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Open data
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Basic information
Entry | Database: PDB / ID: 6gdo | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor 2g (F240) | ||||||
![]() | 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 | ![]() | 216.4 KB | Display | ![]() |
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PDB format | ![]() | 170.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6gckC ![]() 6gclC ![]() 6gcpC ![]() 6gcqC ![]() 6gd0C ![]() 6gd4C ![]() 6gdpC ![]() 6gexC ![]() 6geyC ![]() 5jdcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 30669.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 533 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/EVZ.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EVZ.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.23 % |
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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, pH5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017 |
Radiation | Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→44.72 Å / Num. obs: 93052 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.049 / Rrim(I) all: 0.089 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 13512 / CC1/2: 0.807 / Rpim(I) all: 0.343 / Rrim(I) all: 0.62 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JDC Resolution: 1.78→44.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0.114 / SU B: 3.286 / SU ML: 0.096 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.114 / SU Rfree Cruickshank DPI: 0.114
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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: 27.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.78→44.72 Å
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Refine LS restraints |
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