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- PDB-5j3s: Crystal structure of the catalytic domain of human tyrosyl DNA ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j3s | ||||||
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Title | Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor | ||||||
![]() | Tyrosyl-DNA phosphodiesterase 2 | ||||||
![]() | HYDROLASE / tyrosyl DNA phosphodiesterase 2 catalytic domain | ||||||
Function / homology | ![]() tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair / manganese ion binding / single-stranded DNA binding / cell surface receptor signaling pathway / nuclear body / nucleolus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W. | ||||||
![]() | ![]() Title: Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2. Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S. ...Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S.E. / Atack, J.R. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.3 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786 KB | Display | ![]() |
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Full document | ![]() | 788.7 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j3pSC ![]() 5j3zC ![]() 5j42C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 28824.314 Da / Num. of mol.: 1 / Mutation: C273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O95551, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#2: Chemical | ChemComp-6FQ / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop Details: 1.2M D/L-Malic acid pH7.0, 0.1M Bis-Tris propane pH 7.0, 3% v/v DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→45.22 Å / Num. obs: 7545 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2423 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.4→3.67 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.025 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.54 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5J3P Resolution: 3.4→45.218 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→45.218 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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