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Yorodumi- PDB-5ebk: Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ebk | ||||||
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Title | Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine | ||||||
Components | Trypanothione reductase | ||||||
Keywords | 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 | ||||||
Biological species | Leishmania infantum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Ilari, A. / Angiulli, G. | ||||||
Citation | Journal: J Enzyme Inhib Med Chem / Year: 2017 Title: Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives. Authors: Saccoliti, F. / Angiulli, G. / Pupo, G. / Pescatori, L. / Madia, V.N. / Messore, A. / Colotti, G. / Fiorillo, A. / Scipione, L. / Gramiccia, M. / Di Muccio, T. / Di Santo, R. / Costi, R. / Ilari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ebk.cif.gz | 395.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ebk.ent.gz | 327.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ebk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ebk_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 5ebk_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 5ebk_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 5ebk_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5ebk ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5ebk | HTTPS FTP |
-Related structure data
Related structure data | 2jk6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 10 - 480 / Label seq-ID: 30 - 500
NCS oper:
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-Components
#1: Protein | Mass: 55257.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sandfly / Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: TRYR, LINJ_05_0350 / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A4HSF7, trypanothione-disulfide reductase #2: Chemical | #3: Chemical | ChemComp-RDS / #4: Chemical | ChemComp-SO4 / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density meas: 2017200 Mg/m3 / Density % sol: 73.2 % / Description: Small diamond-shaped yellow crystals |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulphate, Lithium sulphate, Tris HCl / PH range: 7.5 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å | |||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 23, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.51→48.15 Å / Num. all: 24914 / Num. obs: 127631 / % possible obs: 99.6 % / Redundancy: 5.12 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.16 | |||||||||||||||
Reflection shell | Resolution: 3.51→3.72 Å / Redundancy: 5.04 % / Mean I/σ(I) obs: 1.72 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2jk6 Resolution: 3.51→48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.926 / SU B: 40.928 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.04 Å2
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Refinement step | Cycle: 1 / Resolution: 3.51→48 Å
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Refine LS restraints |
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