+Open data
-Basic information
Entry | Database: PDB / ID: 1v3q | ||||||
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Title | Structure of human PNP complexed with DDI | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase / drug design / synchrotorn / DDI | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Canduri, F. / Pereira, J.H. / dos Santos, D.M. / Silva, R.G. / Palma, M.S. / Basso, L.A. / de Azevedo Jr., W.F. / Santos, D.S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Structures of human purine nucleoside phosphorylase complexed with inosine and ddI Authors: Canduri, F. / dos Santos, D.M. / Silva, R.G. / Mendes, M.A. / Basso, L.A. / Palma, M.S. / de Azevedo Jr., W.F. / Santos, D.S. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v3q.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v3q.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 1v3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v3q_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 1v3q_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 1v3q_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1v3q_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v3q ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v3q | HTTPS FTP |
-Related structure data
Related structure data | 1rctC 1m73S S: Starting model for refinement C: citing same article (ref.) |
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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: 32053.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNP / Production host: Escherichia coli (E. coli) References: UniProt: P00491, purine-nucleoside phosphorylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-2DI / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 75 % |
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Crystal grow | pH: 5.3 / Details: pH 5.30 |
-Data collection
Diffraction | Mean temperature: 104 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 / Wavelength: 1.431 Å | |||||||||
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: 2.8→56.796 Å / Num. obs: 46457 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.057 / Net I/σ(I): 7.5 | |||||||||
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.371 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M73 Resolution: 2.8→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: 0.35 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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