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Open data
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Basic information
Entry | Database: PDB / ID: 2yhi | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor WH16 | ||||||
![]() | (PTERIDINE REDUCTASE, ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE | ||||||
Function / homology | ![]() pteridine reductase / pteridine reductase activity / oxidoreductase activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nerini, E. / Dawson, A. / Hunter, W.N. / Costi, M.P. | ||||||
![]() | ![]() Title: Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery. Authors: Linciano, P. / Dawson, A. / Pohner, I. / Costa, D.M. / Sa, M.S. / Cordeiro-da-Silva, A. / Luciani, R. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Gribbon, P. / Reinshagen, J. / Wolf, ...Authors: Linciano, P. / Dawson, A. / Pohner, I. / Costa, D.M. / Sa, M.S. / Cordeiro-da-Silva, A. / Luciani, R. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Gribbon, P. / Reinshagen, J. / Wolf, M. / Behrens, B. / Hannaert, V. / Michels, P.A.M. / Nerini, E. / Pozzi, C. / di Pisa, F. / Landi, G. / Santarem, N. / Ferrari, S. / Saxena, P. / Lazzari, S. / Cannazza, G. / Freitas-Junior, L.H. / Moraes, C.B. / Pascoalino, B.S. / Alcantara, L.M. / Bertolacini, C.P. / Fontana, V. / Wittig, U. / Muller, W. / Wade, R.C. / Hunter, W.N. / 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 | ![]() | 215.8 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 42.5 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yhuC ![]() 4wcdC ![]() 4wcfC ![]() 5izcC ![]() 2x9gS 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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Unit cell |
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Components
-PTERIDINE REDUCTASE, ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 30685.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CYS 59 OXIDIZED TO S-OXY CYSTEINE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 30669.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 550 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/W16.gif)
![](data/chem/img/DTV.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/DTU.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/W16.gif)
![](data/chem/img/DTV.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/DTU.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-W16 / #5: Chemical | ChemComp-DTV / ( | #6: Chemical | #7: Chemical | ChemComp-DTU / ( | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | N TERMINAL TAG SEQUENCE INCLUDED. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.2 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: RESERVOIR CONDITIONS: 100 MM SODIUM CITRATE PH 5, 1.8 M SODIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Oct 4, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.41 Å / Num. obs: 87904 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / % possible all: 88.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X9G Resolution: 1.8→31.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.576 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.41 Å
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Refine LS restraints |
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