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Yorodumi- PDB-8rdz: Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rdz | ||||||
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Title | Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with Ibrutinib | ||||||
Components | ADP-sugar pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix domain / ADPR / ADP-ribose pyrophosphatase / NUDt5 | ||||||
Function / homology | Function and homology information ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ADP-ribose diphosphatase / ribose phosphate metabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ADP-ribose diphosphatase / ribose phosphate metabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity / D-ribose catabolic process / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Raux, B. / Huber, K.V.M. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rdz.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rdz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/8rdz ftp://data.pdbj.org/pub/pdb/validation_reports/rd/8rdz | HTTPS FTP |
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-Related structure data
Related structure data | 8otvC 8riyC 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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2 |
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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.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.557 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.612 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.226 / ESU R Free: 0.211 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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