data_1JNO # _entry.id 1JNO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 1JNO pdb_00001jno 10.2210/pdb1jno/pdb RCSB RCSB013978 ? ? WWPDB D_1000013978 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1TK2 unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE PROTEINASE SAVINASE' PDB 2XDC unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID CUBIC PHASE.' PDB 1AV2 unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE' PDB 1BDW unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS' PDB 1C4D unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE' PDB 1GMK unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM THIOCYANATE' PDB 1GRM unspecified 'SOLUTION STRUCTURE OF THE GRAMICIDIN A' PDB 1KQE unspecified 'SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ACETONE 10:1' PDB 1MAG unspecified 'SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS,' PDB 1MIC unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF CACL' PDB 1NG8 unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE MICELLES' PDB 1NRM unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES' PDB 1NRU unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THE PRESENCE OF EXCESS NA+' PDB 1NT5 unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE MICELLES' PDB 1JO3 unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES' PDB 1JO4 unspecified 'SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES' PDB 1NT6 unspecified 'SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES' PDB 1TKQ unspecified 'SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL' PDB 1W5U unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL' PDB 2IZQ unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL' PDB 3L8L unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI' PDB 1AL4 unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL' PDB 1ALX unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL' PDB 1ALZ unspecified 'CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JNO _pdbx_database_status.recvd_initial_deposition_date 2001-07-24 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Tucker, W.A.' 1 'Sham, S.' 2 'Townsley, L.E.' 3 'Hinton, J.F.' 4 # _citation.id primary _citation.title 'Structures of Gramicidins A, B, and C Incorporated Into Sodium Dodecyl Sulfate Micelles.' _citation.journal_abbrev Biochemistry _citation.journal_volume 40 _citation.page_first 11676 _citation.page_last ? _citation.year 2001 _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 11570868 _citation.pdbx_database_id_DOI 10.1021/BI010942W # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Townsley, L.E.' 1 ? primary 'Tucker, W.A.' 2 ? primary 'Sham, S.' 3 ? primary 'Hinton, J.F.' 4 ? # _cell.entry_id 1JNO _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 1JNO _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 'GRAMICIDIN A' _entity.formula_weight 1882.294 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'VALYL GRAMICIDIN' # _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 '(FVA)GA(DLE)A(DVA)V(DVA)W(DLE)W(DLE)W(DLE)W(ETA)' _entity_poly.pdbx_seq_one_letter_code_can VGALAVVVWLWLWLWX _entity_poly.pdbx_strand_id A,B _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 FVA n 1 2 GLY n 1 3 ALA n 1 4 DLE n 1 5 ALA n 1 6 DVA n 1 7 VAL n 1 8 DVA n 1 9 TRP n 1 10 DLE n 1 11 TRP n 1 12 DLE n 1 13 TRP n 1 14 DLE n 1 15 TRP n 1 16 ETA 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 'BREVIBACILLUS BREVIS' _entity_src_nat.pdbx_ncbi_taxonomy_id 1393 _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 NOR _struct_ref.db_code NOR00243 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession NOR00243 _struct_ref.pdbx_db_isoform ? # 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 1JNO A 1 ? 16 ? NOR00243 1 ? 16 ? 1 16 2 1 1JNO B 1 ? 16 ? NOR00243 1 ? 16 ? 1 16 # 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 DLE 'D-peptide linking' . D-LEUCINE ? 'C6 H13 N O2' 131.173 DVA 'D-peptide linking' . D-VALINE ? 'C5 H11 N O2' 117.146 ETA 'L-peptide COOH carboxy terminus' . ETHANOLAMINE ? 'C2 H7 N O' 61.083 FVA 'L-peptide linking' n N-formyl-L-valine ? 'C6 H11 N O3' 145.156 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type '2D NOESY' _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 328 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure AMBIENT _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '5MM GRAMICIDIN A, 250MM DEUTERATED SODIUM DODECYL SULFATE, 80% 100MM PHOSPHATE BUFFER PH 6.5, 10% D2O, 10% DEUTERATED TFE' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model VXRS _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1JNO _pdbx_nmr_refine.method 'DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION' _pdbx_nmr_refine.details ;THE STRUCTURE WAS MODELED USING 547 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1JNO _pdbx_nmr_details.text 'A 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.' # _pdbx_nmr_ensemble.entry_id 1JNO _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 1JNO _pdbx_nmr_representative.conformer_id ? _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement 'DISCOVER 97.2' ? BIOSYM/MSI 1 'structure solution' 'VNMR 3.2' ? ? 2 'structure solution' 'FELIX 95.0' ? ? 3 'structure solution' 'DSPACE 4.0' ? ? 4 # _exptl.entry_id 1JNO _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1JNO _struct.title 'Gramicidin A in Sodium Dodecyl Sulfate Micelles (NMR)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1JNO _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, SDS MICELLES, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN, ANTIBIOTIC' # 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 1 ? # _struct_biol.id 1 # 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 FVA 1 C ? ? ? 1_555 A GLY 2 N ? ? A FVA 1 A GLY 2 1_555 ? ? ? ? ? ? ? 1.343 ? ? covale2 covale both ? A ALA 3 C ? ? ? 1_555 A DLE 4 N ? ? A ALA 3 A DLE 4 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale3 covale both ? A DLE 4 C ? ? ? 1_555 A ALA 5 N ? ? A DLE 4 A ALA 5 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale4 covale both ? A ALA 5 C ? ? ? 1_555 A DVA 6 N ? ? A ALA 5 A DVA 6 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale5 covale both ? A DVA 6 C ? ? ? 1_555 A VAL 7 N ? ? A DVA 6 A VAL 7 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale6 covale both ? A VAL 7 C ? ? ? 1_555 A DVA 8 N ? ? A VAL 7 A DVA 8 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale7 covale both ? A DVA 8 C ? ? ? 1_555 A TRP 9 N ? ? A DVA 8 A TRP 9 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale8 covale both ? A TRP 9 C ? ? ? 1_555 A DLE 10 N ? ? A TRP 9 A DLE 10 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale9 covale both ? A DLE 10 C ? ? ? 1_555 A TRP 11 N ? ? A DLE 10 A TRP 11 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale10 covale both ? A TRP 11 C ? ? ? 1_555 A DLE 12 N ? ? A TRP 11 A DLE 12 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale11 covale both ? A DLE 12 C ? ? ? 1_555 A TRP 13 N ? ? A DLE 12 A TRP 13 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale12 covale both ? A TRP 13 C ? ? ? 1_555 A DLE 14 N ? ? A TRP 13 A DLE 14 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale13 covale both ? A DLE 14 C ? ? ? 1_555 A TRP 15 N ? ? A DLE 14 A TRP 15 1_555 ? ? ? ? ? ? ? 1.342 ? ? covale14 covale both ? A TRP 15 C ? ? ? 1_555 A ETA 16 N ? ? A TRP 15 A ETA 16 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale15 covale both ? B FVA 1 C ? ? ? 1_555 B GLY 2 N ? ? B FVA 1 B GLY 2 1_555 ? ? ? ? ? ? ? 1.343 ? ? covale16 covale both ? B ALA 3 C ? ? ? 1_555 B DLE 4 N ? ? B ALA 3 B DLE 4 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale17 covale both ? B DLE 4 C ? ? ? 1_555 B ALA 5 N ? ? B DLE 4 B ALA 5 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale18 covale both ? B ALA 5 C ? ? ? 1_555 B DVA 6 N ? ? B ALA 5 B DVA 6 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale19 covale both ? B DVA 6 C ? ? ? 1_555 B VAL 7 N ? ? B DVA 6 B VAL 7 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale20 covale both ? B VAL 7 C ? ? ? 1_555 B DVA 8 N ? ? B VAL 7 B DVA 8 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale21 covale both ? B DVA 8 C ? ? ? 1_555 B TRP 9 N ? ? B DVA 8 B TRP 9 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale22 covale both ? B TRP 9 C ? ? ? 1_555 B DLE 10 N ? ? B TRP 9 B DLE 10 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale23 covale both ? B DLE 10 C ? ? ? 1_555 B TRP 11 N ? ? B DLE 10 B TRP 11 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale24 covale both ? B TRP 11 C ? ? ? 1_555 B DLE 12 N ? ? B TRP 11 B DLE 12 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale25 covale both ? B DLE 12 C ? ? ? 1_555 B TRP 13 N ? ? B DLE 12 B TRP 13 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale26 covale both ? B TRP 13 C ? ? ? 1_555 B DLE 14 N ? ? B TRP 13 B DLE 14 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale27 covale both ? B DLE 14 C ? ? ? 1_555 B TRP 15 N ? ? B DLE 14 B TRP 15 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale28 covale both ? B TRP 15 C ? ? ? 1_555 B ETA 16 N ? ? B TRP 15 B ETA 16 1_555 ? ? ? ? ? ? ? 1.339 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id AA _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id AA _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 GLY A 2 ? TRP A 15 ? GLY A 2 TRP A 15 AA 2 GLY B 2 ? TRP B 15 ? GLY B 2 TRP B 15 # _pdbx_struct_sheet_hbond.sheet_id AA _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id ALA _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 3 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id ALA _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 3 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id ALA _pdbx_struct_sheet_hbond.range_2_label_asym_id B _pdbx_struct_sheet_hbond.range_2_label_seq_id 3 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id ALA _pdbx_struct_sheet_hbond.range_2_auth_asym_id B _pdbx_struct_sheet_hbond.range_2_auth_seq_id 3 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _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 _struct_site.details AC1 Software ? ? ? ? 3 'BINDING SITE FOR CHAIN A OF GRAMICIDIN A' AC2 Software ? ? ? ? 3 'BINDING SITE FOR CHAIN B OF GRAMICIDIN A' # 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 3 ALA B 3 ? ALA B 3 . ? 1_555 ? 2 AC1 3 DLE B 4 ? DLE B 4 . ? 1_555 ? 3 AC1 3 ALA B 5 ? ALA B 5 . ? 1_555 ? 4 AC2 3 ALA A 3 ? ALA A 3 . ? 1_555 ? 5 AC2 3 DLE A 4 ? DLE A 4 . ? 1_555 ? 6 AC2 3 ALA A 5 ? ALA A 5 . ? 1_555 ? # _database_PDB_matrix.entry_id 1JNO _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 1JNO _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 # 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 FVA 1 1 1 FVA FVA A . n A 1 2 GLY 2 2 2 GLY GLY A . n A 1 3 ALA 3 3 3 ALA ALA A . n A 1 4 DLE 4 4 4 DLE DLE A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 DVA 6 6 6 DVA DVA A . n A 1 7 VAL 7 7 7 VAL VAL A . n A 1 8 DVA 8 8 8 DVA DVA A . n A 1 9 TRP 9 9 9 TRP TRP A . n A 1 10 DLE 10 10 10 DLE DLE A . n A 1 11 TRP 11 11 11 TRP TRP A . n A 1 12 DLE 12 12 12 DLE DLE A . n A 1 13 TRP 13 13 13 TRP TRP A . n A 1 14 DLE 14 14 14 DLE DLE A . n A 1 15 TRP 15 15 15 TRP TRP A . n A 1 16 ETA 16 16 16 ETA ETA A . n B 1 1 FVA 1 1 1 FVA FVA B . n B 1 2 GLY 2 2 2 GLY GLY B . n B 1 3 ALA 3 3 3 ALA ALA B . n B 1 4 DLE 4 4 4 DLE DLE B . n B 1 5 ALA 5 5 5 ALA ALA B . n B 1 6 DVA 6 6 6 DVA DVA B . n B 1 7 VAL 7 7 7 VAL VAL B . n B 1 8 DVA 8 8 8 DVA DVA B . n B 1 9 TRP 9 9 9 TRP TRP B . n B 1 10 DLE 10 10 10 DLE DLE B . n B 1 11 TRP 11 11 11 TRP TRP B . n B 1 12 DLE 12 12 12 DLE DLE B . n B 1 13 TRP 13 13 13 TRP TRP B . n B 1 14 DLE 14 14 14 DLE DLE B . n B 1 15 TRP 15 15 15 TRP TRP B . n B 1 16 ETA 16 16 16 ETA ETA B . n # _pdbx_molecule_features.prd_id PRD_000150 _pdbx_molecule_features.name 'GRAMICIDIN A' _pdbx_molecule_features.type Polypeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000150 A 2 PRD_000150 B # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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 # 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)' 810 ? 1 MORE -3.0 ? 1 'SSA (A^2)' 2760 ? # _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 2001-08-08 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 2012-12-12 6 'Structure model' 1 5 2017-11-01 7 'Structure model' 2 0 2023-11-15 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # 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' 'Derived calculations' 10 7 'Structure model' 'Atomic model' 11 7 'Structure model' 'Data collection' 12 7 'Structure model' 'Database references' 13 7 'Structure model' 'Derived calculations' # 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 6 'Structure model' pdbx_struct_assembly 2 7 'Structure model' atom_site 3 7 'Structure model' chem_comp_atom 4 7 'Structure model' chem_comp_bond 5 7 'Structure model' database_2 6 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 6 'Structure model' '_pdbx_struct_assembly.method_details' 2 7 'Structure model' '_atom_site.auth_atom_id' 3 7 'Structure model' '_atom_site.label_atom_id' 4 7 'Structure model' '_database_2.pdbx_DOI' 5 7 'Structure model' '_database_2.pdbx_database_accession' 6 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_entry_details.entry_id 1JNO _pdbx_entry_details.compound_details ;GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A 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_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 DLE N N N N 14 DLE CA C N R 15 DLE CB C N N 16 DLE CG C N N 17 DLE CD1 C N N 18 DLE CD2 C N N 19 DLE C C N N 20 DLE O O N N 21 DLE OXT O N N 22 DLE H H N N 23 DLE H2 H N N 24 DLE HA H N N 25 DLE HB2 H N N 26 DLE HB3 H N N 27 DLE HG H N N 28 DLE HD11 H N N 29 DLE HD12 H N N 30 DLE HD13 H N N 31 DLE HD21 H N N 32 DLE HD22 H N N 33 DLE HD23 H N N 34 DLE HXT H N N 35 DVA N N N N 36 DVA CA C N R 37 DVA CB C N N 38 DVA CG1 C N N 39 DVA CG2 C N N 40 DVA C C N N 41 DVA O O N N 42 DVA OXT O N N 43 DVA H H N N 44 DVA H2 H N N 45 DVA HA H N N 46 DVA HB H N N 47 DVA HG11 H N N 48 DVA HG12 H N N 49 DVA HG13 H N N 50 DVA HG21 H N N 51 DVA HG22 H N N 52 DVA HG23 H N N 53 DVA HXT H N N 54 ETA CA C N N 55 ETA N N N N 56 ETA C C N N 57 ETA O O N N 58 ETA HA1 H N N 59 ETA HA2 H N N 60 ETA H H N N 61 ETA H2 H N N 62 ETA HB1 H N N 63 ETA HB2 H N N 64 ETA HO H N N 65 FVA C C N N 66 FVA N N N N 67 FVA O O N N 68 FVA CA C N S 69 FVA CB C N N 70 FVA CG1 C N N 71 FVA CG2 C N N 72 FVA H H N N 73 FVA HA H N N 74 FVA HB H N N 75 FVA HG11 H N N 76 FVA HG12 H N N 77 FVA HG13 H N N 78 FVA HG21 H N N 79 FVA HG22 H N N 80 FVA HG23 H N N 81 FVA O1 O N N 82 FVA CN C N N 83 FVA HN H N N 84 FVA OXT O N N 85 FVA HXT H N N 86 GLY N N N N 87 GLY CA C N N 88 GLY C C N N 89 GLY O O N N 90 GLY OXT O N N 91 GLY H H N N 92 GLY H2 H N N 93 GLY HA2 H N N 94 GLY HA3 H N N 95 GLY HXT H N N 96 TRP N N N N 97 TRP CA C N S 98 TRP C C N N 99 TRP O O N N 100 TRP CB C N N 101 TRP CG C Y N 102 TRP CD1 C Y N 103 TRP CD2 C Y N 104 TRP NE1 N Y N 105 TRP CE2 C Y N 106 TRP CE3 C Y N 107 TRP CZ2 C Y N 108 TRP CZ3 C Y N 109 TRP CH2 C Y N 110 TRP OXT O N N 111 TRP H H N N 112 TRP H2 H N N 113 TRP HA H N N 114 TRP HB2 H N N 115 TRP HB3 H N N 116 TRP HD1 H N N 117 TRP HE1 H N N 118 TRP HE3 H N N 119 TRP HZ2 H N N 120 TRP HZ3 H N N 121 TRP HH2 H N N 122 TRP HXT H N N 123 VAL N N N N 124 VAL CA C N S 125 VAL C C N N 126 VAL O O N N 127 VAL CB C N N 128 VAL CG1 C N N 129 VAL CG2 C N N 130 VAL OXT O N N 131 VAL H H N N 132 VAL H2 H N N 133 VAL HA H N N 134 VAL HB H N N 135 VAL HG11 H N N 136 VAL HG12 H N N 137 VAL HG13 H N N 138 VAL HG21 H N N 139 VAL HG22 H N N 140 VAL HG23 H N N 141 VAL HXT H N N 142 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 DLE N CA sing N N 13 DLE N H sing N N 14 DLE N H2 sing N N 15 DLE CA CB sing N N 16 DLE CA C sing N N 17 DLE CA HA sing N N 18 DLE CB CG sing N N 19 DLE CB HB2 sing N N 20 DLE CB HB3 sing N N 21 DLE CG CD1 sing N N 22 DLE CG CD2 sing N N 23 DLE CG HG sing N N 24 DLE CD1 HD11 sing N N 25 DLE CD1 HD12 sing N N 26 DLE CD1 HD13 sing N N 27 DLE CD2 HD21 sing N N 28 DLE CD2 HD22 sing N N 29 DLE CD2 HD23 sing N N 30 DLE C O doub N N 31 DLE C OXT sing N N 32 DLE OXT HXT sing N N 33 DVA N CA sing N N 34 DVA N H sing N N 35 DVA N H2 sing N N 36 DVA CA CB sing N N 37 DVA CA C sing N N 38 DVA CA HA sing N N 39 DVA CB CG1 sing N N 40 DVA CB CG2 sing N N 41 DVA CB HB sing N N 42 DVA CG1 HG11 sing N N 43 DVA CG1 HG12 sing N N 44 DVA CG1 HG13 sing N N 45 DVA CG2 HG21 sing N N 46 DVA CG2 HG22 sing N N 47 DVA CG2 HG23 sing N N 48 DVA C O doub N N 49 DVA C OXT sing N N 50 DVA OXT HXT sing N N 51 ETA CA N sing N N 52 ETA CA C sing N N 53 ETA CA HA1 sing N N 54 ETA CA HA2 sing N N 55 ETA N H sing N N 56 ETA N H2 sing N N 57 ETA C O sing N N 58 ETA C HB1 sing N N 59 ETA C HB2 sing N N 60 ETA O HO sing N N 61 FVA O C doub N N 62 FVA C CA sing N N 63 FVA H N sing N N 64 FVA N CN sing N N 65 FVA N CA sing N N 66 FVA CB CA sing N N 67 FVA CA HA sing N N 68 FVA HB CB sing N N 69 FVA CB CG2 sing N N 70 FVA CB CG1 sing N N 71 FVA HG13 CG1 sing N N 72 FVA HG12 CG1 sing N N 73 FVA CG1 HG11 sing N N 74 FVA HG22 CG2 sing N N 75 FVA HG23 CG2 sing N N 76 FVA CG2 HG21 sing N N 77 FVA CN O1 doub N N 78 FVA HN CN sing N N 79 FVA C OXT sing N N 80 FVA OXT HXT sing N N 81 GLY N CA sing N N 82 GLY N H sing N N 83 GLY N H2 sing N N 84 GLY CA C sing N N 85 GLY CA HA2 sing N N 86 GLY CA HA3 sing N N 87 GLY C O doub N N 88 GLY C OXT sing N N 89 GLY OXT HXT sing N N 90 TRP N CA sing N N 91 TRP N H sing N N 92 TRP N H2 sing N N 93 TRP CA C sing N N 94 TRP CA CB sing N N 95 TRP CA HA sing N N 96 TRP C O doub N N 97 TRP C OXT sing N N 98 TRP CB CG sing N N 99 TRP CB HB2 sing N N 100 TRP CB HB3 sing N N 101 TRP CG CD1 doub Y N 102 TRP CG CD2 sing Y N 103 TRP CD1 NE1 sing Y N 104 TRP CD1 HD1 sing N N 105 TRP CD2 CE2 doub Y N 106 TRP CD2 CE3 sing Y N 107 TRP NE1 CE2 sing Y N 108 TRP NE1 HE1 sing N N 109 TRP CE2 CZ2 sing Y N 110 TRP CE3 CZ3 doub Y N 111 TRP CE3 HE3 sing N N 112 TRP CZ2 CH2 doub Y N 113 TRP CZ2 HZ2 sing N N 114 TRP CZ3 CH2 sing Y N 115 TRP CZ3 HZ3 sing N N 116 TRP CH2 HH2 sing N N 117 TRP OXT HXT sing N N 118 VAL N CA sing N N 119 VAL N H sing N N 120 VAL N H2 sing N N 121 VAL CA C sing N N 122 VAL CA CB sing N N 123 VAL CA HA sing N N 124 VAL C O doub N N 125 VAL C OXT sing N N 126 VAL CB CG1 sing N N 127 VAL CB CG2 sing N N 128 VAL CB HB sing N N 129 VAL CG1 HG11 sing N N 130 VAL CG1 HG12 sing N N 131 VAL CG1 HG13 sing N N 132 VAL CG2 HG21 sing N N 133 VAL CG2 HG22 sing N N 134 VAL CG2 HG23 sing N N 135 VAL OXT HXT sing N N 136 #