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- PDB-8of2: Trypanosoma brucei pteridine reductase 1 (TbPTR1) in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8of2 | ||||||
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Title | Trypanosoma brucei pteridine reductase 1 (TbPTR1) in complex with 2,4,6 triamminopyrimidine (TAP) | ||||||
![]() | Pteridine reductase | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / triamminopyrimidine | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassone, G. / Landi, G. / Mangani, S. / Pozzi, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: The discovery of aryl-2-nitroethyl triamino pyrimidines as anti-Trypanosoma brucei agents. Authors: Linciano, P. / Pozzi, C. / Tassone, G. / Landi, G. / Mangani, S. / Santucci, M. / Luciani, R. / Ferrari, S. / Santarem, N. / Tagliazucchi, L. / Cordeiro-da-Silva, A. / Tonelli, M. / Tondi, D. ...Authors: Linciano, P. / Pozzi, C. / Tassone, G. / Landi, G. / Mangani, S. / Santucci, M. / Luciani, R. / Ferrari, S. / Santarem, N. / Tagliazucchi, L. / Cordeiro-da-Silva, A. / Tonelli, M. / Tondi, D. / Bertarini, L. / Gul, S. / Witt, G. / Moraes, C.B. / 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 | ![]() | 233.9 KB | Display | ![]() |
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PDB format | ![]() | 184.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 50.2 KB | Display | |
Data in CIF | ![]() | 74.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1096 molecules ![](data/chem/img/3AY.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-3AY / #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 294 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 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2020 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→74.86 Å / Num. obs: 161484 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24272 / CC1/2: 0.831 / Rpim(I) all: 0.337 / Rrim(I) all: 0.678 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.329 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.48→74.86 Å
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Refine LS restraints |
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