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Open data
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Basic information
Entry | Database: PDB / ID: 6gck | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor 1e (F206) | ||||||
![]() | Pteridine reductase | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / benzothiazole | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Landi, G. / Mangani, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections. Authors: Linciano, P. / Pozzi, C. / Iacono, L.D. / di Pisa, F. / Landi, G. / Bonucci, A. / Gul, S. / Kuzikov, M. / Ellinger, B. / Witt, G. / Santarem, N. / Baptista, C. / Franco, C. / Moraes, C.B. / ...Authors: Linciano, P. / Pozzi, C. / Iacono, L.D. / di Pisa, F. / Landi, G. / Bonucci, A. / Gul, S. / Kuzikov, M. / Ellinger, B. / Witt, G. / Santarem, N. / Baptista, C. / Franco, C. / Moraes, C.B. / Muller, W. / Wittig, U. / Luciani, R. / Sesenna, A. / Quotadamo, A. / Ferrari, S. / Pohner, I. / Cordeiro-da-Silva, A. / Mangani, S. / Costantino, L. / 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 | ![]() | 212.1 KB | Display | ![]() |
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PDB format | ![]() | 169 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gclC ![]() 6gcpC ![]() 6gcqC ![]() 6gd0C ![]() 6gd4C ![]() 6gdoC ![]() 6gdpC ![]() 6gexC ![]() 6geyC ![]() 5jdcS 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
#1: Protein | Mass: 28498.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-EUB / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.57 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2017 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→65.71 Å / Num. obs: 47471 / % possible obs: 88.9 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.069 / Rrim(I) all: 0.121 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.14→2.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7150 / CC1/2: 0.919 / Rpim(I) all: 0.177 / Rrim(I) all: 0.301 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JDC Resolution: 2.14→65.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0.241 / SU B: 7.777 / SU ML: 0.192 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.241 / SU Rfree Cruickshank DPI: 0.241
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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: 27.085 Å2
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Refine analyze | Luzzati coordinate error obs: 0.259 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.14→65.71 Å
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Refine LS restraints |
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