data_2KTN # _entry.id 2KTN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.367 _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 2KTN pdb_00002ktn 10.2210/pdb2ktn/pdb RCSB RCSB101559 ? ? WWPDB D_1000101559 ? ? # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2023-03-22 _pdbx_database_PDB_obs_spr.pdb_id 8C5J _pdbx_database_PDB_obs_spr.replace_pdb_id 2KTN _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1AJ1 unspecified 'SOLUTION STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE' PDB 1MQX unspecified 'SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN MEOH/H2O MIXTURE' PDB 1MQY unspecified 'SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN DPC MICELLES' PDB 1MQZ unspecified 'SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN BOUND TO LIPID II IN DPC MICELLES' PDB 1QOW unspecified 'CRYSTAL STRUCTURE OF THE TUPE B LANTIBIOTIC MERSACIDIN' PDB 1W9N unspecified 'SOLUTION STRUCTURE OF THE LANTIBIOTIC EPILANCIN 15X' PDB 1WCO unspecified 'SOLUTION STRUCTURE OF NISIN AND LIPID II COMPLEX' PDB 2DDE unspecified 'SOLUTION STRUCTURE OF THE LANTIBIOTIC CINNAMYCIN COMPLEXED WITH LYSOPHOSPHATIDYLETHANOLAMINE' PDB 2KTO unspecified 'SOLUTION STRUCTURE OF LCH-BETA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC LICHENICIDIN VK21 A2' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KTN _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-02-05 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_mr OBS _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mineev, K.S.' 1 'Shenkarev, Z.O.' 2 'Ovchinnikova, T.V.' 3 'Arseniev, A.S.' 4 # _citation.id primary _citation.title ;Isolation, Structure Elucidation, and Synergistic Antibacterial Activity of a Novel Two-Component Lantibiotic Lichenicidin from Bacillus Licheniformis Vk21. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 49 _citation.page_first 6462 _citation.page_last ? _citation.year 2010 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20578714 _citation.pdbx_database_id_DOI 10.1021/BI100871B # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shenkarev, Z.O.' 1 ? primary 'Finkina, E.I.' 2 ? primary 'Nurmukhamedova, E.K.' 3 ? primary 'Balandin, S.V.' 4 ? primary 'Mineev, K.S.' 5 ? primary 'Nadezhdin, K.D.' 6 ? primary 'Yakimenko, Z.A.' 7 ? primary 'Tagaev, A.A.' 8 ? primary 'Temirov, Y.V.' 9 ? primary 'Arseniev, A.S.' 10 ? primary 'Ovchinnikova, T.V.' 11 ? # _cell.entry_id 2KTN _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2KTN _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description 'LICHENICIDIN VK21 A1' _entity.formula_weight 3261.921 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'UNP residues 44-74' _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(2KT)I(DBB)L(DHA)(DBU)CAIL(DAL)KPLGNNGYLC(DBB)V(DBB)KECMPSCN' _entity_poly.pdbx_seq_one_letter_code_can XITLSTCAILAKPLGNNGYLCTVTKECMPSCN _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 2KT n 1 2 ILE n 1 3 DBB n 1 4 LEU n 1 5 DHA n 1 6 DBU n 1 7 CYS n 1 8 ALA n 1 9 ILE n 1 10 LEU n 1 11 DAL n 1 12 LYS n 1 13 PRO n 1 14 LEU n 1 15 GLY n 1 16 ASN n 1 17 ASN n 1 18 GLY n 1 19 TYR n 1 20 LEU n 1 21 CYS n 1 22 DBB n 1 23 VAL n 1 24 DBB n 1 25 LYS n 1 26 GLU n 1 27 CYS n 1 28 MET n 1 29 PRO n 1 30 SER n 1 31 CYS n 1 32 ASN 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 ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'BACILLUS LICHENIFORMIS' _entity_src_nat.pdbx_ncbi_taxonomy_id 279010 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain VK21 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LANLA_BACLI _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P86475 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KTN _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 32 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P86475 _struct_ref_seq.db_align_beg 43 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 74 _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 32 # 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 2KT non-polymer . '2-KETOBUTYRIC ACID' '2-OXOBUTANOIC ACID' 'C4 H6 O3' 102.089 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DAL 'D-peptide linking' . D-ALANINE ? 'C3 H7 N O2' 89.093 DBB 'D-peptide linking' . 'D-ALPHA-AMINOBUTYRIC ACID' ? 'C4 H9 N O2' 103.120 DBU 'peptide linking' n '(2Z)-2-AMINOBUT-2-ENOIC ACID' Z-DEHYDROBUTYRINE 'C4 H7 N O2' 101.104 DHA 'peptide linking' n '2-AMINO-ACRYLIC ACID' 2,3-DIDEHYDROALANINE 'C3 H5 N O2' 87.077 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D 1H-1H COSY' 1 2 2 '2D 1H-1H NOESY' 1 3 3 '2D 1H-1H TOCSY' 1 4 4 '2D 1H-13C HSQC' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure AMBIENT _pdbx_nmr_exptl_sample_conditions.pH 3.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '0.5 MM LCHA-1, 500 MG [U-100% 2H] METHANOL-2, METHANOL' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 700 # _pdbx_nmr_refine.entry_id 2KTN _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2KTN _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' # _pdbx_nmr_representative.entry_id 2KTN _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement 'CYANA 2.1' ? 'GUNTERT, MUMENTHALER' 1 'structure solution' 'CARA 1.5.3' ? ? 2 'structure solution' 'TOPSPIN 2.1' ? ? 3 'structure solution' 'CYANA 2.1' ? ? 4 # _exptl.entry_id 2KTN _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2KTN _struct.title 'Spatial structure of Lch-alpha peptide from two-component lantibiotic system Lichenicidin VK21' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KTN _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'LICHENICIDIN VK21, LANTIBIOTICS, LCHA, ANTIBIOTIC, LANTHIONINE, THIOESTER, TWO-COMPONENT LANTIBIOTIC SYSTEM' # _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_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id VAL _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 23 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id CYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 27 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id VAL _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 23 _struct_conf.end_auth_comp_id CYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 27 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A 2KT 1 C1 ? ? ? 1_555 A ILE 2 N ? ? A 2KT 1 A ILE 2 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale2 covale one ? A ILE 2 C ? ? ? 1_555 A DBB 3 N ? ? A ILE 2 A DBB 3 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale3 covale both ? A DBB 3 C ? ? ? 1_555 A LEU 4 N ? ? A DBB 3 A LEU 4 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale4 covale none ? A DBB 3 CB ? ? ? 1_555 A CYS 7 SG ? ? A DBB 3 A CYS 7 1_555 ? ? ? ? ? ? ? 1.823 ? ? covale5 covale both ? A LEU 4 C ? ? ? 1_555 A DHA 5 N ? ? A LEU 4 A DHA 5 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale6 covale both ? A DHA 5 C ? ? ? 1_555 A DBU 6 N ? ? A DHA 5 A DBU 6 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale7 covale both ? A DBU 6 C ? ? ? 1_555 A CYS 7 N ? ? A DBU 6 A CYS 7 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale8 covale both ? A LEU 10 C ? ? ? 1_555 A DAL 11 N ? ? A LEU 10 A DAL 11 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale9 covale both ? A DAL 11 C ? ? ? 1_555 A LYS 12 N ? ? A DAL 11 A LYS 12 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale10 covale none ? A DAL 11 CB ? ? ? 1_555 A CYS 21 SG ? ? A DAL 11 A CYS 21 1_555 ? ? ? ? ? ? ? 1.813 ? ? covale11 covale one ? A CYS 21 C ? ? ? 1_555 A DBB 22 N ? ? A CYS 21 A DBB 22 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale12 covale both ? A DBB 22 C ? ? ? 1_555 A VAL 23 N ? ? A DBB 22 A VAL 23 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale13 covale none ? A DBB 22 CB ? ? ? 1_555 A CYS 27 SG ? ? A DBB 22 A CYS 27 1_555 ? ? ? ? ? ? ? 1.818 ? ? covale14 covale one ? A VAL 23 C ? ? ? 1_555 A DBB 24 N ? ? A VAL 23 A DBB 24 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale15 covale both ? A DBB 24 C ? ? ? 1_555 A LYS 25 N ? ? A DBB 24 A LYS 25 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale16 covale none ? A DBB 24 CB ? ? ? 1_555 A CYS 31 SG ? ? A DBB 24 A CYS 31 1_555 ? ? ? ? ? ? ? 1.868 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2KTN _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2KTN _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 # loop_ _atom_type.symbol C H N O S # 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 2KT 1 1 1 2KT 2KT A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 DBB 3 3 3 DBB DBB A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 DHA 5 5 5 DHA DHA A . n A 1 6 DBU 6 6 6 DBU DBU A . n A 1 7 CYS 7 7 7 CYS CYS A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 ILE 9 9 9 ILE ILE A . n A 1 10 LEU 10 10 10 LEU LEU A . n A 1 11 DAL 11 11 11 DAL DAL A . n A 1 12 LYS 12 12 12 LYS LYS A . n A 1 13 PRO 13 13 13 PRO PRO A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 ASN 16 16 16 ASN ASN A . n A 1 17 ASN 17 17 17 ASN ASN A . n A 1 18 GLY 18 18 18 GLY GLY A . n A 1 19 TYR 19 19 19 TYR TYR A . n A 1 20 LEU 20 20 20 LEU LEU A . n A 1 21 CYS 21 21 21 CYS CYS A . n A 1 22 DBB 22 22 22 DBB DBB A . n A 1 23 VAL 23 23 23 VAL VAL A . n A 1 24 DBB 24 24 24 DBB DBB A . n A 1 25 LYS 25 25 25 LYS LYS A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 CYS 27 27 27 CYS CYS A . n A 1 28 MET 28 28 28 MET MET A . n A 1 29 PRO 29 29 29 PRO PRO A . n A 1 30 SER 30 30 30 SER SER A . n A 1 31 CYS 31 31 31 CYS CYS A . n A 1 32 ASN 32 32 32 ASN ASN A . n # _pdbx_molecule_features.prd_id PRD_000197 _pdbx_molecule_features.name 'ALPHA LICHENICIDIN PREPEPTIDE' _pdbx_molecule_features.type Polypeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AMINO ACIDS AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR. ; # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000197 _pdbx_molecule.asym_id A # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A DBB 3 A DBB 3 ? THR 'POST-TRANSLATIONAL MODIFICATION' 2 A DHA 5 A DHA 5 ? ALA 'POST-TRANSLATIONAL MODIFICATION' 3 A DBU 6 A DBU 6 ? THR 'POST-TRANSLATIONAL MODIFICATION' 4 A DAL 11 A DAL 11 ? SER 'POST-TRANSLATIONAL MODIFICATION' 5 A DBB 22 A DBB 22 ? THR 'POST-TRANSLATIONAL MODIFICATION' 6 A DBB 24 A DBB 24 ? THR 'POST-TRANSLATIONAL MODIFICATION' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_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_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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2010-07-21 2 'Structure model' 1 1 2011-06-14 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-07-27 5 'Structure model' 1 4 2011-08-10 6 'Structure model' 1 5 2012-12-12 7 'Structure model' 1 6 2023-03-22 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 7 'Structure model' repository Obsolete ? ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' Other 9 6 'Structure model' Other 10 7 'Structure model' Advisory 11 7 'Structure model' 'Data collection' 12 7 'Structure model' 'Database references' 13 7 'Structure model' 'Derived calculations' 14 7 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 7 'Structure model' database_2 2 7 'Structure model' pdbx_database_PDB_obs_spr 3 7 'Structure model' pdbx_database_status 4 7 'Structure model' pdbx_nmr_spectrometer 5 7 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 7 'Structure model' '_database_2.pdbx_DOI' 2 7 'Structure model' '_database_2.pdbx_database_accession' 3 7 'Structure model' '_pdbx_database_status.status_code' 4 7 'Structure model' '_pdbx_database_status.status_code_mr' 5 7 'Structure model' '_pdbx_nmr_spectrometer.model' 6 7 'Structure model' '_struct_conn.pdbx_dist_value' 7 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 7 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 7 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 10 7 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 11 7 'Structure model' '_struct_conn.ptnr2_label_atom_id' 12 7 'Structure model' '_struct_conn.ptnr2_label_comp_id' 13 7 'Structure model' '_struct_conn.ptnr2_label_seq_id' # _pdbx_entry_details.entry_id 2KTN _pdbx_entry_details.compound_details ;LICHENICIDIN VK21 A1 IS A LANTIBIOTIC. THE LANTIBIOTICS ARE ARE CHARACTERIZED BY THIOESTER AMINO ACIDS LANTHIONINE AND/OR METHYLLANTHIONINE. HERE, LICHENICIDIN VK21 IS REPRESENTED BY THE SEQUENCE (SEQRES) ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id LchA-1 0.5 ? mM ? 1 methanol-2 500 ? mg/mL '[U-100% 2H]' 1 # 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 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 2 2 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 3 3 O A DBB 24 ? ? N A GLU 26 ? ? 2.18 4 4 O A DBB 24 ? ? N A GLU 26 ? ? 2.18 5 5 O A DBB 24 ? ? N A GLU 26 ? ? 2.18 6 6 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 7 7 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 8 8 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 9 9 O A DBB 24 ? ? N A GLU 26 ? ? 2.18 10 10 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 11 12 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 12 13 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 13 14 O A DBB 24 ? ? N A GLU 26 ? ? 2.18 14 15 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 15 16 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 16 17 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 17 18 O A DBB 24 ? ? N A GLU 26 ? ? 2.19 # 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 LEU A 4 ? ? -30.82 129.07 2 1 LEU A 10 ? ? -83.83 34.48 3 1 DAL A 11 ? ? -44.56 170.39 4 1 LYS A 12 ? ? 173.93 130.19 5 1 LEU A 14 ? ? 44.63 -164.85 6 1 ASN A 17 ? ? -179.50 -80.84 7 1 TYR A 19 ? ? -54.96 -175.30 8 1 LEU A 20 ? ? -75.67 47.73 9 1 LYS A 25 ? ? -23.81 -35.51 10 2 LEU A 4 ? ? -30.61 129.63 11 2 LYS A 12 ? ? -150.09 80.99 12 2 ASN A 17 ? ? -54.43 178.01 13 2 TYR A 19 ? ? -76.98 -166.56 14 2 LEU A 20 ? ? -44.97 157.62 15 2 LYS A 25 ? ? -23.70 -35.42 16 2 SER A 30 ? ? -78.63 26.99 17 3 LEU A 4 ? ? -30.70 130.07 18 3 DAL A 11 ? ? -65.66 177.95 19 3 PRO A 13 ? ? -69.73 -163.70 20 3 LEU A 14 ? ? -57.22 -163.58 21 3 ASN A 16 ? ? 46.27 -164.98 22 3 ASN A 17 ? ? -44.95 -70.15 23 3 LYS A 25 ? ? -23.58 -35.50 24 3 SER A 30 ? ? -78.68 27.87 25 4 LEU A 4 ? ? -30.69 129.23 26 4 CYS A 7 ? ? -56.98 -82.77 27 4 LEU A 10 ? ? -90.22 40.02 28 4 PRO A 13 ? ? -69.71 -163.83 29 4 ASN A 16 ? ? -54.07 -172.50 30 4 TYR A 19 ? ? -56.75 -162.72 31 4 LYS A 25 ? ? -22.99 -36.09 32 4 SER A 30 ? ? -79.25 26.98 33 4 CYS A 31 ? ? -91.00 40.46 34 5 LEU A 4 ? ? -30.70 129.50 35 5 DAL A 11 ? ? -65.56 -140.56 36 5 PRO A 13 ? ? -69.81 -175.31 37 5 LEU A 14 ? ? -79.51 -163.75 38 5 ASN A 16 ? ? 44.45 95.58 39 5 ASN A 17 ? ? 53.42 -177.85 40 5 TYR A 19 ? ? -106.04 -169.75 41 5 LYS A 25 ? ? -23.51 -35.54 42 5 SER A 30 ? ? -78.60 27.58 43 6 LEU A 4 ? ? -30.70 132.19 44 6 LYS A 12 ? ? 34.34 80.96 45 6 ASN A 16 ? ? -54.76 -166.64 46 6 ASN A 17 ? ? 49.89 -85.37 47 6 TYR A 19 ? ? -58.26 -175.05 48 6 LYS A 25 ? ? -23.83 -35.38 49 6 SER A 30 ? ? -78.73 28.04 50 7 LEU A 4 ? ? -30.72 129.61 51 7 DAL A 11 ? ? -62.97 -115.74 52 7 LYS A 12 ? ? -34.08 142.08 53 7 PRO A 13 ? ? -69.76 -175.82 54 7 ASN A 16 ? ? -123.86 -166.37 55 7 TYR A 19 ? ? -62.86 -175.04 56 7 LYS A 25 ? ? -23.60 -35.45 57 7 SER A 30 ? ? -78.73 28.06 58 8 LEU A 4 ? ? -30.66 130.53 59 8 DAL A 11 ? ? -65.93 -168.87 60 8 LEU A 14 ? ? 46.49 -173.90 61 8 ASN A 16 ? ? 52.15 171.63 62 8 LYS A 25 ? ? -23.92 -35.20 63 8 SER A 30 ? ? -78.60 28.13 64 9 LEU A 4 ? ? -30.70 129.58 65 9 DAL A 11 ? ? -62.28 -148.01 66 9 PRO A 13 ? ? -69.75 -173.48 67 9 TYR A 19 ? ? -67.38 -174.77 68 9 LYS A 25 ? ? -23.08 -35.89 69 9 SER A 30 ? ? -79.08 27.82 70 10 DBB A 3 ? ? 144.99 -22.63 71 10 LEU A 4 ? ? -30.74 129.46 72 10 LYS A 12 ? ? 169.47 63.96 73 10 ASN A 16 ? ? -158.82 19.34 74 10 LEU A 20 ? ? -75.49 48.57 75 10 LYS A 25 ? ? -24.12 -35.07 76 10 SER A 30 ? ? -78.81 27.96 77 11 LEU A 4 ? ? -30.70 129.64 78 11 LEU A 10 ? ? -95.60 37.76 79 11 LYS A 12 ? ? 170.77 142.91 80 11 PRO A 13 ? ? -69.74 -163.79 81 11 TYR A 19 ? ? -115.01 -162.48 82 11 LYS A 25 ? ? -24.23 -35.26 83 11 SER A 30 ? ? -78.88 27.96 84 12 DBB A 3 ? ? 144.42 -42.31 85 12 LEU A 4 ? ? -30.56 129.99 86 12 LEU A 10 ? ? -95.17 33.89 87 12 DAL A 11 ? ? 45.56 -173.20 88 12 LYS A 12 ? ? 171.02 156.77 89 12 LEU A 14 ? ? -61.68 -163.61 90 12 ASN A 16 ? ? -157.65 18.67 91 12 ASN A 17 ? ? 46.31 97.77 92 12 TYR A 19 ? ? -55.33 -163.82 93 12 LEU A 20 ? ? -172.62 28.81 94 12 LYS A 25 ? ? -24.18 -35.11 95 12 SER A 30 ? ? -78.82 27.78 96 13 LEU A 4 ? ? -30.62 130.03 97 13 DAL A 11 ? ? -65.57 -165.45 98 13 ASN A 16 ? ? -151.85 19.60 99 13 ASN A 17 ? ? -55.16 -164.99 100 13 LYS A 25 ? ? -23.67 -35.41 101 13 SER A 30 ? ? -78.75 28.01 102 14 LEU A 4 ? ? -30.66 130.80 103 14 DAL A 11 ? ? -65.63 -142.72 104 14 LYS A 12 ? ? -35.06 143.13 105 14 PRO A 13 ? ? -69.73 -166.51 106 14 ASN A 16 ? ? 47.00 -166.05 107 14 ASN A 17 ? ? 50.61 -85.24 108 14 TYR A 19 ? ? -67.92 -174.50 109 14 LYS A 25 ? ? -23.45 -35.60 110 14 SER A 30 ? ? -78.64 27.79 111 15 DBB A 3 ? ? 143.83 -19.97 112 15 LEU A 4 ? ? -30.71 129.59 113 15 PRO A 13 ? ? -69.79 -164.21 114 15 ASN A 17 ? ? -177.81 -84.94 115 15 LEU A 20 ? ? -65.63 -165.05 116 15 LYS A 25 ? ? -23.68 -35.36 117 15 SER A 30 ? ? -78.70 27.86 118 16 LEU A 4 ? ? -30.62 129.55 119 16 DAL A 11 ? ? -65.65 -148.47 120 16 TYR A 19 ? ? -114.95 -169.70 121 16 LYS A 25 ? ? -23.67 -35.50 122 16 SER A 30 ? ? -78.90 28.16 123 17 LYS A 12 ? ? 35.80 51.86 124 17 LEU A 14 ? ? -107.75 -166.10 125 17 ASN A 16 ? ? -143.15 45.64 126 17 ASN A 17 ? ? 66.41 -2.97 127 17 TYR A 19 ? ? -58.73 -175.11 128 17 LEU A 20 ? ? -59.04 -174.75 129 17 LYS A 25 ? ? -23.63 -35.52 130 17 SER A 30 ? ? -78.55 27.16 131 18 LEU A 4 ? ? -30.63 129.52 132 18 DAL A 11 ? ? -65.51 -82.28 133 18 LYS A 12 ? ? -178.74 143.78 134 18 LEU A 14 ? ? 42.16 -167.20 135 18 ASN A 17 ? ? 49.64 -85.58 136 18 TYR A 19 ? ? -65.97 -173.91 137 18 LYS A 25 ? ? -23.76 -35.36 138 18 SER A 30 ? ? -78.72 27.73 139 19 DBB A 3 ? ? 143.92 -18.51 140 19 LEU A 4 ? ? -30.73 129.76 141 19 LEU A 10 ? ? -96.79 37.18 142 19 DAL A 11 ? ? -173.20 -92.34 143 19 LYS A 12 ? ? -179.87 130.17 144 19 ASN A 16 ? ? 54.19 168.79 145 19 ASN A 17 ? ? 179.49 -76.95 146 19 TYR A 19 ? ? -75.83 -164.74 147 19 LYS A 25 ? ? -24.12 -35.22 148 19 SER A 30 ? ? -78.65 27.19 149 20 LEU A 4 ? ? -30.78 129.41 150 20 DAL A 11 ? ? -65.35 -127.14 151 20 PRO A 13 ? ? -69.77 -163.45 152 20 LEU A 14 ? ? -59.47 -163.61 153 20 ASN A 16 ? ? -141.08 57.25 154 20 ASN A 17 ? ? -176.76 127.42 155 20 TYR A 19 ? ? -65.81 -174.71 156 20 LYS A 25 ? ? -25.11 -35.08 157 20 SER A 30 ? ? -79.02 28.20 #