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- PDB-6rxc: Leishmania major pteridine reductase 1 (LmPTR1) in complex with i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rxc | ||||||
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Title | Leishmania major pteridine reductase 1 (LmPTR1) in complex with inhibitor 4 (NMT-C0026) | ||||||
![]() | (Pteridine reductase 1) x 2 | ||||||
![]() | OXIDOREDUCTASE / Leishmania major / pteridine reductase / LmPTR1 / pteridine based inhibitors | ||||||
Function / homology | ![]() pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1. Authors: Pohner, I. / Quotadamo, A. / Panecka-Hofman, J. / Luciani, R. / Santucci, M. / Linciano, P. / Landi, G. / Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. / Gul, S. / Witt, G. / ...Authors: Pohner, I. / Quotadamo, A. / Panecka-Hofman, J. / Luciani, R. / Santucci, M. / Linciano, P. / Landi, G. / Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Santarem, N. / Cordeiro-da-Silva, A. / Costi, M.P. / Venturelli, A. / Wade, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 180.3 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 | ![]() | 50.5 KB | Display | |
Data in CIF | ![]() | 69.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rx0C ![]() 6rx5C ![]() 6rx6C ![]() 5l4nS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 30722.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 30738.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-KMK / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH 5.3 and 10 mM DTT; Crystallization buffer: 12% PEG4600, 100 mM Sodium Acetate pH 5.5 and 120-160 mM Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2015 |
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: 2.1→82.5 Å / Num. obs: 78229 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.057 / Rrim(I) all: 0.124 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 11390 / CC1/2: 0.836 / Rpim(I) all: 0.2 / Rrim(I) all: 0.434 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L4N Resolution: 2.1→82.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.273 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.192
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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: 28.602 Å2
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Refine analyze | Luzzati coordinate error obs: 0.265 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→82.5 Å
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Refine LS restraints |
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