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Yorodumi- PDB-7nvp: Trypanothione reductase from Trypanosoma brucei in complex with N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nvp | ||||||
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Title | Trypanothione reductase from Trypanosoma brucei in complex with N-{4-methoxy-3-[(4-methoxyphenyl)sulfamoyl]phenyl}-5-nitrothiophene-2-carboxamide | ||||||
Components | N(1),N(8)-bis(glutathionyl)spermidine reductase | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å | ||||||
Authors | Battista, T. / Fiorillo, A. / Colotti, G. / Ilari, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nvp.cif.gz | 216.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7nvp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7nvp_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 7nvp_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvp ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvp | HTTPS FTP |
-Related structure data
Related structure data | 2wbaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
NCS ensembles : (Details: Global NCS restraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | 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 | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.51 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.112 Å2
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Refinement step | Cycle: LAST / Resolution: 2.153→102.143 Å
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Refine LS restraints |
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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
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LS refinement shell |
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