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- PDB-5jdc: Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jdc | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin) | ||||||
![]() | (Pteridine reductase) x 2 | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / oxydoreductase / inhibitor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mangani, S. / Pozzi, C. / Di Pisa, F. / Landi, G. / Dello Iacono, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs. Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / ...Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / Gul, S. / Wolf, M. / Kuzikov, M. / Ellinger, B. / Reinshagen, J. / Witt, G. / Gribbon, P. / Kohler, M. / Keminer, O. / Behrens, B. / Costantino, L. / Tejera Nevado, P. / Bifeld, E. / Eick, J. / Clos, J. / Torrado, J. / Jimenez-Anton, M.D. / Corral, M.J. / Alunda, J.M. / Pellati, F. / Wade, R.C. / Ferrari, S. / Mangani, S. / Costi, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.3 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jcjC ![]() 5jcxC ![]() 5jdiC ![]() 2x9gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABDC
#1: Protein | Mass: 30685.787 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 30733.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 268 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/6JP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6JP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-6JP / ( #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10mM DTT; Crystallization buffer: 0.1 M Sodium Citrate pH 5, 2.25 M Sodium Acetate PH range: 5.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→53.68 Å / Num. obs: 92591 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2X9G Resolution: 1.78→53.68 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.873 / Rfactor Rfree error: 0.13 / SU B: 3.475 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.656 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→53.68 Å
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Refine LS restraints |
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