+Open data
-Basic information
Entry | Database: PDB / ID: 6gcl | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor 3a (F020) | ||||||
Components | (Pteridine reductase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / benzothiazole | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Landi, G. / Pozzi, C. / Mangani, S. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gcl.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gcl.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 6gcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gcl ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gcl | HTTPS FTP |
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-Related structure data
Related structure data | 6gckC 6gcpC 6gcqC 6gd0C 6gd4C 6gdoC 6gdpC 6gexC 6geyC 5jdcS C: citing same article (ref.) S: Starting model for refinement |
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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
#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: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O76290 #2: Protein | | Mass: 30717.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O76290 #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-EUE / #5: 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: 2.4 Å3/Da / Density % sol: 48.82 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2014 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→33.26 Å / Num. obs: 72963 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.047 / Rrim(I) all: 0.085 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.474 / Num. unique obs: 10625 / CC1/2: 0.901 / Rpim(I) all: 0.322 / Rrim(I) all: 0.575 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JDC Resolution: 1.95→33.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.118 / SU ML: 0.177 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / SU Rfree Cruickshank DPI: 0.164
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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: 36.084 Å2
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Refine analyze | Luzzati coordinate error obs: 0.297 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→33.26 Å
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Refine LS restraints |
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