Entry | Database: PDB / ID: 5c1p |
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Title | Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis |
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Components | D-alanine--D-alanine ligase |
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Keywords | LIGASE / D-alanine-D-alanine ligase / DDL / drug target / bacterial cell wall synthesis |
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Function / homology | Function and homology information
D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosolSimilarity search - FunctionD-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha BetaSimilarity search - Domain/homology |
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Biological species | ![](img/tx_bacteria.gif) ![](data/taxo/wicon/Yersinia_pestis.jpg) Yersinia pestis (bacteria) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å |
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Authors | Tran, H.T. / Kang, L.W. / Hong, M.K. / Ngo, H.P.T. |
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop. Authors: Tran, H.T. / Hong, M.K. / Ngo, H.P. / Huynh, K.H. / Ahn, Y.J. / Wang, Z. / Kang, L.W. |
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History | Deposition | Jun 15, 2015 | Deposition site: RCSB / Processing site: PDBJ |
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Revision 1.0 | Mar 2, 2016 | Provider: repository / Type: Initial release |
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Revision 1.1 | Mar 20, 2024 | 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_struct_oper_list / struct_conn / struct_conn_type / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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 |
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