登録情報 | データベース: PDB / ID: 6k4g |
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タイトル | Crystal structure of the PI5P4Kbeta-GMPPNP complex |
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要素 | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta |
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キーワード | TRANSFERASE / Lipid kinase / Phosphoinositide signaling |
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機能・相同性 | 機能・相同性情報
1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol類似検索 - 分子機能 Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol-4-phosphate 5-kinase / : / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. ...Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol-4-phosphate 5-kinase / : / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 2-Layer Sandwich / Alpha Beta類似検索 - ドメイン・相同性 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta類似検索 - 構成要素 |
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生物種 | Homo sapiens (ヒト) |
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手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å |
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データ登録者 | Takeuchi, K. / Senda, M. / Senda, T. |
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資金援助 | 日本, 1件 組織 | 認可番号 | 国 |
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Japan Agency for Medical Research and Development (AMED) | JP17am0101001 | 日本 |
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引用 | ジャーナル: Structure / 年: 2022 タイトル: The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. 著者: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / ...著者: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / Sasaki, A.T. / Senda, T. |
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履歴 | 登録 | 2019年5月23日 | 登録サイト: PDBJ / 処理サイト: PDBJ |
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改定 1.0 | 2020年5月27日 | Provider: repository / タイプ: Initial release |
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改定 2.0 | 2021年3月3日 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range / struct_site / struct_site_gen / symmetry Item: _cell.volume / _pdbx_nonpoly_scheme.asym_id ..._cell.volume / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _symmetry.space_group_name_Hall 解説: Real space R-factor / Provider: author / タイプ: Coordinate replacement |
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改定 2.1 | 2022年5月25日 | Group: Database references / カテゴリ: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession |
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改定 2.2 | 2023年11月22日 | Group: Data collection / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model |
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