data_1WCO # _entry.id 1WCO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.330 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1WCO PDBE EBI-21726 WWPDB D_1290021726 # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2005-03-07 _pdbx_database_PDB_obs_spr.pdb_id 1WCO _pdbx_database_PDB_obs_spr.replace_pdb_id 1UZT _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 2DDE unspecified 'SOLUTION STRUCTURE OF THE LANTIBIOTIC CINNAMYCIN COMPLEXED WITH LYSOPHOSPHATIDYLETHANOLAMINE' PDB 2KTN unspecified 'SOLUTION STRUCTURE OF LCH-ALPHA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC SYSTEM LICHENICIDIN VK21 A1' PDB 2KTO unspecified 'SOLUTION STRUCTURE OF LCH-BETA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC LICHENICIDIN VK21 A2' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1WCO _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2004-11-19 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Hsu, S.-T.D.' 1 ? 'Breukink, E.' 2 ? 'Tischenko, E.' 3 ? 'Lutters, M.A.G.' 4 ? 'de Kruijff, B.' 5 ? 'Kaptein, R.' 6 ? 'Bonvin, A.M.J.J.' 7 ? 'van Nuland, N.A.J.' 8 ? # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics.' 'Nat. Struct. Mol. Biol.' 11 963 967 2004 ? US 1545-9993 ? ? 15361862 10.1038/nsmb830 1 'Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR: The Nisin Z and Lipid II Interaction in Sds Micelles' Biochemistry 41 7670 ? 2002 BICHAW US 0006-2960 0033 ? 12056898 10.1021/BI025679T 2 'Use of the Cell Wall Precursor Lipid II by a Pore- Forming Peptide Antibiotic' Science 286 2361 ? 1999 SCIEAS US 0036-8075 0038 ? 10600751 10.1126/SCIENCE.286.5448.2361 3 'Refinement of Protein Structures in Explicit Solvent' 'Proteins: Struct.,Funct., Genet.' 50 496 ? 2003 PSFGEY US 0887-3585 0867 ? 12557191 10.1002/PROT.10299 4 'Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information' J.Am.Chem.Soc. 125 1731 ? 2003 JACSAT US 0002-7863 0004 ? 12580598 10.1021/JA026939X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hsu, S.T.' 1 ? primary 'Breukink, E.' 2 ? primary 'Tischenko, E.' 3 ? primary 'Lutters, M.A.' 4 ? primary 'de Kruijff, B.' 5 ? primary 'Kaptein, R.' 6 ? primary 'Bonvin, A.M.' 7 ? primary 'van Nuland, N.A.' 8 ? 1 'Hsu, S.-T.D.' 9 ? 1 'Breukink, E.' 10 ? 1 'de Kruijff, B.' 11 ? 1 'Kaptein, R.' 12 ? 1 'Bonvin, A.M.J.J.' 13 ? 1 'van Nuland, N.A.J.' 14 ? 2 'Breukink, E.' 15 ? 2 'Wiedemann, I.' 16 ? 2 'van Kraaij, C.' 17 ? 2 'Kuipers, O.P.' 18 ? 2 'Sahl, H.G.' 19 ? 2 'de Kruijff, B.' 20 ? 3 'Linge, J.' 21 ? 3 'Williams, M.A.' 22 ? 3 'Spronk, C.A.E.M.' 23 ? 3 'Bonvin, A.M.J.J.' 24 ? 3 'Nilges, M.' 25 ? 4 'Dominguez, C.' 26 ? 4 'Boelens, R.' 27 ? 4 'Bonvin, A.M.J.J.' 28 ? # _cell.entry_id 1WCO _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 1WCO _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer nat 'ALA-FGA-LYS-DAL-DAL PEPTIDE' 489.542 1 ? ? ? ? 2 polymer nat Lantibiotic 3345.146 1 ? ? ? ? 3 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid' 496.463 1 ? ? ? ? 4 non-polymer syn '(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate' 418.307 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes 'A(FGA)K(DAL)(DAL)' AEKAA L ? 2 'polypeptide(L)' no yes 'I(DBU)(DAL)I(DHA)LC(DBB)PGCK(DBB)GALMGCNMK(DBB)A(DBB)CNCSIHV(DHA)K' ITAISLCTPGCKTGALMGCNMKTATCNCSIHVSK N ? # 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 FGA n 1 3 LYS n 1 4 DAL n 1 5 DAL n 2 1 ILE n 2 2 DBU n 2 3 DAL n 2 4 ILE n 2 5 DHA n 2 6 LEU n 2 7 CYS n 2 8 DBB n 2 9 PRO n 2 10 GLY n 2 11 CYS n 2 12 LYS n 2 13 DBB n 2 14 GLY n 2 15 ALA n 2 16 LEU n 2 17 MET n 2 18 GLY n 2 19 CYS n 2 20 ASN n 2 21 MET n 2 22 LYS n 2 23 DBB n 2 24 ALA n 2 25 DBB n 2 26 CYS n 2 27 ASN n 2 28 CYS n 2 29 SER n 2 30 ILE n 2 31 HIS n 2 32 VAL n 2 33 DHA n 2 34 LYS n # loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_alt_source_flag _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 _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.strain _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 1 1 sample 1 5 ? 'MONARTHROPALPUS FLAVUS' 71816 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 1 34 ? 'Lactococcus lactis' 1358 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 1WCO 1WCO ? 1 ? 1 2 UNP Q7BB86_9LACT Q7BB86 ? 2 ITSISLCTPGCKTGALMGCNMKTATCNCSIHVSK 24 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1WCO L 1 ? 5 ? 1WCO 3 ? 7 ? 3 7 2 2 1WCO N 1 ? 34 ? Q7BB86 24 ? 57 ? 1 34 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 2 1WCO DAL N 3 ? UNP Q7BB86 SER 26 conflict 3 1 2 1WCO DBB N 8 ? UNP Q7BB86 THR 31 conflict 8 2 2 1WCO DBB N 13 ? UNP Q7BB86 THR 36 conflict 13 3 2 1WCO DBB N 23 ? UNP Q7BB86 THR 46 conflict 23 4 2 1WCO DBB N 25 ? UNP Q7BB86 THR 48 conflict 25 5 # 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 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 FDF non-polymer . '(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate' ? 'C15 H26 F2 O7 P2' 418.307 FGA 'D-gamma-peptide, C-delta linking' . 'GAMMA-D-GLUTAMIC ACID' 'D-GLUTAMIC ACID' 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 MUB 'D-saccharide, alpha linking' . 'N-acetyl-alpha-muramic acid' ? 'C11 H19 N O8' 293.270 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 '1H-15N CT HSQC' 1 2 1 '31P 1D' 1 3 1 '1H-13C HSQC' 1 4 1 '1H-13C HMBC' 1 5 1 '31P 1D' 1 6 1 '1H-15N-NOESY HSQC' 1 7 1 '1H-1H NOESY' 1 8 1 '1H-15N TOCSY- HSQC' 1 9 1 '1H-1H TOCSY' 1 10 1 '1H-1H COSY' 1 11 1 '1H-15N-NOESY HSQC' 1 12 1 '1H-1H NOESY' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300.0 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pH ? _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? _pdbx_nmr_exptl_sample_conditions.pH_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label ? # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '100% D6-DMSO' _pdbx_nmr_sample_details.solvent_system ? _pdbx_nmr_sample_details.label ? _pdbx_nmr_sample_details.type ? _pdbx_nmr_sample_details.details ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 AVANCE Bruker 500 ? 2 AVANCE Bruker 600 ? 3 AVANCE Bruker 750 ? 4 AVANCE Bruker 900 ? # _pdbx_nmr_refine.entry_id 1WCO _pdbx_nmr_refine.method HADDOCK _pdbx_nmr_refine.details ;REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED ON THE CA OF NISIN RESIDUES 1-12 (CHAIN N), THE HEAVY ATOMS OF MURNAC, PYROPHOSPHATE AND THE FIRST ISOPRENE OF 3-LIPID II (CHAIN L) AS THESE ARE THE ONLY SEGMENTS THAT HAVE SUFFICIENT DISTANCE RESTRAINTS TO DEFINE THE COMPLEX STRUCTURE. OTHER RESIDUES NAMELY RESIDUES 13-34 (ESPECIALLY RESIDUES 20-34) OF NISIN, THE PENTAPEPTIDE AND TERMINAL ISOPRENE UNITS OF 3-LIPID II ARE FLEXIBLE AS SUPPORTED BY DYNAMICS DATA. THE ATOM OCCUPANCY OF THE C- TERMINAL TAIL OF NISIN (RESIDUES 20-34) HAS BEEN MODIFIED TO BE 0.3 TO REFLECT THEIR DISORDER/FLEXIBILITY. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1WCO _pdbx_nmr_details.text ;THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL NMR SPECTROSCOPY ON 15N-LABELLED NISIN IN COMPLEX WITH UNLABELLED 3-LIPID II. INTERMOLECULAR HYDROGEN BONDS WERE IDENTIFIED AND USED IN STRUCTURAL CALCULATION BY 31P- EDITED 1H-15N CT HSQC. ; # _pdbx_nmr_ensemble.entry_id 1WCO _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'RMSD CLUSTERING AND LOWEST TOTAL ENERGY' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement CNS 1.1 'BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN' 1 'structure solution' NMRView VIEW ? 2 'structure solution' CNS ? ? 3 # _exptl.entry_id 1WCO _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1WCO _struct.title 'The solution structure of the nisin-lipid II complex' _struct.pdbx_descriptor 'NAG-MUB-ALA-FGA-LYS-DAL-DAL PEPTIDE, NISIN Z' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1WCO _struct_keywords.pdbx_keywords PEPTIDE/ANTIBIOTIC _struct_keywords.text ;PEPTIDE-ANTIBIOTIC COMPLEX, LANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, THIOESTER, PORE FORMATION, PYROPHOSPHATE CAGE, FOOD PRESERVATIVE ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _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 DBB _struct_conf.beg_label_asym_id B _struct_conf.beg_label_seq_id 8 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id DBB _struct_conf.end_label_asym_id B _struct_conf.end_label_seq_id 13 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id DBB _struct_conf.beg_auth_asym_id N _struct_conf.beg_auth_seq_id 8 _struct_conf.end_auth_comp_id DBB _struct_conf.end_auth_asym_id N _struct_conf.end_auth_seq_id 13 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 6 # _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 ALA 1 C ? ? ? 1_555 A FGA 2 N ? ? L ALA 3 L FGA 4 1_555 ? ? ? ? ? ? ? 1.318 ? ? covale2 covale one ? A ALA 1 N ? ? ? 1_555 C MUB . C10 ? ? L ALA 3 A MUB 1 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale3 covale both ? A FGA 2 CD ? ? ? 1_555 A LYS 3 N ? ? L FGA 4 L LYS 5 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale4 covale both ? A LYS 3 C ? ? ? 1_555 A DAL 4 N ? ? L LYS 5 L DAL 6 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale5 covale both ? A DAL 4 C ? ? ? 1_555 A DAL 5 N ? ? L DAL 6 L DAL 7 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale6 covale one ? D FDF . PB ? ? ? 1_555 C MUB . O1 ? ? L FDF 101 A MUB 1 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale7 covale both ? B ILE 1 C ? ? ? 1_555 B DBU 2 N ? ? N ILE 1 N DBU 2 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale8 covale both ? B DBU 2 C ? ? ? 1_555 B DAL 3 N ? ? N DBU 2 N DAL 3 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale9 covale both ? B DAL 3 C ? ? ? 1_555 B ILE 4 N ? ? N DAL 3 N ILE 4 1_555 ? ? ? ? ? ? ? 1.318 ? ? covale10 covale none ? B DAL 3 CB ? ? ? 1_555 B CYS 7 SG ? ? N DAL 3 N CYS 7 1_555 ? ? ? ? ? ? ? 1.794 ? ? covale11 covale both ? B ILE 4 C ? ? ? 1_555 B DHA 5 N ? ? N ILE 4 N DHA 5 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale12 covale both ? B DHA 5 C ? ? ? 1_555 B LEU 6 N ? ? N DHA 5 N LEU 6 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale13 covale one ? B CYS 7 C ? ? ? 1_555 B DBB 8 N ? ? N CYS 7 N DBB 8 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale14 covale both ? B DBB 8 C ? ? ? 1_555 B PRO 9 N ? ? N DBB 8 N PRO 9 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale15 covale none ? B DBB 8 CB ? ? ? 1_555 B CYS 11 SG ? ? N DBB 8 N CYS 11 1_555 ? ? ? ? ? ? ? 1.815 ? ? covale16 covale one ? B LYS 12 C ? ? ? 1_555 B DBB 13 N ? ? N LYS 12 N DBB 13 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale17 covale both ? B DBB 13 C ? ? ? 1_555 B GLY 14 N ? ? N DBB 13 N GLY 14 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale18 covale none ? B DBB 13 CB ? ? ? 1_555 B CYS 19 SG ? ? N DBB 13 N CYS 19 1_555 ? ? ? ? ? ? ? 1.828 ? ? covale19 covale one ? B LYS 22 C ? ? ? 1_555 B DBB 23 N ? ? N LYS 22 N DBB 23 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale20 covale both ? B DBB 23 C ? ? ? 1_555 B ALA 24 N ? ? N DBB 23 N ALA 24 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale21 covale none ? B DBB 23 CB ? ? ? 1_555 B CYS 26 SG ? ? N DBB 23 N CYS 26 1_555 ? ? ? ? ? ? ? 1.823 ? ? covale22 covale one ? B ALA 24 C ? ? ? 1_555 B DBB 25 N ? ? N ALA 24 N DBB 25 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale23 covale both ? B DBB 25 C ? ? ? 1_555 B CYS 26 N ? ? N DBB 25 N CYS 26 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale24 covale none ? B DBB 25 CB ? ? ? 1_555 B CYS 28 SG ? ? N DBB 25 N CYS 28 1_555 ? ? ? ? ? ? ? 1.817 ? ? covale25 covale both ? B VAL 32 C ? ? ? 1_555 B DHA 33 N ? ? N VAL 32 N DHA 33 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale26 covale both ? B DHA 33 C ? ? ? 1_555 B LYS 34 N ? ? N DHA 33 N LYS 34 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale27 covale both ? C MUB . O4 ? ? ? 1_555 C NAG . C1 ? ? A MUB 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.424 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1WCO _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 1WCO _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 P S # loop_ _database_PDB_caveat.text 'MUB A 1 HAS WRONG CHIRALITY AT ATOM C9' # 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 3 3 ALA ALA L . n A 1 2 FGA 2 4 4 FGA FGA L . n A 1 3 LYS 3 5 5 LYS LYS L . n A 1 4 DAL 4 6 6 DAL DAL L . n A 1 5 DAL 5 7 7 DAL DAL L . n B 2 1 ILE 1 1 1 ILE ILE N . n B 2 2 DBU 2 2 2 DBU DBU N . n B 2 3 DAL 3 3 3 DAL DAL N . n B 2 4 ILE 4 4 4 ILE ILE N . n B 2 5 DHA 5 5 5 DHA DHA N . n B 2 6 LEU 6 6 6 LEU LEU N . n B 2 7 CYS 7 7 7 CYS CYS N . n B 2 8 DBB 8 8 8 DBB DBB N . n B 2 9 PRO 9 9 9 PRO PRO N . n B 2 10 GLY 10 10 10 GLY GLY N . n B 2 11 CYS 11 11 11 CYS CYS N . n B 2 12 LYS 12 12 12 LYS LYS N . n B 2 13 DBB 13 13 13 DBB DBB N . n B 2 14 GLY 14 14 14 GLY GLY N . n B 2 15 ALA 15 15 15 ALA ALA N . n B 2 16 LEU 16 16 16 LEU LEU N . n B 2 17 MET 17 17 17 MET MET N . n B 2 18 GLY 18 18 18 GLY GLY N . n B 2 19 CYS 19 19 19 CYS CYS N . n B 2 20 ASN 20 20 20 ASN ASN N . n B 2 21 MET 21 21 21 MET MET N . n B 2 22 LYS 22 22 22 LYS LYS N . n B 2 23 DBB 23 23 23 DBB DBB N . n B 2 24 ALA 24 24 24 ALA ALA N . n B 2 25 DBB 25 25 25 DBB DBB N . n B 2 26 CYS 26 26 26 CYS CYS N . n B 2 27 ASN 27 27 27 ASN ASN N . n B 2 28 CYS 28 28 28 CYS CYS N . n B 2 29 SER 29 29 29 SER SER N . n B 2 30 ILE 30 30 30 ILE ILE N . n B 2 31 HIS 31 31 31 HIS HIS N . n B 2 32 VAL 32 32 32 VAL VAL N . n B 2 33 DHA 33 33 33 DHA DHA N . n B 2 34 LYS 34 34 34 LYS LYS N . n # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id FDF _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 35 _pdbx_nonpoly_scheme.pdb_mon_id FDF _pdbx_nonpoly_scheme.auth_mon_id FPP _pdbx_nonpoly_scheme.pdb_strand_id L _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_molecule_features.prd_id PRD_000200 _pdbx_molecule_features.name 'Nisin A' _pdbx_molecule_features.type Polypeptide _pdbx_molecule_features.class Lantibiotic _pdbx_molecule_features.details ;Nisin Z is a heptacyclic peptide. Post Translational maturation of lantibiotics involves the enzymic conversion of Thr, and Ser into dehydrated AA and the formation of thioether bonds with cysteine. Thioether bonds with cysteine result in five cyclic structures along the peptide chain. This is followed by membrane translocation and cleavage of the modified precursor. ; # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000200 _pdbx_molecule.asym_id B # 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 B DBU 2 N DBU 2 ? THR 'modified residue' 2 B DHA 5 N DHA 5 ? SER 'modified residue' 3 B DHA 33 N DHA 33 ? SER 'modified residue' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1610 ? 1 MORE 3 ? 1 'SSA (A^2)' 3620 ? # _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 ? _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 2005-03-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-11-30 4 'Structure model' 2 0 2018-01-17 5 'Structure model' 3 0 2020-07-08 6 'Structure model' 4 0 2020-07-29 # 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 6 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Atomic model' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' 'Structure summary' 5 2 'Structure model' 'Version format compliance' 6 3 'Structure model' Other 7 4 'Structure model' Advisory 8 4 'Structure model' 'Atomic model' 9 4 'Structure model' 'Data collection' 10 4 'Structure model' 'Database references' 11 5 'Structure model' Advisory 12 5 'Structure model' 'Atomic model' 13 5 'Structure model' 'Data collection' 14 5 'Structure model' 'Database references' 15 5 'Structure model' 'Derived calculations' 16 5 'Structure model' 'Non-polymer description' 17 5 'Structure model' Other 18 5 'Structure model' 'Polymer sequence' 19 5 'Structure model' 'Source and taxonomy' 20 5 'Structure model' 'Structure summary' 21 6 'Structure model' Advisory 22 6 'Structure model' 'Atomic model' 23 6 'Structure model' 'Data collection' 24 6 'Structure model' 'Derived calculations' 25 6 'Structure model' 'Structure summary' # 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 4 'Structure model' atom_site 2 4 'Structure model' citation 3 4 'Structure model' citation_author 4 4 'Structure model' database_PDB_caveat 5 4 'Structure model' pdbx_nmr_spectrometer 6 4 'Structure model' pdbx_validate_polymer_linkage 7 5 'Structure model' atom_site 8 5 'Structure model' chem_comp 9 5 'Structure model' database_PDB_caveat 10 5 'Structure model' entity 11 5 'Structure model' entity_poly 12 5 'Structure model' entity_poly_seq 13 5 'Structure model' entity_src_nat 14 5 'Structure model' pdbx_database_status 15 5 'Structure model' pdbx_entity_nonpoly 16 5 'Structure model' pdbx_nmr_software 17 5 'Structure model' pdbx_nmr_spectrometer 18 5 'Structure model' pdbx_nonpoly_scheme 19 5 'Structure model' pdbx_poly_seq_scheme 20 5 'Structure model' pdbx_struct_assembly_gen 21 5 'Structure model' pdbx_struct_assembly_prop 22 5 'Structure model' pdbx_struct_mod_residue 23 5 'Structure model' pdbx_struct_oper_list 24 5 'Structure model' pdbx_unobs_or_zero_occ_atoms 25 5 'Structure model' pdbx_validate_chiral 26 5 'Structure model' pdbx_validate_close_contact 27 5 'Structure model' struct_asym 28 5 'Structure model' struct_conn 29 5 'Structure model' struct_ref 30 5 'Structure model' struct_ref_seq 31 5 'Structure model' struct_ref_seq_dif 32 5 'Structure model' struct_site_gen 33 6 'Structure model' atom_site 34 6 'Structure model' chem_comp 35 6 'Structure model' database_PDB_caveat 36 6 'Structure model' entity 37 6 'Structure model' pdbx_branch_scheme 38 6 'Structure model' pdbx_chem_comp_identifier 39 6 'Structure model' pdbx_entity_branch 40 6 'Structure model' pdbx_entity_branch_descriptor 41 6 'Structure model' pdbx_entity_branch_link 42 6 'Structure model' pdbx_entity_branch_list 43 6 'Structure model' pdbx_entity_nonpoly 44 6 'Structure model' pdbx_nonpoly_scheme 45 6 'Structure model' pdbx_struct_assembly_gen 46 6 'Structure model' pdbx_unobs_or_zero_occ_atoms 47 6 'Structure model' pdbx_validate_chiral 48 6 'Structure model' pdbx_validate_close_contact 49 6 'Structure model' struct_asym 50 6 'Structure model' struct_conn 51 6 'Structure model' struct_site 52 6 'Structure model' struct_site_gen # 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 4 'Structure model' '_atom_site.B_iso_or_equiv' 2 4 'Structure model' '_atom_site.Cartn_x' 3 4 'Structure model' '_atom_site.Cartn_y' 4 4 'Structure model' '_atom_site.Cartn_z' 5 4 'Structure model' '_atom_site.auth_atom_id' 6 4 'Structure model' '_atom_site.label_atom_id' 7 4 'Structure model' '_citation.journal_abbrev' 8 4 'Structure model' '_citation.page_last' 9 4 'Structure model' '_citation.pdbx_database_id_DOI' 10 4 'Structure model' '_citation.title' 11 4 'Structure model' '_citation_author.name' 12 4 'Structure model' '_pdbx_nmr_spectrometer.manufacturer' 13 4 'Structure model' '_pdbx_nmr_spectrometer.model' 14 5 'Structure model' '_atom_site.B_iso_or_equiv' 15 5 'Structure model' '_atom_site.Cartn_x' 16 5 'Structure model' '_atom_site.Cartn_y' 17 5 'Structure model' '_atom_site.Cartn_z' 18 5 'Structure model' '_atom_site.auth_asym_id' 19 5 'Structure model' '_atom_site.auth_atom_id' 20 5 'Structure model' '_atom_site.auth_comp_id' 21 5 'Structure model' '_atom_site.auth_seq_id' 22 5 'Structure model' '_atom_site.group_PDB' 23 5 'Structure model' '_atom_site.label_asym_id' 24 5 'Structure model' '_atom_site.label_atom_id' 25 5 'Structure model' '_atom_site.label_comp_id' 26 5 'Structure model' '_atom_site.label_entity_id' 27 5 'Structure model' '_atom_site.label_seq_id' 28 5 'Structure model' '_atom_site.type_symbol' 29 5 'Structure model' '_chem_comp.formula' 30 5 'Structure model' '_chem_comp.formula_weight' 31 5 'Structure model' '_chem_comp.id' 32 5 'Structure model' '_chem_comp.name' 33 5 'Structure model' '_chem_comp.pdbx_synonyms' 34 5 'Structure model' '_chem_comp.type' 35 5 'Structure model' '_database_PDB_caveat.text' 36 5 'Structure model' '_entity_poly.pdbx_seq_one_letter_code' 37 5 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 38 5 'Structure model' '_entity_src_nat.pdbx_beg_seq_num' 39 5 'Structure model' '_entity_src_nat.pdbx_end_seq_num' 40 5 'Structure model' '_entity_src_nat.pdbx_organism_scientific' 41 5 'Structure model' '_entity_src_nat.strain' 42 5 'Structure model' '_pdbx_database_status.status_code_mr' 43 5 'Structure model' '_pdbx_nmr_software.name' 44 5 'Structure model' '_pdbx_nmr_spectrometer.model' 45 5 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 46 5 'Structure model' '_pdbx_struct_assembly_prop.value' 47 5 'Structure model' '_pdbx_struct_mod_residue.details' 48 5 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 49 5 'Structure model' '_pdbx_validate_chiral.auth_seq_id' 50 5 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_2' 51 5 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_1' 52 5 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_2' 53 5 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_1' 54 5 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_2' 55 5 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_1' 56 5 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 57 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 58 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 59 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 60 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 61 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 62 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 63 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 64 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 65 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 66 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 67 5 'Structure model' '_struct_ref.db_code' 68 5 'Structure model' '_struct_ref.pdbx_align_begin' 69 5 'Structure model' '_struct_ref.pdbx_db_accession' 70 5 'Structure model' '_struct_ref.pdbx_seq_one_letter_code' 71 5 'Structure model' '_struct_ref_seq.db_align_beg' 72 5 'Structure model' '_struct_ref_seq.pdbx_auth_seq_align_beg' 73 5 'Structure model' '_struct_ref_seq.pdbx_db_accession' 74 5 'Structure model' '_struct_ref_seq.seq_align_end' 75 5 'Structure model' '_struct_site_gen.auth_asym_id' 76 5 'Structure model' '_struct_site_gen.auth_comp_id' 77 5 'Structure model' '_struct_site_gen.auth_seq_id' 78 5 'Structure model' '_struct_site_gen.label_asym_id' 79 5 'Structure model' '_struct_site_gen.label_comp_id' 80 5 'Structure model' '_struct_site_gen.label_seq_id' 81 6 'Structure model' '_atom_site.B_iso_or_equiv' 82 6 'Structure model' '_atom_site.Cartn_x' 83 6 'Structure model' '_atom_site.Cartn_y' 84 6 'Structure model' '_atom_site.Cartn_z' 85 6 'Structure model' '_atom_site.auth_asym_id' 86 6 'Structure model' '_atom_site.auth_atom_id' 87 6 'Structure model' '_atom_site.auth_comp_id' 88 6 'Structure model' '_atom_site.auth_seq_id' 89 6 'Structure model' '_atom_site.label_asym_id' 90 6 'Structure model' '_atom_site.label_atom_id' 91 6 'Structure model' '_atom_site.label_comp_id' 92 6 'Structure model' '_atom_site.label_entity_id' 93 6 'Structure model' '_atom_site.type_symbol' 94 6 'Structure model' '_chem_comp.name' 95 6 'Structure model' '_database_PDB_caveat.text' 96 6 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 97 6 'Structure model' '_pdbx_unobs_or_zero_occ_atoms.label_asym_id' 98 6 'Structure model' '_pdbx_validate_chiral.auth_asym_id' 99 6 'Structure model' '_pdbx_validate_chiral.auth_seq_id' 100 6 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_1' 101 6 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_2' 102 6 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_1' 103 6 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_2' 104 6 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_1' 105 6 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_2' 106 6 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_1' 107 6 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 108 6 'Structure model' '_struct_conn.pdbx_dist_value' 109 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 110 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 111 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 112 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 113 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 114 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 115 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 116 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 117 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 118 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 119 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 120 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 121 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 122 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 123 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' # _pdbx_entry_details.entry_id 1WCO _pdbx_entry_details.compound_details ;NISIN Z IS A LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE AND/OR METHYLLANTHIONINE NONPROTEINOGENIC AMINO ACIDS. HERE, NISIN Z IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: NISIN Z CHAIN: N COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 34 DESCRIPTION: NISIN Z IS A PENTACYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN FIVE CYCLIC STRUCTURES ALONG THE PEPTIDE CHAIN. CROSSLINK 3-7 METHYLLANTHIONINE (DAL-CYS) CROSSLINK 8-11 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 13-19 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 23-26 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 25-28 BETA-METHYLLANTHIONINE (DBB-CYS) ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 HZ3 L LYS 5 ? ? O L DAL 7 ? ? 1.56 2 3 HG2 L FGA 4 ? ? H62 A MUB 1 ? ? 1.15 3 3 HB2 N PRO 9 ? ? H5 L FDF 101 ? ? 1.33 4 3 HG22 N ILE 1 ? ? O1 L FDF 101 ? ? 1.54 5 4 HD3 L LYS 5 ? ? H5 A MUB 1 ? ? 1.30 6 4 O N GLY 14 ? ? H N GLY 18 ? ? 1.60 7 5 HG22 N ILE 1 ? ? O1 L FDF 101 ? ? 1.58 8 5 HD1 N HIS 31 ? ? O N LYS 34 ? ? 1.58 9 6 HG2 L FGA 4 ? ? H62 A MUB 1 ? ? 1.23 10 9 HB2 N PRO 9 ? ? H5 L FDF 101 ? ? 1.28 11 9 HG22 N ILE 1 ? ? O1 L FDF 101 ? ? 1.52 12 9 O N GLY 14 ? ? H N GLY 18 ? ? 1.59 13 10 HZ3 L LYS 5 ? ? OXT L DAL 7 ? ? 1.56 14 13 HG3 L FGA 4 ? ? H62 A MUB 1 ? ? 1.33 15 14 HG2 L FGA 4 ? ? H62 A MUB 1 ? ? 1.26 16 14 OXT L FGA 4 ? ? H61 A MUB 1 ? ? 1.56 17 16 HD1 N HIS 31 ? ? O N LYS 34 ? ? 1.59 18 16 OXT L FGA 4 ? ? HO6 A MUB 1 ? ? 1.60 19 17 H1 L ALA 3 ? ? H4 A MUB 1 ? ? 0.84 20 18 O3 A MUB 1 ? ? H1 A NAG 2 ? ? 1.55 21 19 HZ2 L LYS 5 ? ? O4 A MUB 1 ? ? 1.58 22 20 HB1 L ALA 3 ? ? H61 A MUB 1 ? ? 1.29 # 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 DBB N 8 ? ? 147.76 -58.97 2 1 LYS N 12 ? ? -151.30 1.93 3 1 MET N 17 ? ? -154.38 -46.71 4 1 CYS N 19 ? ? 63.18 82.90 5 1 ASN N 20 ? ? -57.88 -81.18 6 1 HIS N 31 ? ? -126.21 -82.45 7 2 DAL L 6 ? ? -71.81 -73.98 8 2 DBB N 13 ? ? -73.72 46.61 9 2 MET N 17 ? ? -160.00 -33.77 10 2 CYS N 19 ? ? 65.39 91.33 11 2 MET N 21 ? ? 73.82 39.53 12 3 DAL L 6 ? ? -74.60 21.26 13 3 DBB N 8 ? ? 150.47 -53.57 14 3 DBB N 13 ? ? -73.72 46.83 15 3 MET N 17 ? ? -138.14 -30.53 16 3 CYS N 19 ? ? 60.11 79.16 17 3 ASN N 20 ? ? -68.09 -80.10 18 3 MET N 21 ? ? 75.27 -31.16 19 3 DBB N 23 ? ? 174.54 38.88 20 3 ALA N 24 ? ? -117.37 74.54 21 3 ILE N 30 ? ? -90.11 55.63 22 4 DAL L 6 ? ? -178.22 -82.63 23 4 LEU N 6 ? ? -101.79 68.85 24 4 CYS N 7 ? ? -63.52 99.10 25 4 DBB N 8 ? ? 150.92 -57.27 26 4 DBB N 13 ? ? -73.79 44.97 27 4 MET N 17 ? ? -150.61 -36.02 28 4 CYS N 19 ? ? 70.22 87.97 29 4 MET N 21 ? ? 74.53 -49.92 30 5 DAL L 6 ? ? 145.50 40.04 31 5 DBB N 8 ? ? 153.14 -53.07 32 5 DBB N 13 ? ? -81.60 25.69 33 5 MET N 17 ? ? -149.99 -57.69 34 5 CYS N 19 ? ? 65.63 70.83 35 5 ASN N 20 ? ? 70.51 -81.51 36 6 DAL L 6 ? ? -75.27 46.55 37 6 CYS N 7 ? ? -59.40 90.44 38 6 DBB N 8 ? ? 150.13 -54.95 39 6 DBB N 13 ? ? -73.93 32.70 40 6 MET N 17 ? ? -152.97 -42.41 41 6 ASN N 20 ? ? 174.42 -23.20 42 6 ILE N 30 ? ? -91.79 32.34 43 7 DAL L 6 ? ? 170.25 -37.64 44 7 CYS N 7 ? ? -59.99 99.45 45 7 DBB N 8 ? ? 146.75 -53.50 46 7 DBB N 13 ? ? -70.51 52.35 47 7 MET N 17 ? ? -136.07 -58.47 48 7 CYS N 19 ? ? 64.80 177.59 49 7 ASN N 20 ? ? -119.19 -71.63 50 7 MET N 21 ? ? 73.57 -47.13 51 7 DBB N 23 ? ? 155.26 33.29 52 8 DBB N 13 ? ? -70.92 50.83 53 8 ALA N 15 ? ? -79.02 21.81 54 8 MET N 17 ? ? -172.30 -30.90 55 8 ASN N 20 ? ? 179.32 -22.05 56 8 MET N 21 ? ? 75.76 -65.11 57 9 DBB N 8 ? ? 150.53 -55.48 58 9 DBB N 13 ? ? -76.75 28.34 59 9 MET N 17 ? ? -158.99 -41.37 60 9 CYS N 19 ? ? 63.11 88.32 61 9 MET N 21 ? ? 72.13 -49.53 62 10 DBB N 8 ? ? 140.28 -51.06 63 10 LYS N 12 ? ? -140.84 14.19 64 10 DBB N 13 ? ? -72.49 53.85 65 10 MET N 17 ? ? -163.81 -42.48 66 10 CYS N 19 ? ? 65.03 77.38 67 10 ASN N 20 ? ? -68.84 -85.39 68 11 DBB N 8 ? ? 143.70 -49.16 69 11 DBB N 13 ? ? -71.95 50.51 70 11 ALA N 15 ? ? -75.07 28.20 71 11 MET N 17 ? ? 179.56 -26.65 72 11 DBB N 23 ? ? -177.58 46.61 73 12 DBB N 8 ? ? 143.59 -55.55 74 12 DBB N 13 ? ? -71.21 58.25 75 12 MET N 17 ? ? -154.64 -49.22 76 12 CYS N 19 ? ? 63.45 99.75 77 12 ASN N 20 ? ? -72.79 -98.27 78 12 ILE N 30 ? ? -81.86 35.64 79 13 DBB N 13 ? ? -76.07 35.24 80 13 ASN N 20 ? ? 73.71 -88.65 81 14 CYS N 7 ? ? -61.82 99.58 82 14 DBB N 13 ? ? -68.14 46.07 83 14 ALA N 15 ? ? -75.16 29.46 84 14 MET N 17 ? ? 178.46 -33.69 85 14 CYS N 19 ? ? 75.05 -65.87 86 14 ASN N 20 ? ? -173.18 -39.26 87 14 MET N 21 ? ? 74.54 -43.78 88 14 DBB N 23 ? ? -174.89 26.50 89 15 DAL L 6 ? ? 148.83 -34.55 90 15 DBB N 8 ? ? 150.40 -58.71 91 15 DBB N 13 ? ? -75.98 24.17 92 15 MET N 17 ? ? -156.02 -44.07 93 15 CYS N 19 ? ? 75.01 -24.27 94 15 ASN N 20 ? ? -172.07 -68.37 95 15 SER N 29 ? ? -69.29 98.60 96 16 DBB N 8 ? ? 146.93 -53.89 97 16 DBB N 13 ? ? -71.36 54.04 98 16 MET N 17 ? ? -132.83 -66.27 99 16 ASN N 20 ? ? -83.05 -97.80 100 16 DBB N 23 ? ? 147.54 32.18 101 16 ALA N 24 ? ? -92.82 57.44 102 16 ILE N 30 ? ? -86.91 49.49 103 17 DBB N 13 ? ? -73.49 50.91 104 17 ALA N 15 ? ? -76.73 28.51 105 17 MET N 17 ? ? -174.22 -28.53 106 17 CYS N 19 ? ? 64.22 70.08 107 17 ASN N 20 ? ? -128.41 -68.79 108 17 DBB N 23 ? ? -70.61 58.28 109 18 DAL L 6 ? ? 171.54 -80.63 110 18 DBB N 13 ? ? -73.58 52.26 111 18 ALA N 15 ? ? -77.60 37.21 112 18 MET N 17 ? ? 175.46 -34.28 113 18 MET N 21 ? ? 76.41 -28.66 114 19 DAL L 6 ? ? 168.96 29.97 115 19 DBB N 8 ? ? 151.16 -52.95 116 19 DBB N 13 ? ? -73.79 52.82 117 19 ALA N 15 ? ? -78.18 28.35 118 19 MET N 17 ? ? -143.10 -12.74 119 19 MET N 21 ? ? 70.87 -1.49 120 19 DBB N 23 ? ? 137.40 33.35 121 19 HIS N 31 ? ? -95.08 -71.87 122 20 DAL L 6 ? ? -71.59 0.68 123 20 CYS N 7 ? ? -66.03 97.78 124 20 DBB N 8 ? ? 145.18 -50.86 125 20 DBB N 13 ? ? -71.67 52.44 126 20 ALA N 15 ? ? -78.86 29.70 127 20 MET N 17 ? ? -174.47 -46.32 128 20 CYS N 19 ? ? 65.31 62.64 129 20 ASN N 20 ? ? 70.42 -57.45 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C9 ? A MUB 1 ? PLANAR . 2 2 C9 ? A MUB 1 ? PLANAR . 3 4 C9 ? A MUB 1 ? PLANAR . 4 5 C9 ? A MUB 1 ? PLANAR . 5 7 C9 ? A MUB 1 ? PLANAR . 6 10 C9 ? A MUB 1 ? PLANAR . 7 11 C9 ? A MUB 1 ? PLANAR . 8 12 C9 ? A MUB 1 ? PLANAR . 9 13 C9 ? A MUB 1 ? PLANAR . 10 15 C9 ? A MUB 1 ? PLANAR . 11 16 C9 ? A MUB 1 ? PLANAR . 12 17 C9 ? A MUB 1 ? PLANAR . 13 18 C9 ? A MUB 1 ? PLANAR . 14 19 C9 ? A MUB 1 ? PLANAR . 15 20 C9 ? A MUB 1 ? PLANAR . # 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 N 1 L FDF 101 ? F1 ? D FDF 1 F1 2 1 N 1 L FDF 101 ? F2 ? D FDF 1 F2 3 2 N 1 L FDF 101 ? F1 ? D FDF 1 F1 4 2 N 1 L FDF 101 ? F2 ? D FDF 1 F2 5 3 N 1 L FDF 101 ? F1 ? D FDF 1 F1 6 3 N 1 L FDF 101 ? F2 ? D FDF 1 F2 7 4 N 1 L FDF 101 ? F1 ? D FDF 1 F1 8 4 N 1 L FDF 101 ? F2 ? D FDF 1 F2 9 5 N 1 L FDF 101 ? F1 ? D FDF 1 F1 10 5 N 1 L FDF 101 ? F2 ? D FDF 1 F2 11 6 N 1 L FDF 101 ? F1 ? D FDF 1 F1 12 6 N 1 L FDF 101 ? F2 ? D FDF 1 F2 13 7 N 1 L FDF 101 ? F1 ? D FDF 1 F1 14 7 N 1 L FDF 101 ? F2 ? D FDF 1 F2 15 8 N 1 L FDF 101 ? F1 ? D FDF 1 F1 16 8 N 1 L FDF 101 ? F2 ? D FDF 1 F2 17 9 N 1 L FDF 101 ? F1 ? D FDF 1 F1 18 9 N 1 L FDF 101 ? F2 ? D FDF 1 F2 19 10 N 1 L FDF 101 ? F1 ? D FDF 1 F1 20 10 N 1 L FDF 101 ? F2 ? D FDF 1 F2 21 11 N 1 L FDF 101 ? F1 ? D FDF 1 F1 22 11 N 1 L FDF 101 ? F2 ? D FDF 1 F2 23 12 N 1 L FDF 101 ? F1 ? D FDF 1 F1 24 12 N 1 L FDF 101 ? F2 ? D FDF 1 F2 25 13 N 1 L FDF 101 ? F1 ? D FDF 1 F1 26 13 N 1 L FDF 101 ? F2 ? D FDF 1 F2 27 14 N 1 L FDF 101 ? F1 ? D FDF 1 F1 28 14 N 1 L FDF 101 ? F2 ? D FDF 1 F2 29 15 N 1 L FDF 101 ? F1 ? D FDF 1 F1 30 15 N 1 L FDF 101 ? F2 ? D FDF 1 F2 31 16 N 1 L FDF 101 ? F1 ? D FDF 1 F1 32 16 N 1 L FDF 101 ? F2 ? D FDF 1 F2 33 17 N 1 L FDF 101 ? F1 ? D FDF 1 F1 34 17 N 1 L FDF 101 ? F2 ? D FDF 1 F2 35 18 N 1 L FDF 101 ? F1 ? D FDF 1 F1 36 18 N 1 L FDF 101 ? F2 ? D FDF 1 F2 37 19 N 1 L FDF 101 ? F1 ? D FDF 1 F1 38 19 N 1 L FDF 101 ? F2 ? D FDF 1 F2 39 20 N 1 L FDF 101 ? F1 ? D FDF 1 F1 40 20 N 1 L FDF 101 ? F2 ? D FDF 1 F2 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero C 3 MUB 1 A MUB 1 L MUB 2 n C 3 NAG 2 A NAG 2 L NAG 1 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier MUB 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GlcpNAc3 MUB 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 MurNAc NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 3 DGlcpNAcb1-4MurNAc1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 3 'WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1' WURCS PDB2Glycan 1.1.0 3 3 '[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 MUB _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 3 MUB 1 n 3 NAG 2 n # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name '(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate' _pdbx_entity_nonpoly.comp_id FDF #