data_PRD_000217 # _pdbx_reference_molecule.prd_id PRD_000217 _pdbx_reference_molecule.name Daptomycin _pdbx_reference_molecule.represent_as polymer _pdbx_reference_molecule.type "Cyclic lipopeptide" _pdbx_reference_molecule.type_evidence_code ? _pdbx_reference_molecule.class Antibiotic _pdbx_reference_molecule.class_evidence_code ? _pdbx_reference_molecule.formula "C72 H101 N17 O26" _pdbx_reference_molecule.formula_weight 1620.671 _pdbx_reference_molecule.chem_comp_id ? _pdbx_reference_molecule.release_status REL _pdbx_reference_molecule.replaces ? _pdbx_reference_molecule.replaced_by ? _pdbx_reference_molecule.compound_details ;DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA. ; _pdbx_reference_molecule.description ; DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION. ; _pdbx_reference_molecule.representative_PDB_id_code 1xt7 # loop_ _pdbx_reference_entity_list.prd_id _pdbx_reference_entity_list.ref_entity_id _pdbx_reference_entity_list.component_id _pdbx_reference_entity_list.type _pdbx_reference_entity_list.details PRD_000217 1 1 polymer "PEPTIDE LIKE SEQUENCE RESIDUES 2 TO 14" PRD_000217 2 2 non-polymer "FATTY ACID RESIDUE" # _pdbx_reference_entity_nonpoly.prd_id PRD_000217 _pdbx_reference_entity_nonpoly.ref_entity_id 2 _pdbx_reference_entity_nonpoly.name "DECANOIC ACID" _pdbx_reference_entity_nonpoly.chem_comp_id DKA _pdbx_reference_entity_nonpoly.details ? # _pdbx_reference_entity_link.prd_id PRD_000217 _pdbx_reference_entity_link.link_id 1 _pdbx_reference_entity_link.link_class PN _pdbx_reference_entity_link.ref_entity_id_1 1 _pdbx_reference_entity_link.entity_seq_num_1 1 _pdbx_reference_entity_link.comp_id_1 TRP _pdbx_reference_entity_link.atom_id_1 N _pdbx_reference_entity_link.ref_entity_id_2 2 _pdbx_reference_entity_link.entity_seq_num_2 ? _pdbx_reference_entity_link.comp_id_2 DKA _pdbx_reference_entity_link.atom_id_2 C1 _pdbx_reference_entity_link.value_order sing _pdbx_reference_entity_link.component_1 1 _pdbx_reference_entity_link.component_2 2 _pdbx_reference_entity_link.details ? _pdbx_reference_entity_link.nonpoly_res_num_1 ? _pdbx_reference_entity_link.nonpoly_res_num_2 ? # loop_ _pdbx_reference_entity_poly_link.prd_id _pdbx_reference_entity_poly_link.ref_entity_id _pdbx_reference_entity_poly_link.link_id _pdbx_reference_entity_poly_link.atom_id_1 _pdbx_reference_entity_poly_link.comp_id_1 _pdbx_reference_entity_poly_link.entity_seq_num_1 _pdbx_reference_entity_poly_link.atom_id_2 _pdbx_reference_entity_poly_link.comp_id_2 _pdbx_reference_entity_poly_link.entity_seq_num_2 _pdbx_reference_entity_poly_link.value_order _pdbx_reference_entity_poly_link.component_id _pdbx_reference_entity_poly_link.details _pdbx_reference_entity_poly_link.insert_code_1 _pdbx_reference_entity_poly_link.insert_code_2 PRD_000217 1 1 C TRP 1 N DSG 2 sing 1 ? ? ? PRD_000217 1 2 C DSG 2 N ASP 3 sing 1 ? ? ? PRD_000217 1 3 C ASP 3 N THR 4 sing 1 ? ? ? PRD_000217 1 4 OG1 THR 4 C KYN 13 sing 1 ? ? ? PRD_000217 1 5 C THR 4 N GLY 5 sing 1 ? ? ? PRD_000217 1 6 C GLY 5 N ORN 6 sing 1 ? ? ? PRD_000217 1 7 C ORN 6 N ASP 7 sing 1 ? ? ? PRD_000217 1 8 C ASP 7 N DAL 8 sing 1 ? ? ? PRD_000217 1 9 C DAL 8 N ASP 9 sing 1 ? ? ? PRD_000217 1 10 C ASP 9 N GLY 10 sing 1 ? ? ? PRD_000217 1 11 C GLY 10 N DSN 11 sing 1 ? ? ? PRD_000217 1 12 C DSN 11 N LME 12 sing 1 ? ? ? PRD_000217 1 13 C LME 12 N KYN 13 sing 1 ? ? ? # _pdbx_reference_entity_poly.prd_id PRD_000217 _pdbx_reference_entity_poly.ref_entity_id 1 _pdbx_reference_entity_poly.db_code NOR00001 _pdbx_reference_entity_poly.db_name NOR _pdbx_reference_entity_poly.type peptide-like # _pdbx_reference_entity_sequence.prd_id PRD_000217 _pdbx_reference_entity_sequence.ref_entity_id 1 _pdbx_reference_entity_sequence.type peptide-like _pdbx_reference_entity_sequence.NRP_flag Y # loop_ _pdbx_reference_entity_poly_seq.prd_id _pdbx_reference_entity_poly_seq.ref_entity_id _pdbx_reference_entity_poly_seq.num _pdbx_reference_entity_poly_seq.mon_id _pdbx_reference_entity_poly_seq.parent_mon_id _pdbx_reference_entity_poly_seq.hetero _pdbx_reference_entity_poly_seq.observed PRD_000217 1 1 TRP TRP N Y PRD_000217 1 2 DSG ASN N Y PRD_000217 1 3 ASP ASP N Y PRD_000217 1 4 THR THR N Y PRD_000217 1 5 GLY GLY N Y PRD_000217 1 6 ORN ARG N Y PRD_000217 1 7 ASP ASP N Y PRD_000217 1 8 DAL ALA N Y PRD_000217 1 9 ASP ASP N Y PRD_000217 1 10 GLY GLY N Y PRD_000217 1 11 DSN SER N Y PRD_000217 1 12 LME GLU N Y PRD_000217 1 13 KYN ? N Y # _pdbx_reference_entity_src_nat.prd_id PRD_000217 _pdbx_reference_entity_src_nat.ref_entity_id 1 _pdbx_reference_entity_src_nat.ordinal 1 _pdbx_reference_entity_src_nat.taxid 67294 _pdbx_reference_entity_src_nat.organism_scientific "Streptomyces roseosporus" _pdbx_reference_entity_src_nat.source ? _pdbx_reference_entity_src_nat.db_code NOR00001 _pdbx_reference_entity_src_nat.db_name Norine _pdbx_reference_entity_src_nat.strain ? # loop_ _pdbx_prd_audit.prd_id _pdbx_prd_audit.date _pdbx_prd_audit.processing_site _pdbx_prd_audit.action_type PRD_000217 2012-02-08 RCSB "Create molecule" PRD_000217 2012-07-09 PDBE "Other modification" PRD_000217 2012-07-31 RCSB "Other modification" PRD_000217 2012-12-12 RCSB "Initial release" PRD_000217 2013-06-03 RCSB "Other modification" PRD_000217 2017-05-04 RCSB "Other modification" PRD_000217 2023-09-20 PDBE "Modify audit" #