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Open data
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Basic information
Entry | Database: PDB / ID: 6gd0 | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor 4g (F133) | ||||||
![]() | Pteridine reductase | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / benzothiazole | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Landi, G. / Pozzi, C. / 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 | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 48.8 KB | Display | |
Data in CIF | ![]() | 70.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gckC ![]() 6gclC ![]() 6gcpC ![]() 6gcqC ![]() 6gd4C ![]() 6gdoC ![]() 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
#1: Protein | Mass: 30669.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % |
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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-F / Detector: PIXEL / Date: May 4, 2015 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→67.43 Å / Num. obs: 102374 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.037 / Rrim(I) all: 0.074 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 14739 / CC1/2: 0.889 / Rpim(I) all: 0.169 / Rrim(I) all: 0.324 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JDC Resolution: 1.74→67.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.154 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101
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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: 16.304 Å2
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Refine analyze | Luzzati coordinate error obs: 0.154 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.74→67.43 Å
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Refine LS restraints |
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