020X-RAY DIFFRACTION99.9525
6.795-9.5880.203780.1651600X-RAY DIFFRACTION100
9.588-102.143X-RAY DIFFRACTION

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