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Open data
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Basic information
Entry | Database: PDB / ID: 3euf | ||||||
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Title | Crystal structure of BAU-bound human uridine phosphorylase 1 | ||||||
![]() | Uridine phosphorylase 1 | ||||||
![]() | TRANSFERASE / nucleoside phosphorylase / uridine rescue / 5-benzylacyclouridine / Alternative splicing / Glycosyltransferase | ||||||
Function / homology | ![]() deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / dUMP catabolic process / Pyrimidine catabolism / uridine catabolic process / Pyrimidine salvage ...deoxyuridine phosphorylase activity / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / thymidine phosphorylase activity / dUMP catabolic process / Pyrimidine catabolism / uridine catabolic process / Pyrimidine salvage / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleobase-containing compound metabolic process / cellular response to glucose starvation / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roosild, T.P. | ||||||
![]() | ![]() Title: Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy. Authors: Roosild, T.P. / Castronovo, S. / Fabbiani, M. / Pizzorno, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.2 KB | Display | ![]() |
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PDB format | ![]() | 195.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3eueC ![]() 1u1cS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 36050.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BAU / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG 3350, 300mM KCl, 30mM MgCl2, 100mM Bis-Tris Buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 103357 / Num. obs: 103213 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible obs: 100 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2 / Num. unique all: 10192 / Num. unique obs: 10192 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U1C Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.403 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.999 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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