登録情報 | データベース: PDB / ID: 3itb |
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タイトル | Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment |
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要素 | - D-alanyl-D-alanine carboxypeptidase DacC
- Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)
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キーワード | HYDROLASE / Penicillin-Binding Protein / PBP6 / DD-carboxypeptidase / peptidoglycan / substrate fragment / Carboxypeptidase / Cell inner membrane / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis / Protease |
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機能・相同性 | 機能・相同性情報
serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to xenobiotic stimulus / protein homodimerization activity ...serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to xenobiotic stimulus / protein homodimerization activity / proteolysis / plasma membrane類似検索 - 分子機能 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta類似検索 - ドメイン・相同性 sucrose / Chem-AMV / D-alanyl-D-alanine carboxypeptidase DacC類似検索 - 構成要素 |
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生物種 | ![](img/tx_bacteria.gif) Escherichia coli (大腸菌) synthetic construct (人工物) |
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手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å |
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データ登録者 | Chen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K. |
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引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2009 タイトル: Crystal structures of penicillin-binding protein 6 from Escherichia coli. 著者: Chen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K. |
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履歴 | 登録 | 2009年8月27日 | 登録サイト: RCSB / 処理サイト: RCSB |
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改定 1.0 | 2009年10月20日 | Provider: repository / タイプ: Initial release |
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改定 1.1 | 2011年7月13日 | Group: Version format compliance |
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改定 1.2 | 2011年7月27日 | Group: Database references / Derived calculations / Non-polymer description |
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改定 1.3 | 2017年11月1日 | Group: Advisory / Refinement description / カテゴリ: pdbx_validate_polymer_linkage / software |
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改定 2.0 | 2020年7月29日 | Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details 解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation |
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改定 3.0 | 2024年3月27日 | Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end |
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改定 3.1 | 2024年4月3日 | Group: Refinement description / カテゴリ: pdbx_initial_refinement_model |
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