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- PDB-8rdz: Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rdz | ||||||
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Title | Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with Ibrutinib | ||||||
![]() | ADP-sugar pyrophosphatase | ||||||
![]() | HYDROLASE / Nudix domain / ADPR / ADP-ribose pyrophosphatase / NUDt5 | ||||||
Function / homology | ![]() ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raux, B. / Huber, K.V.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. Authors: Balikci, E. / Marques, A.M.C. / Bauer, L.G. / Seupel, R. / Bennett, J. / Raux, B. / Buchan, K. / Simelis, K. / Singh, U. / Rogers, C. / Ward, J. / Cheng, C. / Szommer, T. / Schutzenhofer, K. ...Authors: Balikci, E. / Marques, A.M.C. / Bauer, L.G. / Seupel, R. / Bennett, J. / Raux, B. / Buchan, K. / Simelis, K. / Singh, U. / Rogers, C. / Ward, J. / Cheng, C. / Szommer, T. / Schutzenhofer, K. / Elkins, J.M. / Sloman, D.L. / Ahel, I. / Fedorov, O. / Brennan, P.E. / Huber, K.V.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8otvC ![]() 8riyC 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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Unit cell |
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Components
#1: Protein | Mass: 24355.596 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-A1H14 / Mass: 440.497 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H24N6O2 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG4K, magnesium chloride |
-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: Sep 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→49.56 Å / Num. obs: 53078 / % possible obs: 96.87 % / Redundancy: 2.8 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.05739 / Rpim(I) all: 0.04047 / Rrim(I) all: 0.07063 / Net I/σ(I): 7.35 |
Reflection shell | Resolution: 2.02→2.092 Å / Rmerge(I) obs: 0.8753 / Num. unique obs: 5256 / CC1/2: 0.243 / CC star: 0.625 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.269 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→49.557 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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