+Open data
-Basic information
Entry | Database: PDB / ID: 6gcp | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor 2d (F186) | ||||||
Components | Pteridine reductase | ||||||
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: 1.52 Å | ||||||
Authors | Pozzi, C. / Landi, G. / 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 | 6gcp.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gcp.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gcp_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6gcp_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6gcp_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 6gcp_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gcp ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gcp | HTTPS FTP |
-Related structure data
Related structure data | 6gckC 6gclC 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
-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.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O76290 |
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-Non-polymers , 5 types, 870 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-EUK / #4: Chemical | ChemComp-GOL / #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: 2.1 Å3/Da / Density % sol: 41.37 % |
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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: 0.9795 Å |
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: 1.52→67.48 Å / Num. obs: 149204 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.52→1.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 21375 / CC1/2: 0.921 / Rpim(I) all: 0.259 / Rrim(I) all: 0.514 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JDC Resolution: 1.52→67.48 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Rfactor Rfree error: 0.075 / SU B: 1.833 / SU ML: 0.062 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / SU Rfree Cruickshank DPI: 0.075
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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: 20.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.169 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.52→67.48 Å
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Refine LS restraints |
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