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Open data
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Basic information
Entry | Database: PDB / ID: 7zsq | ||||||
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Title | human purine nucleoside phosphorylase in complex with JS-555 | ||||||
![]() | Purine nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / PNP-inhibitor complex | ||||||
Function / homology | ![]() nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Djukic, S. / Pachl, P. / Rezacova, P. | ||||||
Funding support | European Union, 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168 KB | Display | ![]() |
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PDB format | ![]() | 130 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zslC ![]() 7zsmC ![]() 7zsnC ![]() 7zsoC ![]() 7zspC ![]() 7zsrC ![]() 8c25C ![]() 1g2oS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 27724.584 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: deoD, E5M05_03615, E5M23_14660, E5M52_18960, E5M78_19105, ERS013440_01955, ERS027646_00621, ERS027659_03654, SAMEA2683035_02840 Production host: ![]() ![]() References: UniProt: A0A045IAS2, purine-nucleoside phosphorylase |
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-Non-polymers , 7 types, 425 molecules ![](data/chem/img/JTO.gif)
![](data/chem/img/TEW.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/P4K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TEW.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/P4K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TEW / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-P4K / | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 30.00 % v/v Polyethylene glycol 400; 100 mM HEPES; pH 7.5; 200 mM Magnesium chloride; 1 mM TEW |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→48.38 Å / Num. obs: 140249 / % possible obs: 99.9 % / Redundancy: 6.96 % / Biso Wilson estimate: 34.629 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.174 / Χ2: 0.887 / Net I/σ(I): 8.39 / Num. measured all: 976139 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1g2o Resolution: 1.77→48.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.547 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.112 / 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: 104.63 Å2 / Biso mean: 30.516 Å2 / Biso min: 17.52 Å2
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Refinement step | Cycle: final / Resolution: 1.77→48.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.815 Å / Rfactor Rfree error: 0
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