data_1T5M # _entry.id 1T5M # _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 1T5M RCSB RCSB022341 WWPDB D_1000022341 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1XT7 unspecified 'SOLUTION STRUCTURE OF THE ANTIBIOTIC DAPTOMYCIN' PDB 1T5N unspecified 'SOLUTION STRUCTURE OF THE CALCIUM-DEPENDENT ANTIBIOTIC DAPTOMYCIN' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1T5M _pdbx_database_status.recvd_initial_deposition_date 2004-05-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Jung, D.' 1 'Rozek, A.' 2 'Okon, M.' 3 'Hancock, R.E.' 4 # _citation.id primary _citation.title 'Structural Transitions as Determinants of the Action of the Calcium-Dependent Antibiotic Daptomycin.' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 11 _citation.page_first 949 _citation.page_last ? _citation.year 2004 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15271353 _citation.pdbx_database_id_DOI 10.1016/J.CHEMBIOL.2004.04.020 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Jung, D.' 1 primary 'Rozek, A.' 2 primary 'Okon, M.' 3 primary 'Hancock, R.E.' 4 # _cell.entry_id 1T5M _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 1T5M _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 syn DAPTOMYCIN 1484.440 1 ? ? ? ? 2 non-polymer syn 'DECANOIC ACID' 172.265 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'A21978C, CUBICIN' # _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 'W(DSG)DTG(ORN)D(DAL)DG(DSN)(LME)(KYN)' _entity_poly.pdbx_seq_one_letter_code_can WNDTGADADGSEW _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 TRP n 1 2 DSG n 1 3 ASP n 1 4 THR n 1 5 GLY n 1 6 ORN n 1 7 ASP n 1 8 DAL n 1 9 ASP n 1 10 GLY n 1 11 DSN n 1 12 LME n 1 13 KYN n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'STREPTOMYCES ROSEOSPORUS' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 67294 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name NOR _struct_ref.db_code NOR00001 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession NOR00001 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1T5M _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 13 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession NOR00001 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 14 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 14 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 DAL 'D-peptide linking' . D-ALANINE ? 'C3 H7 N O2' 89.093 DKA non-polymer . 'DECANOIC ACID' ? 'C10 H20 O2' 172.265 DSG 'D-peptide linking' . D-ASPARAGINE ? 'C4 H8 N2 O3' 132.118 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 KYN 'L-peptide linking' n '(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid' L-KYNURENINE 'C10 H12 N2 O3' 208.214 LME 'L-peptide linking' n '(2S,3R)-2-azanyl-3-methyl-pentanedioic acid' '(3R)-3-methyl-L-glutamic acid' 'C6 H11 N O4' 161.156 ORN 'L-peptide linking' n L-ornithine ? 'C5 H12 N2 O2' 132.161 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 '2D TOCSY' 1 3 1 DQF-COSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 290.15 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure AMBIENT _pdbx_nmr_exptl_sample_conditions.pH 6.6 _pdbx_nmr_exptl_sample_conditions.ionic_strength '100mM KCL' _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2MM DAPTOMYCIN, 100MM KCL, 2MM EGTA, 0.2MM EDTA, 93% H2O, 7% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_details.entry_id 1T5M _pdbx_nmr_details.text 'THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.' # _pdbx_nmr_ensemble.entry_id 1T5M _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' # _pdbx_nmr_representative.entry_id 1T5M _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement 'DGII MODULE OF INSIGHT II VER 97.2' ? 'ACCYLRYS INC.' 1 'structure solution' 'DGII MODULE OF INSIGHT II VER 97.2' ? ? 2 'structure solution' 'NMRPIPE 1' ? ? 3 'structure solution' 'NMRVIEW 5.0.4' ? ? 4 # _exptl.entry_id 1T5M _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1T5M _struct.title 'Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin' _struct.pdbx_descriptor DAPTOMYCIN _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1T5M _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'DAPTOMYCIN, CUBICIN, ANTIBIOTIC, LIPOPEPTIDE, CALCIUM-DEPENDENT' # 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 ? # _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 covale1 covale ? ? B DKA . C1 ? ? ? 1_555 A TRP 1 N ? ? A DKA 1 A TRP 2 1_555 ? ? ? ? ? ? ? 1.349 ? covale2 covale ? ? A TRP 1 C ? ? ? 1_555 A DSG 2 N ? ? A TRP 2 A DSG 3 1_555 ? ? ? ? ? ? ? 1.353 ? covale3 covale ? ? A DSG 2 C ? ? ? 1_555 A ASP 3 N ? ? A DSG 3 A ASP 4 1_555 ? ? ? ? ? ? ? 1.347 ? covale4 covale ? ? A THR 4 OG1 ? ? ? 1_555 A KYN 13 C ? ? A THR 5 A KYN 14 1_555 ? ? ? ? ? ? ? 1.390 ? covale5 covale ? ? A GLY 5 C ? ? ? 1_555 A ORN 6 N ? ? A GLY 6 A ORN 7 1_555 ? ? ? ? ? ? ? 1.349 ? covale6 covale ? ? A ORN 6 C ? ? ? 1_555 A ASP 7 N ? ? A ORN 7 A ASP 8 1_555 ? ? ? ? ? ? ? 1.349 ? covale7 covale ? ? A ASP 7 C ? ? ? 1_555 A DAL 8 N ? ? A ASP 8 A DAL 9 1_555 ? ? ? ? ? ? ? 1.348 ? covale8 covale ? ? A DAL 8 C ? ? ? 1_555 A ASP 9 N ? ? A DAL 9 A ASP 10 1_555 ? ? ? ? ? ? ? 1.350 ? covale9 covale ? ? A GLY 10 C ? ? ? 1_555 A DSN 11 N ? ? A GLY 11 A DSN 12 1_555 ? ? ? ? ? ? ? 1.348 ? covale10 covale ? ? A DSN 11 C ? ? ? 1_555 A LME 12 N ? ? A DSN 12 A LME 13 1_555 ? ? ? ? ? ? ? 1.346 ? covale11 covale ? ? A LME 12 C ? ? ? 1_555 A KYN 13 N ? ? A LME 13 A KYN 14 1_555 ? ? ? ? ? ? ? 1.354 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 3 25.02 2 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 6 -24.81 3 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 7 -27.84 4 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 8 -26.17 5 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 9 24.78 6 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 10 27.85 7 GLY 5 A . ? GLY 6 A ORN 6 A ? ORN 7 A 11 29.06 8 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 11 27.22 9 GLY 5 A . ? GLY 6 A ORN 6 A ? ORN 7 A 12 -28.84 10 GLY 5 A . ? GLY 6 A ORN 6 A ? ORN 7 A 13 21.78 11 GLY 10 A . ? GLY 11 A DSN 11 A ? DSN 12 A 14 -10.99 # _database_PDB_matrix.entry_id 1T5M _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 1T5M _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_ _database_PDB_caveat.text ;THR A 5 C-BETA WRONG HAND IN ALL MODELS, THR A 5 C-ALPHA WRONG HAND IN ALL MODELS, LME A 13 C-BETA WRONG HAND IN ALL MODELS, KYN A 14 C-ALPHA WRONG HAND IN ALL MODELS ; # 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 TRP 1 2 2 TRP TRP A . n A 1 2 DSG 2 3 3 DSG DSG A . n A 1 3 ASP 3 4 4 ASP ASP A . n A 1 4 THR 4 5 5 THR THR A . n A 1 5 GLY 5 6 6 GLY GLY A . n A 1 6 ORN 6 7 7 ORN ORN A . n A 1 7 ASP 7 8 8 ASP ASP A . n A 1 8 DAL 8 9 9 DAL DAL A . n A 1 9 ASP 9 10 10 ASP ASP A . n A 1 10 GLY 10 11 11 GLY GLY A . n A 1 11 DSN 11 12 12 DSN DSN A . n A 1 12 LME 12 13 13 LME LME A . n A 1 13 KYN 13 14 14 KYN KYN A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id DKA _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id DKA _pdbx_nonpoly_scheme.auth_mon_id DKA _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_molecule_features.prd_id PRD_000217 _pdbx_molecule_features.name Daptomycin _pdbx_molecule_features.type 'Cyclic lipopeptide' _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000217 A 1 PRD_000217 B # _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 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,B # _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 2004-08-31 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 # _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' '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 # _pdbx_entry_details.entry_id 1T5M _pdbx_entry_details.compound_details ;DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.76 110.10 9.66 1.40 N 2 1 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.29 110.10 16.19 1.90 N 3 2 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.99 110.10 9.89 1.40 N 4 2 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.45 110.10 16.35 1.90 N 5 3 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.82 110.10 9.72 1.40 N 6 3 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.17 110.10 16.07 1.90 N 7 4 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.86 110.10 9.76 1.40 N 8 4 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.13 110.10 16.03 1.90 N 9 5 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.80 110.10 9.70 1.40 N 10 5 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 125.90 110.10 15.80 1.90 N 11 6 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.77 110.10 9.67 1.40 N 12 6 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.27 110.10 16.17 1.90 N 13 7 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.79 110.10 9.69 1.40 N 14 7 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.25 110.10 16.15 1.90 N 15 8 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.77 110.10 9.67 1.40 N 16 8 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.16 110.10 16.06 1.90 N 17 9 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.73 110.10 9.63 1.40 N 18 9 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 125.97 110.10 15.87 1.90 N 19 10 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.73 110.10 9.63 1.40 N 20 10 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.08 110.10 15.98 1.90 N 21 11 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.72 110.10 9.62 1.40 N 22 11 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.39 110.10 16.29 1.90 N 23 12 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.85 110.10 9.75 1.40 N 24 12 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.25 110.10 16.15 1.90 N 25 13 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.86 110.10 9.76 1.40 N 26 13 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.25 110.10 16.15 1.90 N 27 14 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.78 110.10 9.68 1.40 N 28 14 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.17 110.10 16.07 1.90 N 29 15 N A DAL 9 ? ? CA A DAL 9 ? ? CB A DAL 9 ? ? 119.82 110.10 9.72 1.40 N 30 15 CB A DSN 12 ? ? CA A DSN 12 ? ? C A DSN 12 ? ? 126.42 110.10 16.32 1.90 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 DSG A 3 ? ? 95.49 -50.47 2 1 ASP A 4 ? ? -18.22 -51.98 3 1 THR A 5 ? ? -100.91 54.93 4 1 DAL A 9 ? ? 156.27 -84.79 5 2 DSG A 3 ? ? 53.28 -171.41 6 2 THR A 5 ? ? 88.53 56.26 7 2 DAL A 9 ? ? 176.25 -91.57 8 3 DSG A 3 ? ? 31.05 -165.89 9 3 THR A 5 ? ? 93.14 94.87 10 3 ORN A 7 ? ? -46.41 150.97 11 3 ASP A 10 ? ? -113.21 -76.30 12 4 ASP A 4 ? ? 35.30 -139.26 13 4 THR A 5 ? ? -116.76 51.22 14 4 ASP A 8 ? ? -56.26 101.97 15 4 DAL A 9 ? ? 158.37 -65.21 16 4 ASP A 10 ? ? -119.57 -76.11 17 5 ASP A 4 ? ? 26.59 -127.05 18 5 THR A 5 ? ? 96.07 56.64 19 5 DAL A 9 ? ? 156.18 -72.63 20 6 THR A 5 ? ? 99.87 57.17 21 6 DAL A 9 ? ? 162.06 -61.38 22 6 ASP A 10 ? ? -106.99 -67.76 23 7 DSG A 3 ? ? 43.39 177.06 24 7 ASP A 4 ? ? -82.82 -98.09 25 7 THR A 5 ? ? 92.20 78.41 26 8 DSG A 3 ? ? 23.92 -64.64 27 8 DAL A 9 ? ? 158.24 -89.50 28 9 THR A 5 ? ? 98.40 84.06 29 9 DAL A 9 ? ? 159.05 -81.45 30 9 LME A 13 ? ? -54.88 -178.62 31 10 DSG A 3 ? ? 58.13 -177.59 32 10 THR A 5 ? ? 100.71 57.72 33 10 DAL A 9 ? ? 152.69 -73.24 34 10 ASP A 10 ? ? -85.78 -71.28 35 10 LME A 13 ? ? -44.67 155.42 36 11 DSG A 3 ? ? 63.91 -76.80 37 11 ASP A 4 ? ? 29.32 -94.96 38 11 THR A 5 ? ? 121.95 69.60 39 11 DAL A 9 ? ? 155.76 -73.09 40 12 DSG A 3 ? ? -3.69 -68.37 41 12 ASP A 4 ? ? -117.06 -103.98 42 12 THR A 5 ? ? 76.70 57.06 43 12 DAL A 9 ? ? 156.49 -71.55 44 13 DSG A 3 ? ? 33.84 -171.46 45 13 THR A 5 ? ? -27.97 -70.47 46 13 ORN A 7 ? ? -100.51 -161.81 47 13 ASP A 8 ? ? -20.06 104.69 48 13 DAL A 9 ? ? 154.19 -76.50 49 14 ASP A 4 ? ? -65.94 -94.88 50 14 THR A 5 ? ? 101.76 69.74 51 15 ASP A 4 ? ? 18.48 -95.39 52 15 THR A 5 ? ? 109.14 68.84 53 15 DAL A 9 ? ? 152.73 -68.99 # loop_ _pdbx_validate_peptide_omega.id _pdbx_validate_peptide_omega.PDB_model_num _pdbx_validate_peptide_omega.auth_comp_id_1 _pdbx_validate_peptide_omega.auth_asym_id_1 _pdbx_validate_peptide_omega.auth_seq_id_1 _pdbx_validate_peptide_omega.PDB_ins_code_1 _pdbx_validate_peptide_omega.label_alt_id_1 _pdbx_validate_peptide_omega.auth_comp_id_2 _pdbx_validate_peptide_omega.auth_asym_id_2 _pdbx_validate_peptide_omega.auth_seq_id_2 _pdbx_validate_peptide_omega.PDB_ins_code_2 _pdbx_validate_peptide_omega.label_alt_id_2 _pdbx_validate_peptide_omega.omega 1 13 ASP A 4 ? ? THR A 5 ? ? -149.41 2 15 GLY A 6 ? ? ORN A 7 ? ? -30.26 # 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 CA ? A THR 5 ? 'WRONG HAND' . 2 1 CB ? A THR 5 ? 'WRONG HAND' . 3 1 CB ? A LME 13 ? 'WRONG HAND' . 4 1 CA ? A KYN 14 ? 'WRONG HAND' . 5 2 CA ? A THR 5 ? 'WRONG HAND' . 6 2 CB ? A THR 5 ? 'WRONG HAND' . 7 2 CB ? A LME 13 ? 'WRONG HAND' . 8 2 CA ? A KYN 14 ? 'WRONG HAND' . 9 3 CA ? A THR 5 ? 'WRONG HAND' . 10 3 CB ? A THR 5 ? 'WRONG HAND' . 11 3 CB ? A LME 13 ? 'WRONG HAND' . 12 3 CA ? A KYN 14 ? 'WRONG HAND' . 13 4 CA ? A THR 5 ? 'WRONG HAND' . 14 4 CB ? A THR 5 ? 'WRONG HAND' . 15 4 CB ? A LME 13 ? 'WRONG HAND' . 16 4 CA ? A KYN 14 ? 'WRONG HAND' . 17 5 CA ? A THR 5 ? 'WRONG HAND' . 18 5 CB ? A THR 5 ? 'WRONG HAND' . 19 5 CB ? A LME 13 ? 'WRONG HAND' . 20 5 CA ? A KYN 14 ? 'WRONG HAND' . 21 6 CA ? A THR 5 ? 'WRONG HAND' . 22 6 CB ? A THR 5 ? 'WRONG HAND' . 23 6 CB ? A LME 13 ? 'WRONG HAND' . 24 6 CA ? A KYN 14 ? 'WRONG HAND' . 25 7 CA ? A THR 5 ? 'WRONG HAND' . 26 7 CB ? A THR 5 ? 'WRONG HAND' . 27 7 CB ? A LME 13 ? 'WRONG HAND' . 28 7 CA ? A KYN 14 ? 'WRONG HAND' . 29 8 CA ? A THR 5 ? 'WRONG HAND' . 30 8 CB ? A THR 5 ? 'WRONG HAND' . 31 8 CB ? A LME 13 ? 'WRONG HAND' . 32 8 CA ? A KYN 14 ? 'WRONG HAND' . 33 9 CA ? A THR 5 ? 'WRONG HAND' . 34 9 CB ? A THR 5 ? 'WRONG HAND' . 35 9 CB ? A LME 13 ? 'WRONG HAND' . 36 9 CA ? A KYN 14 ? 'WRONG HAND' . 37 10 CA ? A THR 5 ? 'WRONG HAND' . 38 10 CB ? A THR 5 ? 'WRONG HAND' . 39 10 CB ? A LME 13 ? 'WRONG HAND' . 40 10 CA ? A KYN 14 ? 'WRONG HAND' . 41 11 CA ? A THR 5 ? 'WRONG HAND' . 42 11 CB ? A THR 5 ? 'WRONG HAND' . 43 11 CB ? A LME 13 ? 'WRONG HAND' . 44 11 CA ? A KYN 14 ? 'WRONG HAND' . 45 12 CA ? A THR 5 ? 'WRONG HAND' . 46 12 CB ? A THR 5 ? 'WRONG HAND' . 47 12 CB ? A LME 13 ? 'WRONG HAND' . 48 12 CA ? A KYN 14 ? 'WRONG HAND' . 49 13 CA ? A THR 5 ? 'WRONG HAND' . 50 13 CB ? A THR 5 ? 'WRONG HAND' . 51 13 CB ? A LME 13 ? 'WRONG HAND' . 52 13 CA ? A KYN 14 ? 'WRONG HAND' . 53 14 CA ? A THR 5 ? 'WRONG HAND' . 54 14 CB ? A THR 5 ? 'WRONG HAND' . 55 14 CB ? A LME 13 ? 'WRONG HAND' . 56 14 CA ? A KYN 14 ? 'WRONG HAND' . 57 15 CA ? A THR 5 ? 'WRONG HAND' . 58 15 CB ? A THR 5 ? 'WRONG HAND' . 59 15 CB ? A LME 13 ? 'WRONG HAND' . 60 15 CA ? A KYN 14 ? 'WRONG HAND' . # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'DECANOIC ACID' _pdbx_entity_nonpoly.comp_id DKA #