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Open data
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Basic information
Entry | Database: PDB / ID: 1v2h | ||||||
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Title | Crystal structure of human PNP complexed with guanine | ||||||
![]() | Purine nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / purine nucleoside phosphorylase / drug design / synchrotron / guanine | ||||||
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 / nucleotide biosynthetic process / dAMP catabolic 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 / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / response to xenobiotic stimulus / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Azevedo Jr., W.F. / Canduri, F. / Pereira, J.H. / Dos Santos, D.M. / Bertacine Dias, M.V. / Silva, R.G. / Palma, M.S. / Basso, L.A. / Santos, D.S. | ||||||
![]() | ![]() Title: Crystal structure of human PNP complexed with guanine. Authors: de Azevedo Jr., W.F. / Canduri, F. / dos Santos, D.M. / Pereira, J.H. / Bertacine Dias, M.V. / Silva, R.G. / Mendes, M.A. / Basso, L.A. / Palma, M.S. / Santos, D.S. #1: ![]() Title: Crystal Structure of Human Purine Nucleoside Phosphorylase at 2.3A Resolution Authors: De Azevedo Jr., 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.4 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m73S 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, purine-nucleoside phosphorylase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GUN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.65 Å3/Da / Density % sol: 74 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||
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: CCD / Date: Apr 16, 2003 | |||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→56.381 Å / Num. all: 46457 / Num. obs: 18226 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.07 / Net I/σ(I): 7.5 | |||||||||
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.371 / % possible all: 96 | |||||||||
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 56.8 Å / Rmerge(I) obs: 0.07 | |||||||||
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.371 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M73 Resolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.82 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 8 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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