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Open data
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Basic information
Entry | Database: PDB / ID: 1m73 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN PNP AT 2.3A RESOLUTION | ||||||
![]() | PURINE NUCLEOSIDE PHOSPHORYLASE![]() | ||||||
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Function / homology | ![]() nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Azevedo Jr., W.F. / Marangoni Dos Santos, D. / Canduri, F. / Santos, G.C. / Olivieri, J.R. / Silva, R.G. / Basso, L.A. / Palma, M.S. / Santos, D.S. | ||||||
![]() | ![]() Title: Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution. Authors: de Azevedo, W.F. / Canduri, F. / dos Santos, D.M. / Silva, R.G. / de Oliveira, J.S. / de Carvalho, L.P. / Basso, L.A. / Mendes, M.A. / Palma, M.S. / Santos, D.S. #1: ![]() Title: Application of Crystallographic and Modeling Methods in the Design of Purine Nucleoside Phosphorylase Inhibitors Authors: Ealick, S.E. / Babu, Y.S. / Bugg, C.E. / Erion, M.D. / Guida, W.C. / Montgomery, J.A. / Secrist, J.A.3rd. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ulaS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 32053.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P00491, ![]() | ||
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#2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.92 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.05M citrate buffer, 19% ammonium sulphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 19, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→24.25 Å / Num. all: 26429 / Num. obs: 26429 / % possible obs: 94.13 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.842 % / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.197 / % possible all: 87.6 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20.25 Å / Num. measured all: 48682 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 87.6 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ULA Resolution: 2.3→8 Å / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.75 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 8 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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