data_2L2W # _entry.id 2L2W # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2L2W RCSB RCSB101888 WWPDB D_1000101888 # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 1E9W PDB . unspecified 2JQ7 PDB . unspecified 2L2X PDB . unspecified 2L2Y PDB . unspecified 2L2Z PDB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2L2W _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-08-27 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Jonker, H.R.A.' 1 'Baumann, S.' 2 'Wolf, A.' 3 'Schoof, S.' 4 'Hiller, F.' 5 'Schulte, K.W.' 6 'Kirschner, K.N.' 7 'Schwalbe, H.' 8 'Arndt, H.-D.' 9 # _citation.id primary _citation.title 'NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site.' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 50 _citation.page_first 3308 _citation.page_last 3312 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21365717 _citation.pdbx_database_id_DOI 10.1002/anie.201003582 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Jonker, H.R.' 1 primary 'Baumann, S.' 2 primary 'Wolf, A.' 3 primary 'Schoof, S.' 4 primary 'Hiller, F.' 5 primary 'Schulte, K.W.' 6 primary 'Kirschner, K.N.' 7 primary 'Schwalbe, H.' 8 primary 'Arndt, H.D.' 9 # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description Thiostrepton _entity.formula_weight 1805.985 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Alaninamide, Bryamycin, Gargon, Thiactin' # _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 '(QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)' _entity_poly.pdbx_seq_one_letter_code_can XIASASCTTCXCTCXCSSX _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 QUA n 1 2 ILE n 1 3 ALA n 1 4 DHA n 1 5 ALA n 1 6 SER n 1 7 BB9 n 1 8 THR n 1 9 DBU n 1 10 DCY n 1 11 TS9 n 1 12 BB9 n 1 13 THR n 1 14 BB9 n 1 15 MH6 n 1 16 BB9 n 1 17 DHA n 1 18 DHA n 1 19 NH2 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 'Streptomyces azureus' _entity_src_nat.pdbx_ncbi_taxonomy_id 146537 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code THCL_STRAJ _struct_ref.pdbx_db_accession P0C8P8 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code IASASCTTCICTCSCSS _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2L2W _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 18 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0C8P8 _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 # 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 1 2L2W QUA A 1 ? UNP P0C8P8 ? ? 'SEE REMARK 999' 0 1 1 2L2W NH2 A 19 ? UNP P0C8P8 ? ? AMIDATION 18 2 # 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 BB9 'peptide linking' n '(2Z)-2-amino-3-sulfanylprop-2-enoic acid' ? 'C3 H5 N O2 S' 119.142 DBU 'peptide linking' n '(2Z)-2-AMINOBUT-2-ENOIC ACID' Z-DEHYDROBUTYRINE 'C4 H7 N O2' 101.104 DCY 'D-peptide linking' . D-CYSTEINE ? 'C3 H7 N O2 S' 121.158 DHA 'peptide linking' n '2-AMINO-ACRYLIC ACID' 2,3-DIDEHYDROALANINE 'C3 H5 N O2' 87.077 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 MH6 'peptide linking' n '3-hydroxy-2-iminopropanoic acid' ? 'C3 H5 N O3' 103.077 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 QUA non-polymer . '8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID' ? 'C12 H13 N O4' 235.236 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TS9 'L-peptide linking' n '(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid' ? 'C6 H13 N O4' 163.172 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-15N HSQC' 1 2 1 '2D 1H-13C HSQC' 1 3 1 '2D 1H-13C TOCSY-HSQC' 1 4 1 '2D 1H-13C HMBC' 1 5 1 '2D 1H-1H NOESY' 1 6 1 '2D 1H-1H ROESY' 1 7 1 '2D 1H-1H TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH . _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '10 mM thiostrepton, chloroform-d/ethanol-d5 5:1' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system 'chloroform-d/ethanol-d5 5:1' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker DRX' # _pdbx_nmr_refine.entry_id 2L2W _pdbx_nmr_refine.method 'simulated annealing, torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2L2W _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2L2W _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TOPSPIN 1.3 1 'Bruker Biospin' processing TOPSPIN 1.3 2 Goddard 'peak picking' SPARKY 3.113 3 Goddard 'chemical shift assignment' SPARKY 3.113 4 Goddard 'data analysis' SPARKY 3.113 5 ;Linge, O'Donoghue and Nilges ; refinement ARIA 1.2 6 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.1 7 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details 'Thiostrepton wt (in 5:1 chloroform-d ethanol-d5)' _exptl.entry_id 2L2W _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2L2W _struct.title Thiostrepton _struct.pdbx_descriptor thiostrepton _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2L2W _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'Natural antibiotic, Thiopeptide, Antibiotic, Antimicrobial, ANTIBACTERIAL, thiazole, thiazoline' # _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_biol.details ? # 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 covale1 covale ? ? A ALA 3 C ? ? ? 1_555 A DHA 4 N ? ? A ALA 2 A DHA 3 1_555 ? ? ? ? ? ? ? 1.334 ? covale2 covale ? ? A DHA 4 C ? ? ? 1_555 A ALA 5 N ? ? A DHA 3 A ALA 4 1_555 ? ? ? ? ? ? ? 1.325 ? covale3 covale ? ? A DHA 17 C ? ? ? 1_555 A DHA 18 N ? ? A DHA 16 A DHA 17 1_555 ? ? ? ? ? ? ? 1.336 ? covale4 covale ? ? A SER 6 C ? ? ? 1_555 A BB9 7 N ? ? A SER 5 A BB9 6 1_555 ? ? ? ? ? ? ? 1.296 ? covale5 covale ? ? A BB9 7 C ? ? ? 1_555 A THR 8 N ? ? A BB9 6 A THR 7 1_555 ? ? ? ? ? ? ? 1.332 ? covale6 covale ? ? A THR 8 C ? ? ? 1_555 A DBU 9 N ? ? A THR 7 A DBU 8 1_555 ? ? ? ? ? ? ? 1.329 ? covale7 covale ? ? A DBU 9 C ? ? ? 1_555 A DCY 10 N ? ? A DBU 8 A DCY 9 1_555 ? ? ? ? ? ? ? 1.307 ? covale8 covale ? ? A DCY 10 C ? ? ? 1_555 A TS9 11 N ? ? A DCY 9 A TS9 10 1_555 ? ? ? ? ? ? ? 1.332 ? covale9 covale ? ? A TS9 11 C ? ? ? 1_555 A BB9 12 N ? ? A TS9 10 A BB9 11 1_555 ? ? ? ? ? ? ? 1.298 ? covale10 covale ? ? A BB9 12 C ? ? ? 1_555 A THR 13 N ? ? A BB9 11 A THR 12 1_555 ? ? ? ? ? ? ? 1.333 ? covale11 covale ? ? A THR 13 C ? ? ? 1_555 A BB9 14 N ? ? A THR 12 A BB9 13 1_555 ? ? ? ? ? ? ? 1.285 ? covale12 covale ? ? A BB9 14 C ? ? ? 1_555 A MH6 15 N ? ? A BB9 13 A MH6 14 1_555 ? ? ? ? ? ? ? 1.471 ? covale13 covale ? ? A MH6 15 C ? ? ? 1_555 A BB9 16 N ? ? A MH6 14 A BB9 15 1_555 ? ? ? ? ? ? ? 1.291 ? covale14 covale ? ? A BB9 16 C ? ? ? 1_555 A DHA 17 N ? ? A BB9 15 A DHA 16 1_555 ? ? ? ? ? ? ? 1.335 ? covale15 covale ? ? A QUA 1 C11 ? ? ? 1_555 A THR 13 OG1 ? ? A QUA 0 A THR 12 1_555 ? ? ? ? ? ? ? 1.334 ? covale16 covale ? ? A QUA 1 C7 ? ? ? 1_555 A ILE 2 N ? ? A QUA 0 A ILE 1 1_555 ? ? ? ? ? ? ? 1.494 ? covale17 covale ? ? A SER 6 CB ? ? ? 1_555 A MH6 15 CB ? ? A SER 5 A MH6 14 1_555 ? ? ? ? ? ? ? 1.526 ? covale18 covale ? ? A SER 6 CA ? ? ? 1_555 A BB9 14 C ? ? A SER 5 A BB9 13 1_555 ? ? ? ? ? ? ? 1.574 ? covale19 covale ? ? A TS9 11 C ? ? ? 1_555 A BB9 12 SG ? ? A TS9 10 A BB9 11 1_555 ? ? ? ? ? ? ? 1.718 ? covale20 covale ? ? A MH6 15 C ? ? ? 1_555 A BB9 16 SG ? ? A MH6 14 A BB9 15 1_555 ? ? ? ? ? ? ? 1.719 ? covale21 covale ? ? A THR 13 C ? ? ? 1_555 A BB9 14 SG ? ? A THR 12 A BB9 13 1_555 ? ? ? ? ? ? ? 1.719 ? covale22 covale ? ? A SER 6 C ? ? ? 1_555 A BB9 7 SG ? ? A SER 5 A BB9 6 1_555 ? ? ? ? ? ? ? 1.724 ? covale23 covale ? ? A DBU 9 C ? ? ? 1_555 A DCY 10 SG ? ? A DBU 8 A DCY 9 1_555 ? ? ? ? ? ? ? 1.732 ? covale24 covale ? ? A DHA 18 C ? ? ? 1_555 A NH2 19 N ? ? A DHA 17 A NH2 18 1_555 ? ? ? ? ? ? ? 1.330 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE DCY A 9' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 THR A 8 ? THR A 7 . ? 1_555 ? 2 AC1 4 DBU A 9 ? DBU A 8 . ? 1_555 ? 3 AC1 4 TS9 A 11 ? TS9 A 10 . ? 1_555 ? 4 AC1 4 BB9 A 12 ? BB9 A 11 . ? 1_555 ? # _atom_sites.entry_id 2L2W _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 QUA 1 0 0 QUA QUA A . n A 1 2 ILE 2 1 1 ILE ILE A . n A 1 3 ALA 3 2 2 ALA ALA A . n A 1 4 DHA 4 3 3 DHA DHA A . n A 1 5 ALA 5 4 4 ALA ALA A . n A 1 6 SER 6 5 5 SER SER A . n A 1 7 BB9 7 6 6 BB9 BB9 A . n A 1 8 THR 8 7 7 THR THR A . n A 1 9 DBU 9 8 8 DBU DBU A . n A 1 10 DCY 10 9 9 DCY DCY A . n A 1 11 TS9 11 10 10 TS9 TS9 A . n A 1 12 BB9 12 11 11 BB9 BB9 A . n A 1 13 THR 13 12 12 THR THR A . n A 1 14 BB9 14 13 13 BB9 BB9 A . n A 1 15 MH6 15 14 14 MH6 MH6 A . n A 1 16 BB9 16 15 15 BB9 BB9 A . n A 1 17 DHA 17 16 16 DHA DHA A . n A 1 18 DHA 18 17 17 DHA DHA A . n A 1 19 NH2 19 18 17 NH2 DHA A . n # _pdbx_molecule_features.prd_id PRD_000223 _pdbx_molecule_features.name THIOSTREPTON _pdbx_molecule_features.type Thiopeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes. ; # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000223 _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 DHA 4 A DHA 3 ? SER '2-AMINO-ACRYLIC ACID' 2 A BB9 7 A BB9 6 ? CYS ? 3 A DBU 9 A DBU 8 ? THR '(2E)-2-AMINOBUT-2-ENOIC ACID' 4 A TS9 11 A TS9 10 ? ILE ? 5 A BB9 12 A BB9 11 ? CYS ? 6 A BB9 14 A BB9 13 ? CYS ? 7 A MH6 15 A MH6 14 ? SER '3-HYDROXY-2-IMINOPROPANOIC ACID' 8 A BB9 16 A BB9 15 ? CYS ? 9 A DHA 17 A DHA 16 ? SER '2-AMINO-ACRYLIC ACID' 10 A DHA 18 A DHA 17 ? SER '2-AMINO-ACRYLIC ACID' # _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 2011-02-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-12-12 4 'Structure model' 1 3 2013-05-08 # _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 ? # 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' Other 3 4 'Structure model' 'Derived calculations' # _pdbx_entry_details.entry_id 2L2W _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'A MODIFIED QUINOLINE LINKED TO THE MAIN-CHAIN OF RESIDUE 1 AND THE SIDE-CHAIN OF RESIDUE 12.' _pdbx_entry_details.compound_details ;THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) ; _pdbx_entry_details.source_details ? # _pdbx_nmr_exptl_sample.component thiostrepton _pdbx_nmr_exptl_sample.concentration 10 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2L2W _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 231 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 76 _pdbx_nmr_constraints.NOE_long_range_total_count 55 _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 62 _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 10 _pdbx_validate_close_contact.auth_atom_id_1 H _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ILE _pdbx_validate_close_contact.auth_seq_id_1 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 H _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ALA _pdbx_validate_close_contact.auth_seq_id_2 2 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.35 # 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 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.85 117.20 -13.35 2.20 Y 2 2 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.95 117.20 -13.25 2.20 Y 3 3 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.95 117.20 -13.25 2.20 Y 4 4 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.84 117.20 -13.36 2.20 Y 5 6 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.92 117.20 -13.28 2.20 Y 6 7 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.83 117.20 -13.37 2.20 Y 7 9 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.92 117.20 -13.28 2.20 Y 8 11 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.95 117.20 -13.25 2.20 Y 9 12 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.96 117.20 -13.24 2.20 Y 10 14 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.85 117.20 -13.35 2.20 Y 11 15 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.93 117.20 -13.27 2.20 Y 12 16 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.87 117.20 -13.33 2.20 Y 13 18 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.89 117.20 -13.31 2.20 Y 14 19 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.79 117.20 -13.41 2.20 Y 15 20 CA A BB9 13 ? ? C A BB9 13 ? ? N A MH6 14 ? ? 103.90 117.20 -13.30 2.20 Y # 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 ALA A 2 ? ? -172.56 124.19 2 1 SER A 5 ? ? 73.30 90.44 3 1 DCY A 9 ? ? -145.32 -37.98 4 2 ALA A 2 ? ? -172.12 119.19 5 2 SER A 5 ? ? 72.56 89.15 6 2 DCY A 9 ? ? -145.26 -37.74 7 3 ALA A 2 ? ? -171.24 128.02 8 3 SER A 5 ? ? 72.90 90.21 9 3 DCY A 9 ? ? -144.35 -38.01 10 4 ALA A 2 ? ? -172.27 123.88 11 4 SER A 5 ? ? 73.73 90.82 12 4 DCY A 9 ? ? -145.27 -36.60 13 5 ALA A 2 ? ? -172.33 126.44 14 5 SER A 5 ? ? 72.25 90.22 15 5 DCY A 9 ? ? -143.92 -40.55 16 6 ALA A 2 ? ? -173.51 121.89 17 6 SER A 5 ? ? 71.63 89.90 18 6 DCY A 9 ? ? -144.50 -40.52 19 7 ALA A 2 ? ? -172.71 122.14 20 7 SER A 5 ? ? 73.00 90.56 21 7 DCY A 9 ? ? -144.83 -42.50 22 8 ALA A 2 ? ? -170.64 125.15 23 8 SER A 5 ? ? 73.72 90.24 24 8 DCY A 9 ? ? -145.34 -29.32 25 9 ALA A 2 ? ? -171.57 121.04 26 9 SER A 5 ? ? 71.95 89.07 27 9 DCY A 9 ? ? -144.94 -29.84 28 10 ALA A 2 ? ? -173.13 118.58 29 10 SER A 5 ? ? 71.39 89.16 30 10 DCY A 9 ? ? -144.22 -37.36 31 11 ALA A 2 ? ? -170.41 126.72 32 11 SER A 5 ? ? 73.40 89.91 33 11 DCY A 9 ? ? -145.07 -30.45 34 12 ALA A 2 ? ? -172.80 119.08 35 12 SER A 5 ? ? 72.33 90.34 36 12 DCY A 9 ? ? -144.43 -41.98 37 13 ALA A 2 ? ? -171.70 123.29 38 13 SER A 5 ? ? 72.13 89.09 39 13 DCY A 9 ? ? -144.07 -39.17 40 14 SER A 5 ? ? 72.64 89.74 41 14 DCY A 9 ? ? -144.27 -38.47 42 15 ALA A 2 ? ? -172.86 119.95 43 15 SER A 5 ? ? 71.89 90.02 44 15 DCY A 9 ? ? -145.04 -36.98 45 16 ALA A 2 ? ? -171.74 122.41 46 16 SER A 5 ? ? 71.68 89.77 47 16 DCY A 9 ? ? -144.31 -43.05 48 17 ALA A 2 ? ? -171.06 123.94 49 17 SER A 5 ? ? 72.09 91.55 50 17 DCY A 9 ? ? -145.17 -41.77 51 18 ALA A 2 ? ? -171.05 120.25 52 18 SER A 5 ? ? 73.26 89.18 53 18 DCY A 9 ? ? -144.61 -28.67 54 19 ALA A 2 ? ? -170.61 124.43 55 19 SER A 5 ? ? 72.29 90.05 56 19 DCY A 9 ? ? -144.27 -38.54 57 20 ALA A 2 ? ? -173.62 119.19 58 20 SER A 5 ? ? 72.24 90.33 59 20 DCY A 9 ? ? -145.45 -35.86 #