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Yorodumi- PDB-6rxc: Leishmania major pteridine reductase 1 (LmPTR1) in complex with i... -
+Open data
-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) | ||||||
Components | (Pteridine reductase 1) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Leishmania major / pteridine reductase / LmPTR1 / pteridine based inhibitors | ||||||
Function / homology | Function and homology information pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxc.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxc.ent.gz | 180.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rxc_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6rxc_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6rxc_validation.xml.gz | 50.5 KB | Display | |
Data in CIF | 6rxc_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxc ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxc | HTTPS FTP |
-Related structure data
Related structure data | 6rx0C 6rx5C 6rx6C 5l4nS 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
#1: Protein | Mass: 30722.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01782, pteridine reductase #2: Protein | Mass: 30738.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01782, pteridine reductase #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-KMK / #5: 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: 2.74 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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