+Open data
-Basic information
Entry | Database: PDB / ID: 7zso | ||||||
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Title | human purine nucleoside phosphorylase in complex with JS-554 | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / PNP-inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Djukic, S. / Pachl, P. / Rezacova, P. | ||||||
Funding support | European Union, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / ...Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / Pachl, P. / Brynda, J. / Vuckova, T. / Fabry, M. / Snasel, J. / Pichova, I. / Rezacova, P. / Mertlikova-Kaiserova, H. / Janeba, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zso.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zso.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zso_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zso_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7zso_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 7zso_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/7zso ftp://data.pdbj.org/pub/pdb/validation_reports/zs/7zso | HTTPS FTP |
-Related structure data
Related structure data | 7zslSC 7zsmC 7zsnC 7zspC 7zsqC 7zsrC 8c25C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 32154.854 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNP, NP / Production host: Escherichia coli (E. coli) References: UniProt: P00491, purine-nucleoside phosphorylase |
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-Non-polymers , 5 types, 371 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 500 mM Ammonium sulfate; 1.00 M Lithium sulfate 100 mM; tri-Sodium citrate; pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 65544 / % possible obs: 97.5 % / Redundancy: 6.64 % / CC1/2: 0.996 / Net I/σ(I): 9.29 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 4612 / CC1/2: 0.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZSL Resolution: 1.95→40.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.044 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 107.7 Å2 / Biso mean: 31.157 Å2 / Biso min: 8.78 Å2
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Refinement step | Cycle: final / Resolution: 1.95→40.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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