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Open data
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Basic information
Entry | Database: PDB / ID: 5izc | ||||||
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Title | Trypanosoma brucei PTR1 in complex with inhibitor F032 | ||||||
![]() | (Pteridine reductase) x 2 | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / inhibitor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Landi, G. / Di Pisa, F. / Mangani, S. | ||||||
Funding support | ![]()
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![]() | ![]() 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 KB | Display | ![]() |
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PDB format | ![]() | 170.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 62.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yhiC ![]() 2yhuC ![]() 4wcdSC ![]() 4wcfC 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
-Protein , 2 types, 4 molecules ABDC
#1: Protein | Mass: 28574.559 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Only in subunit C Cys60 has been oxidized to OCS. In all subunits Cys168 has been chemically modified by BME Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 28622.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Only in subunit C Cys60 has been oxidized to OCS. In all subunits Cys168 has been chemically modified by BME Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 585 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/6F4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6F4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-6F4 / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: TbPTR1 6-10 mg/mL in 20 mM Tris-HCl pH 7.5 and 10 mM DTT or BME) and precipitant (1.5-2.5 M Sodium Acetate and 0.1 M Sodium Citrate pH 5) PH range: 5.0 - 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 18, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→74.364 Å / Num. all: 73011 / Num. obs: 73011 / % possible obs: 98 % / Redundancy: 3 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Rsym value: 0.089 / Net I/av σ(I): 6.025 / Net I/σ(I): 7.7 / Num. measured all: 217984 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WCD Resolution: 1.92→74.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.1 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.14 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 73.93 Å2 / Biso mean: 20.565 Å2 / Biso min: 8.29 Å2
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Refinement step | Cycle: final / Resolution: 1.92→74.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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