data_9Z8J # _entry.id 9Z8J # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.414 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9Z8J pdb_00009z8j 10.2210/pdb9z8j/pdb WWPDB D_1000302219 ? ? BMRB 31284 ? 10.13018/BMR31284 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-05-27 _pdbx_audit_revision_history.part_number ? # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 9Z8J _pdbx_database_status.recvd_initial_deposition_date 2025-11-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs . _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Gelatinamin A: a figure-of-eight lasso peptide' _pdbx_database_related.db_id 31284 _pdbx_database_related.content_type unspecified # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 ajlink@princeton.edu Jamie Link ? 'principal investigator/group leader' 0000-0001-5066-9691 3 thomast@bce.au.dk Thomas Torring ? 'principal investigator/group leader' 0000-0001-5257-2121 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Johnson, T.G.' 1 0000-0002-6475-769X 'Zhu, A.' 2 0009-0007-0567-4740 'Svenningsen, T.' 3 0009-0004-3472-7627 'Merrild, A.' 4 0009-0005-0360-6176 'Wang, F.' 5 ? 'Andersen, F.D.' 6 ? 'Iwase, R.' 7 ? 'Viennet, T.' 8 ? 'Larsen, M.K.' 9 ? 'Link, A.J.' 10 0000-0001-5066-9691 'Torring, T.' 11 0000-0001-5257-2121 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Chembiochem _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1439-7633 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 27 _citation.language ? _citation.page_first e70378 _citation.page_last e70378 _citation.title 'Biosynthesis, Structure, and Antibiotic Properties of Gelatinamin A, a Triculamin-Like Lasso Peptide.' _citation.year 2026 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/cbic.70378 _citation.pdbx_database_id_PubMed 42138325 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Svenningsen, T.' 1 ? primary 'Merrild, A.' 2 ? primary 'Wang, F.' 3 ? primary 'Hansen, F.D.' 4 ? primary 'Johnson, T.G.' 5 ? primary 'Iwase, R.' 6 ? primary 'Viennet, T.' 7 ? primary 'Larsen, M.K.' 8 ? primary 'Link, A.J.' 9 0000-0001-5066-9691 primary 'Torring, T.' 10 0000-0001-5257-2121 # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description 'Gelatinamin A' _entity.formula_weight 1786.131 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code AKKSKPGDGKHGRGVKK _entity_poly.pdbx_seq_one_letter_code_can AKKSKPGDGKHGRGVKK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ALA n 1 2 LYS n 1 3 LYS n 1 4 SER n 1 5 LYS n 1 6 PRO n 1 7 GLY n 1 8 ASP n 1 9 GLY n 1 10 LYS n 1 11 HIS n 1 12 GLY n 1 13 ARG n 1 14 GLY n 1 15 VAL n 1 16 LYS n 1 17 LYS n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 17 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Brevibacillus gelatini' _entity_src_nat.pdbx_ncbi_taxonomy_id 1655277 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain PDF4 _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ALA 1 1 1 ALA ALA A . n A 1 2 LYS 2 2 2 LYS LYS A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 SER 4 4 4 SER SER A . n A 1 5 LYS 5 5 5 LYS LYS A . n A 1 6 PRO 6 6 6 PRO PRO A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 HIS 11 11 11 HIS HIS A . n A 1 12 GLY 12 12 12 GLY GLY A . n A 1 13 ARG 13 13 13 ARG ARG A . n A 1 14 GLY 14 14 14 GLY GLY A . n A 1 15 VAL 15 15 15 VAL VAL A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 LYS 17 17 17 LYS LYS A . n # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 2 2 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 3 3 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 4 4 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 5 5 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 6 6 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 7 7 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 8 8 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 9 9 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 10 10 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 11 11 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 12 12 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 13 13 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 14 14 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 15 15 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 16 16 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 17 17 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 18 18 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 19 19 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 20 20 Y 1 A ASP 8 ? OD2 ? A ASP 8 OD2 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9Z8J _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 9Z8J _struct.title 'Gelatinamin A: a figure-of-eight lasso peptide' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9Z8J _struct_keywords.text 'Lasso peptide, Antimycobacterial, Mechanically Interlocked Peptide, ANTIBIOTIC' _struct_keywords.pdbx_keywords ANTIBIOTIC # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9Z8J _struct_ref.pdbx_db_accession 9Z8J _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9Z8J _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 9Z8J _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 17 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # _pdbx_entry_details.entry_id 9Z8J _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 2 1 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 3 1 HZ1 A LYS 3 ? ? O A SER 4 ? ? 1.56 4 2 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 5 2 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 6 3 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 7 3 N A ALA 1 ? ? CG A ASP 8 ? ? 1.38 8 4 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.36 9 4 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 10 5 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 11 5 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 12 5 H A SER 4 ? ? O A ARG 13 ? ? 1.60 13 6 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.38 14 6 N A ALA 1 ? ? CG A ASP 8 ? ? 1.38 15 6 HZ1 A LYS 3 ? ? O A ARG 13 ? ? 1.60 16 7 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 17 7 N A ALA 1 ? ? CG A ASP 8 ? ? 1.38 18 8 N A ALA 1 ? ? CG A ASP 8 ? ? 1.36 19 8 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 20 9 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.36 21 9 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 22 10 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 23 10 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 24 11 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 25 11 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 26 12 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 27 12 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 28 13 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.36 29 13 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 30 14 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 31 14 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 32 15 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 33 15 N A ALA 1 ? ? CG A ASP 8 ? ? 1.38 34 16 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 35 16 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 36 17 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 37 17 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 38 17 O A VAL 15 ? ? HZ3 A LYS 17 ? ? 1.60 39 18 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.36 40 18 N A ALA 1 ? ? CG A ASP 8 ? ? 1.39 41 19 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.36 42 19 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 43 20 NZ A LYS 2 ? ? C A LYS 17 ? ? 1.37 44 20 N A ALA 1 ? ? CG A ASP 8 ? ? 1.37 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 123.92 118.30 5.62 0.90 N 2 2 N A ALA 1 ? ? CA A ALA 1 ? ? CB A ALA 1 ? ? 118.66 110.10 8.56 1.40 N 3 3 NE A ARG 13 ? ? CZ A ARG 13 ? ? NH1 A ARG 13 ? ? 123.70 120.30 3.40 0.50 N 4 4 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 124.49 118.30 6.19 0.90 N 5 5 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 124.04 118.30 5.74 0.90 N 6 7 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 124.73 118.30 6.43 0.90 N 7 11 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 123.97 118.30 5.67 0.90 N 8 18 CB A ASP 8 ? ? CG A ASP 8 ? ? OD1 A ASP 8 ? ? 124.05 118.30 5.75 0.90 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LYS A 2 ? ? -85.77 -97.34 2 1 SER A 4 ? ? -171.41 -167.53 3 1 ASP A 8 ? ? -142.93 -6.27 4 1 HIS A 11 ? ? -164.15 40.23 5 1 LYS A 16 ? ? -148.82 -159.99 6 2 LYS A 2 ? ? -112.32 -80.66 7 2 SER A 4 ? ? 174.25 -169.29 8 2 ASP A 8 ? ? 168.39 -0.02 9 2 HIS A 11 ? ? 72.08 47.77 10 2 ARG A 13 ? ? -89.75 -95.04 11 3 LYS A 2 ? ? -86.02 -149.44 12 3 SER A 4 ? ? 166.51 -173.43 13 3 ASP A 8 ? ? 106.76 -58.35 14 3 LYS A 10 ? ? -59.77 -5.76 15 3 HIS A 11 ? ? -175.25 58.40 16 4 LYS A 2 ? ? -100.29 -100.04 17 4 SER A 4 ? ? -176.73 -171.75 18 4 LYS A 10 ? ? -146.46 -57.25 19 5 LYS A 2 ? ? -88.91 -93.56 20 5 LYS A 3 ? ? 172.09 105.89 21 5 SER A 4 ? ? -165.41 -90.62 22 5 LYS A 5 ? ? -164.14 -55.18 23 5 ASP A 8 ? ? 139.71 -15.36 24 5 LYS A 10 ? ? -69.76 98.15 25 6 LYS A 2 ? ? -91.33 -106.66 26 6 SER A 4 ? ? -171.84 -168.87 27 6 ASP A 8 ? ? -160.09 38.74 28 6 HIS A 11 ? ? 76.16 56.82 29 6 ARG A 13 ? ? -82.48 -78.58 30 7 LYS A 2 ? ? -98.23 -79.30 31 7 LYS A 3 ? ? -170.66 -177.42 32 7 SER A 4 ? ? 93.88 178.71 33 7 ASP A 8 ? ? -142.34 35.80 34 7 LYS A 16 ? ? -69.83 97.97 35 8 LYS A 2 ? ? -86.69 -115.94 36 8 LYS A 3 ? ? -166.23 119.74 37 8 SER A 4 ? ? -176.96 -64.71 38 8 LYS A 5 ? ? -177.58 -53.35 39 8 HIS A 11 ? ? 90.28 50.50 40 8 ARG A 13 ? ? -74.95 -100.91 41 8 VAL A 15 ? ? -87.32 32.46 42 8 LYS A 16 ? ? -147.67 -112.21 43 9 LYS A 2 ? ? -79.76 -157.18 44 9 SER A 4 ? ? 173.11 -163.84 45 9 ASP A 8 ? ? 172.85 -20.60 46 9 LYS A 10 ? ? -77.86 41.73 47 9 HIS A 11 ? ? -171.95 75.18 48 9 LYS A 16 ? ? -164.37 -158.75 49 10 LYS A 3 ? ? 82.36 118.33 50 10 SER A 4 ? ? -163.43 -47.50 51 10 LYS A 5 ? ? 160.95 -61.49 52 10 ASP A 8 ? ? 83.85 26.82 53 10 LYS A 10 ? ? -147.23 53.67 54 10 HIS A 11 ? ? 77.56 -169.23 55 10 ARG A 13 ? ? -88.16 -112.98 56 11 LYS A 2 ? ? -89.57 -122.00 57 11 SER A 4 ? ? 177.59 166.62 58 11 PRO A 6 ? ? -81.48 35.73 59 11 ASP A 8 ? ? -160.74 26.19 60 11 HIS A 11 ? ? 79.16 86.94 61 12 LYS A 2 ? ? -126.93 -94.14 62 12 SER A 4 ? ? 174.06 179.99 63 12 PRO A 6 ? ? -81.29 48.31 64 12 ASP A 8 ? ? 175.42 1.08 65 12 HIS A 11 ? ? 76.37 36.44 66 12 ARG A 13 ? ? -87.77 -91.06 67 13 LYS A 3 ? ? 80.71 149.31 68 13 SER A 4 ? ? 170.37 -95.00 69 13 LYS A 5 ? ? -143.78 -58.04 70 13 PRO A 6 ? ? -79.53 47.65 71 13 ASP A 8 ? ? -179.85 24.82 72 13 HIS A 11 ? ? 91.69 156.23 73 13 ARG A 13 ? ? -113.28 -151.35 74 14 LYS A 2 ? ? -147.20 45.78 75 14 LYS A 3 ? ? 84.04 87.55 76 14 HIS A 11 ? ? 66.88 -154.29 77 14 ARG A 13 ? ? -137.59 -112.97 78 15 LYS A 3 ? ? 144.69 177.11 79 15 SER A 4 ? ? 122.01 -111.64 80 15 LYS A 5 ? ? -154.67 -51.26 81 15 ASP A 8 ? ? -160.47 -8.91 82 16 HIS A 11 ? ? 75.79 165.30 83 16 LYS A 16 ? ? -69.48 91.96 84 17 LYS A 2 ? ? -96.02 -77.88 85 17 SER A 4 ? ? 86.63 178.40 86 17 PRO A 6 ? ? -69.63 99.64 87 18 LYS A 3 ? ? 65.03 179.70 88 18 SER A 4 ? ? 77.50 176.90 89 18 ASP A 8 ? ? 129.07 -58.06 90 18 HIS A 11 ? ? 84.96 68.20 91 19 LYS A 2 ? ? -84.37 -146.53 92 19 SER A 4 ? ? -179.31 -170.37 93 19 PRO A 6 ? ? -81.74 34.36 94 19 HIS A 11 ? ? 67.81 175.52 95 20 SER A 4 ? ? 173.90 168.94 96 20 LYS A 16 ? ? -69.40 93.75 # loop_ _pdbx_validate_peptide_omega.id _pdbx_validate_peptide_omega.PDB_model_num _pdbx_validate_peptide_omega.auth_comp_id_1 _pdbx_validate_peptide_omega.auth_asym_id_1 _pdbx_validate_peptide_omega.auth_seq_id_1 _pdbx_validate_peptide_omega.PDB_ins_code_1 _pdbx_validate_peptide_omega.label_alt_id_1 _pdbx_validate_peptide_omega.auth_comp_id_2 _pdbx_validate_peptide_omega.auth_asym_id_2 _pdbx_validate_peptide_omega.auth_seq_id_2 _pdbx_validate_peptide_omega.PDB_ins_code_2 _pdbx_validate_peptide_omega.label_alt_id_2 _pdbx_validate_peptide_omega.omega 1 1 GLY A 12 ? ? ARG A 13 ? ? -145.85 2 2 LYS A 10 ? ? HIS A 11 ? ? 147.04 3 3 GLY A 9 ? ? LYS A 10 ? ? -144.82 4 4 ASP A 8 ? ? GLY A 9 ? ? 144.65 5 5 VAL A 15 ? ? LYS A 16 ? ? -141.56 6 6 VAL A 15 ? ? LYS A 16 ? ? -135.18 7 8 LYS A 10 ? ? HIS A 11 ? ? 146.42 8 12 VAL A 15 ? ? LYS A 16 ? ? -132.51 9 18 ASP A 8 ? ? GLY A 9 ? ? 145.42 # _pdbx_nmr_ensemble.entry_id 9Z8J _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 9Z8J _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '10 mg/mL Gelatinamin A, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label 'Gelatinamin A' _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component 'Gelatinamin A' _pdbx_nmr_exptl_sample.concentration 10 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mg/mL _pdbx_nmr_exptl_sample.isotopic_labeling 'natural abundance' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.1 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units M _pdbx_nmr_exptl_sample_conditions.label NMR _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '1H NMR with water suppression' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 1 '2D 1H-1H NOESY' 1 isotropic 4 1 1 '2D 1H-15N HSQC' 1 isotropic 5 1 1 '2D 1H-13C HSQC' 1 isotropic 6 1 1 '3D 1H-13C HSQC-TOCSY' 1 isotropic 8 1 1 '3D 1H-15N HSQC-TOCSY' 1 isotropic 9 1 1 '3D 1H-13C HSQC-NOESY' 1 isotropic 10 1 1 '3D 1H-15N HSQC-NOESY' 1 isotropic # _pdbx_nmr_refine.entry_id 9Z8J _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details 'MMFF94 using Avogadro' _pdbx_nmr_refine.software_ordinal 2 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' 'MestreLab (Mnova / MestReNova / MestReC)' ? MestreLab 2 'structure calculation' CYANA 2.1 'Guntert, Mumenthaler and Wuthrich' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASP N N N N 41 ASP CA C N S 42 ASP C C N N 43 ASP O O N N 44 ASP CB C N N 45 ASP CG C N N 46 ASP OD1 O N N 47 ASP OD2 O N N 48 ASP OXT O N N 49 ASP H H N N 50 ASP H2 H N N 51 ASP HA H N N 52 ASP HB2 H N N 53 ASP HB3 H N N 54 ASP HD2 H N N 55 ASP HXT H N N 56 GLY N N N N 57 GLY CA C N N 58 GLY C C N N 59 GLY O O N N 60 GLY OXT O N N 61 GLY H H N N 62 GLY H2 H N N 63 GLY HA2 H N N 64 GLY HA3 H N N 65 GLY HXT H N N 66 HIS N N N N 67 HIS CA C N S 68 HIS C C N N 69 HIS O O N N 70 HIS CB C N N 71 HIS CG C Y N 72 HIS ND1 N Y N 73 HIS CD2 C Y N 74 HIS CE1 C Y N 75 HIS NE2 N Y N 76 HIS OXT O N N 77 HIS H H N N 78 HIS H2 H N N 79 HIS HA H N N 80 HIS HB2 H N N 81 HIS HB3 H N N 82 HIS HD1 H N N 83 HIS HD2 H N N 84 HIS HE1 H N N 85 HIS HE2 H N N 86 HIS HXT H N N 87 LYS N N N N 88 LYS CA C N S 89 LYS C C N N 90 LYS O O N N 91 LYS CB C N N 92 LYS CG C N N 93 LYS CD C N N 94 LYS CE C N N 95 LYS NZ N N N 96 LYS OXT O N N 97 LYS H H N N 98 LYS H2 H N N 99 LYS HA H N N 100 LYS HB2 H N N 101 LYS HB3 H N N 102 LYS HG2 H N N 103 LYS HG3 H N N 104 LYS HD2 H N N 105 LYS HD3 H N N 106 LYS HE2 H N N 107 LYS HE3 H N N 108 LYS HZ1 H N N 109 LYS HZ2 H N N 110 LYS HZ3 H N N 111 LYS HXT H N N 112 PRO N N N N 113 PRO CA C N S 114 PRO C C N N 115 PRO O O N N 116 PRO CB C N N 117 PRO CG C N N 118 PRO CD C N N 119 PRO OXT O N N 120 PRO H H N N 121 PRO HA H N N 122 PRO HB2 H N N 123 PRO HB3 H N N 124 PRO HG2 H N N 125 PRO HG3 H N N 126 PRO HD2 H N N 127 PRO HD3 H N N 128 PRO HXT H N N 129 SER N N N N 130 SER CA C N S 131 SER C C N N 132 SER O O N N 133 SER CB C N N 134 SER OG O N N 135 SER OXT O N N 136 SER H H N N 137 SER H2 H N N 138 SER HA H N N 139 SER HB2 H N N 140 SER HB3 H N N 141 SER HG H N N 142 SER HXT H N N 143 VAL N N N N 144 VAL CA C N S 145 VAL C C N N 146 VAL O O N N 147 VAL CB C N N 148 VAL CG1 C N N 149 VAL CG2 C N N 150 VAL OXT O N N 151 VAL H H N N 152 VAL H2 H N N 153 VAL HA H N N 154 VAL HB H N N 155 VAL HG11 H N N 156 VAL HG12 H N N 157 VAL HG13 H N N 158 VAL HG21 H N N 159 VAL HG22 H N N 160 VAL HG23 H N N 161 VAL HXT H N N 162 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASP N CA sing N N 39 ASP N H sing N N 40 ASP N H2 sing N N 41 ASP CA C sing N N 42 ASP CA CB sing N N 43 ASP CA HA sing N N 44 ASP C O doub N N 45 ASP C OXT sing N N 46 ASP CB CG sing N N 47 ASP CB HB2 sing N N 48 ASP CB HB3 sing N N 49 ASP CG OD1 doub N N 50 ASP CG OD2 sing N N 51 ASP OD2 HD2 sing N N 52 ASP OXT HXT sing N N 53 GLY N CA sing N N 54 GLY N H sing N N 55 GLY N H2 sing N N 56 GLY CA C sing N N 57 GLY CA HA2 sing N N 58 GLY CA HA3 sing N N 59 GLY C O doub N N 60 GLY C OXT sing N N 61 GLY OXT HXT sing N N 62 HIS N CA sing N N 63 HIS N H sing N N 64 HIS N H2 sing N N 65 HIS CA C sing N N 66 HIS CA CB sing N N 67 HIS CA HA sing N N 68 HIS C O doub N N 69 HIS C OXT sing N N 70 HIS CB CG sing N N 71 HIS CB HB2 sing N N 72 HIS CB HB3 sing N N 73 HIS CG ND1 sing Y N 74 HIS CG CD2 doub Y N 75 HIS ND1 CE1 doub Y N 76 HIS ND1 HD1 sing N N 77 HIS CD2 NE2 sing Y N 78 HIS CD2 HD2 sing N N 79 HIS CE1 NE2 sing Y N 80 HIS CE1 HE1 sing N N 81 HIS NE2 HE2 sing N N 82 HIS OXT HXT sing N N 83 LYS N CA sing N N 84 LYS N H sing N N 85 LYS N H2 sing N N 86 LYS CA C sing N N 87 LYS CA CB sing N N 88 LYS CA HA sing N N 89 LYS C O doub N N 90 LYS C OXT sing N N 91 LYS CB CG sing N N 92 LYS CB HB2 sing N N 93 LYS CB HB3 sing N N 94 LYS CG CD sing N N 95 LYS CG HG2 sing N N 96 LYS CG HG3 sing N N 97 LYS CD CE sing N N 98 LYS CD HD2 sing N N 99 LYS CD HD3 sing N N 100 LYS CE NZ sing N N 101 LYS CE HE2 sing N N 102 LYS CE HE3 sing N N 103 LYS NZ HZ1 sing N N 104 LYS NZ HZ2 sing N N 105 LYS NZ HZ3 sing N N 106 LYS OXT HXT sing N N 107 PRO N CA sing N N 108 PRO N CD sing N N 109 PRO N H sing N N 110 PRO CA C sing N N 111 PRO CA CB sing N N 112 PRO CA HA sing N N 113 PRO C O doub N N 114 PRO C OXT sing N N 115 PRO CB CG sing N N 116 PRO CB HB2 sing N N 117 PRO CB HB3 sing N N 118 PRO CG CD sing N N 119 PRO CG HG2 sing N N 120 PRO CG HG3 sing N N 121 PRO CD HD2 sing N N 122 PRO CD HD3 sing N N 123 PRO OXT HXT sing N N 124 SER N CA sing N N 125 SER N H sing N N 126 SER N H2 sing N N 127 SER CA C sing N N 128 SER CA CB sing N N 129 SER CA HA sing N N 130 SER C O doub N N 131 SER C OXT sing N N 132 SER CB OG sing N N 133 SER CB HB2 sing N N 134 SER CB HB3 sing N N 135 SER OG HG sing N N 136 SER OXT HXT sing N N 137 VAL N CA sing N N 138 VAL N H sing N N 139 VAL N H2 sing N N 140 VAL CA C sing N N 141 VAL CA CB sing N N 142 VAL CA HA sing N N 143 VAL C O doub N N 144 VAL C OXT sing N N 145 VAL CB CG1 sing N N 146 VAL CB CG2 sing N N 147 VAL CB HB sing N N 148 VAL CG1 HG11 sing N N 149 VAL CG1 HG12 sing N N 150 VAL CG1 HG13 sing N N 151 VAL CG2 HG21 sing N N 152 VAL CG2 HG22 sing N N 153 VAL CG2 HG23 sing N N 154 VAL OXT HXT sing N N 155 # _pdbx_audit_support.funding_organization 'The Carlsberg Foundation' _pdbx_audit_support.country Denmark _pdbx_audit_support.grant_number CF22-1239 _pdbx_audit_support.ordinal 1 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 950 _pdbx_nmr_spectrometer.details 'equipped with a cryogenically cooled triple resonance probe' # _atom_sites.entry_id 9Z8J _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O # loop_ #