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Yorodumi- PDB-5jdi: Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jdi | ||||||
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Title | Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NMT-H024 (compound 2) | ||||||
Components | (Pteridine reductase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / oxydoreductase / inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Landi, G. / Pozzi, C. / Di Pisa, F. / Dello lacono, L. / Mangani, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdi.cif.gz | 410.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdi.ent.gz | 334.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdi ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdi | HTTPS FTP |
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-Related structure data
Related structure data | 5jcjC 5jcxC 5jdcC 2x9gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 30669.791 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290 #2: Protein | | Mass: 30685.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290 |
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-Non-polymers , 4 types, 915 molecules
#3: Chemical | ChemComp-NAP / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein solution: 6 g/L in 20 mM Tris-HCl pH 7.5, 10 mM DTT; Crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate PH range: 5.0-6.0 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→57.7 Å / Num. obs: 204222 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.38→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x9g Resolution: 1.38→57.7 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Rfactor Rfree error: 0.045 / SU B: 1.573 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / 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: 15.672 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→57.7 Å
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