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"       
# 
