data_PRD_002404
# 
_pdbx_reference_molecule.prd_id                       PRD_002404 
_pdbx_reference_molecule.name                         "Dynobactin A" 
_pdbx_reference_molecule.represent_as                 polymer 
_pdbx_reference_molecule.type                         "Cyclic peptide" 
_pdbx_reference_molecule.type_evidence_code           "Dynobactin A structure elucidation by Cryo-EM microED" 
_pdbx_reference_molecule.class                        "Antibiotic, Antimicrobial" 
_pdbx_reference_molecule.class_evidence_code          "MICs for 8-64 micrograms per mL against Gram-negative bacteria (e.g. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) " 
_pdbx_reference_molecule.formula                      "C60 H78 N18 O16" 
_pdbx_reference_molecule.formula_weight               1307.372 
_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             "Dynobactin A is a decapeptide (1-WNSNVHSYRF-10) with 2 closed rings. One carbon-carbon bond formed between the C6 of Trp (W1) and the beta-carbon of Asn (N4). Second an unusual nitrogen-carbon linkage formed between the imidazole N-Epsilon-2 of His (H6) and the beta-carbon of Tyr (Y8)." 
_pdbx_reference_molecule.description                  "10mer peptide with distinct cyclophane rings." 
_pdbx_reference_molecule.representative_PDB_id_code   7R1V 
# 
_pdbx_reference_entity_list.prd_id          PRD_002404 
_pdbx_reference_entity_list.ref_entity_id   1 
_pdbx_reference_entity_list.component_id    1 
_pdbx_reference_entity_list.type            polymer 
_pdbx_reference_entity_list.details         . 
# 
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_002404 1 1  C   TRP 1 N  ASN 2  sing 1 . . . 
PRD_002404 1 2  CH2 TRP 1 CB ASN 4  sing 1 . . . 
PRD_002404 1 3  C   ASN 2 N  SER 3  sing 1 . . . 
PRD_002404 1 4  C   SER 3 N  ASN 4  sing 1 . . . 
PRD_002404 1 5  C   ASN 4 N  VAL 5  sing 1 . . . 
PRD_002404 1 6  C   VAL 5 N  HIS 6  sing 1 . . . 
PRD_002404 1 7  C   HIS 6 N  SER 7  sing 1 . . . 
PRD_002404 1 8  NE2 HIS 6 CB TYR 8  sing 1 . . . 
PRD_002404 1 9  C   SER 7 N  TYR 8  sing 1 . . . 
PRD_002404 1 10 C   TYR 8 N  ARG 9  sing 1 . . . 
PRD_002404 1 11 C   ARG 9 N  PHE 10 sing 1 . . . 
# 
_pdbx_reference_entity_poly.prd_id          PRD_002404 
_pdbx_reference_entity_poly.ref_entity_id   1 
_pdbx_reference_entity_poly.db_code         A0A1C0U7H2 
_pdbx_reference_entity_poly.db_name         UNP 
_pdbx_reference_entity_poly.type            peptide-like 
# 
_pdbx_reference_entity_sequence.prd_id          PRD_002404 
_pdbx_reference_entity_sequence.ref_entity_id   1 
_pdbx_reference_entity_sequence.type            peptide-like 
_pdbx_reference_entity_sequence.NRP_flag        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_002404 1 1  TRP TRP N Y 
PRD_002404 1 2  ASN ASN N Y 
PRD_002404 1 3  SER SER N Y 
PRD_002404 1 4  ASN ASN N Y 
PRD_002404 1 5  VAL VAL N Y 
PRD_002404 1 6  HIS HIS N Y 
PRD_002404 1 7  SER SER N Y 
PRD_002404 1 8  TYR TYR N Y 
PRD_002404 1 9  ARG ARG N Y 
PRD_002404 1 10 PHE PHE N Y 
# 
loop_
_pdbx_prd_audit.prd_id 
_pdbx_prd_audit.date 
_pdbx_prd_audit.processing_site 
_pdbx_prd_audit.action_type 
PRD_002404 2022-03-02 PDBE "Create molecule"    
PRD_002404 2022-09-28 RCSB "Initial release"    
PRD_002404 2024-03-26 PDBE "Other modification" 
# 
_pdbx_reference_entity_src_nat.db_code               ? 
_pdbx_reference_entity_src_nat.db_name               ? 
_pdbx_reference_entity_src_nat.ordinal               1 
_pdbx_reference_entity_src_nat.organism_scientific   "Photorhabdus australis" 
_pdbx_reference_entity_src_nat.prd_id                PRD_002404 
_pdbx_reference_entity_src_nat.ref_entity_id         1 
_pdbx_reference_entity_src_nat.source                ? 
_pdbx_reference_entity_src_nat.strain                ? 
_pdbx_reference_entity_src_nat.taxid                 286156 
# 
