Entry | Database: PDB / ID: 6ca4 |
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Title | Crystal structure of humanized D. rerio TDP2 by 14 mutations |
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Components | Tyrosyl-DNA phosphodiesterase 2 |
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Keywords | HYDROLASE / TDP2 |
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Function / homology | Function and homology information
tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair ...tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair / single-stranded DNA binding / manganese ion binding / magnesium ion binding / DNA binding / cytoplasmSimilarity search - Function UBA-like domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / 4-Layer Sandwich / Alpha BetaSimilarity search - Domain/homology |
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Biological species | ![](img/tx_fish.gif) Danio rerio (zebrafish) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.623 Å |
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Authors | Shi, K. / Aihrara, H. |
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Funding support | United States, 2items Organization | Grant number | Country |
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National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | GM095558 | United States | National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | GM118047 | United States |
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Citation | Journal: Eur J Pharm Sci / Year: 2018 Title: New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2). Authors: Ribeiro, C.J.A. / Kankanala, J. / Shi, K. / Kurahashi, K. / Kiselev, E. / Ravji, A. / Pommier, Y. / Aihara, H. / Wang, Z. |
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History | Deposition | Jan 29, 2018 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | May 2, 2018 | Provider: repository / Type: Initial release |
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Revision 1.1 | Feb 20, 2019 | Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization |
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Revision 1.2 | Jan 1, 2020 | Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization |
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Revision 1.3 | Oct 4, 2023 | Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id |
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