data_PRD_002583
# 
_pdbx_reference_molecule.prd_id                       PRD_002583 
_pdbx_reference_molecule.name                         "Peptidoglycan disaccharide tetrapeptide" 
_pdbx_reference_molecule.represent_as                 polymer 
_pdbx_reference_molecule.type                         Glycopeptide 
_pdbx_reference_molecule.type_evidence_code           "Peptidoglycan monomer from Corynebacterium jeikeium or Mycobacterium tuberculosis." 
_pdbx_reference_molecule.class                        Inducer 
_pdbx_reference_molecule.class_evidence_code          "Peptidoglycan components can induce immune response." 
_pdbx_reference_molecule.formula                      "C37 H63 N9 O19" 
_pdbx_reference_molecule.formula_weight               937.945 
_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             GlcNAc-MurNAc-L-ALA-D-iGluNH2-m-DAPNH2-D-ALA 
_pdbx_reference_molecule.description                  "Peptidoglycan is composed of glycan strands and peptide stems. In this instance the glycan strands are made of N-acetylmuramic acid/MurNAc (MUB) and N-acetylglucosamine/GlcNAc (NAG) linked by beta-1,4 glycosidic bonds.  Peptide stems, in this instance, are attach to MurNAc and consist of L-alanine, gamma D-glutamine/D-Gln (ZGL), meso-diaminopimelic acid/m-DAP (JGO), and D-alanine (DAP)." 
_pdbx_reference_molecule.representative_PDB_id_code   8PXY 
# 
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_002583 1 1 polymer  . 
PRD_002583 2 2 branched . 
# 
_pdbx_reference_entity_link.prd_id              PRD_002583 
_pdbx_reference_entity_link.link_id             1 
_pdbx_reference_entity_link.link_class          PP 
_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           ALA 
_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    1 
_pdbx_reference_entity_link.comp_id_2           MUB 
_pdbx_reference_entity_link.atom_id_2           C10 
_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_002583 1 1 C  ALA 1 N  ZGL 2 sing 1 . . . 
PRD_002583 1 2 C  ZGL 2 N  JGO 3 sing 1 . . . 
PRD_002583 1 3 C  JGO 3 N  DAL 4 sing 1 . . . 
PRD_002583 2 4 O4 MUB 1 C1 NAG 2 sing 2 . . . 
# 
loop_
_pdbx_reference_entity_poly.prd_id 
_pdbx_reference_entity_poly.ref_entity_id 
_pdbx_reference_entity_poly.db_code 
_pdbx_reference_entity_poly.db_name 
_pdbx_reference_entity_poly.type 
PRD_002583 1 . . peptide-like    
PRD_002583 2 . . oligosaccharide 
# 
loop_
_pdbx_reference_entity_sequence.prd_id 
_pdbx_reference_entity_sequence.ref_entity_id 
_pdbx_reference_entity_sequence.type 
_pdbx_reference_entity_sequence.NRP_flag 
PRD_002583 1 peptide-like N 
PRD_002583 2 saccharide   N 
# 
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_002583 1 1 ALA ALA N Y 
PRD_002583 1 2 ZGL .   N Y 
PRD_002583 1 3 JGO LYS N Y 
PRD_002583 1 4 DAL .   N Y 
PRD_002583 2 1 MUB .   N Y 
PRD_002583 2 2 NAG .   N Y 
# 
_pdbx_reference_entity_src_nat.prd_id                PRD_002583 
_pdbx_reference_entity_src_nat.ref_entity_id         1 
_pdbx_reference_entity_src_nat.ordinal               1 
_pdbx_reference_entity_src_nat.taxid                 38289 
_pdbx_reference_entity_src_nat.organism_scientific   "Corynebacterium jeikeium" 
_pdbx_reference_entity_src_nat.source                . 
_pdbx_reference_entity_src_nat.db_code               . 
_pdbx_reference_entity_src_nat.db_name               . 
_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_002583 2024-10-05 PDBE "Create molecule" 
PRD_002583 2024-10-16 RCSB "Initial release" 
# 
