data_1XVR # _entry.id 1XVR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1XVR NDB DD0068 RCSB RCSB030820 WWPDB D_1000030820 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 185D unspecified 'SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A' PDB 193D unspecified 'SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305' PDB 1PFE unspecified 'CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P6322' PDB 1VS2 unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A' PDB 1XVK unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 1XVN unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 2ADW unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212' PDB 2DA8 unspecified 'SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8' PDB 3GO3 unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XVR _pdbx_database_status.recvd_initial_deposition_date 2004-10-28 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 'Cuesta-Seijo, J.A.' 1 'Sheldrick, G.M.' 2 # _citation.id primary _citation.title 'Structures of Complexes between Echinomycin and Duplex DNA.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 61 _citation.page_first 442 _citation.page_last ? _citation.year 2005 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15805599 _citation.pdbx_database_id_DOI 10.1107/S090744490500137X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Cuesta-Seijo, J.A.' 1 primary 'Sheldrick, G.M.' 2 # _cell.entry_id 1XVR _cell.length_a 29.512 _cell.length_b 62.616 _cell.length_c 34.143 _cell.angle_alpha 90.00 _cell.angle_beta 114.99 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1XVR _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # 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 "5'-D(*CP*GP*TP*AP*CP*G)-3'" 1809.217 2 ? ? ? ? 2 polymer nat ECHINOMYCIN 809.008 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer syn 2-CARBOXYQUINOXALINE 174.156 4 ? ? ? ? 5 water nat water 18.015 43 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name 'QUINOMYCIN A' # 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 polydeoxyribonucleotide no no '(DC)(DG)(DT)(DA)(DC)(DG)' CGTACG A,C ? 2 'polypeptide(L)' no yes '(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)' SAXVSAXV D,E ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 DG n 2 1 DSN n 2 2 ALA n 2 3 N2C n 2 4 MVA n 2 5 DSN n 2 6 ALA n 2 7 NCY n 2 8 MVA n # _entity_src_nat.entity_id 2 _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 ECHINATUS' _entity_src_nat.pdbx_ncbi_taxonomy_id 67293 _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 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 1XVR 1 ? ? 1XVR ? 2 NOR NOR01126 2 ? ? NOR01126 ? # 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 1XVR A 1 ? 6 ? 1XVR 2 ? 7 ? 2 7 2 1 1XVR C 1 ? 6 ? 1XVR 102 ? 107 ? 102 107 3 2 1XVR D 1 ? 8 ? NOR01126 1 ? 8 ? 1 8 4 2 1XVR E 1 ? 8 ? NOR01126 1 ? 8 ? 1 8 # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MVA 'L-peptide linking' n N-METHYLVALINE ? 'C6 H13 N O2' 131.173 N2C 'L-peptide linking' . N,S-DIMETHYLCYSTEINE ? 'C5 H11 N O2 S' 149.211 NCY 'L-peptide linking' . N-METHYLCYSTEINE ? 'C4 H9 N O2 S' 135.185 QUI non-polymer . 2-CARBOXYQUINOXALINE ? 'C9 H6 N2 O2' 174.156 # _exptl.entry_id 1XVR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.35 _exptl_crystal.density_percent_sol 47.32 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'MPD, MGCL2, MES, SPERMINE-HCL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K' # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 MES ? ? ? 1 4 1 spermine-HCl ? ? ? 1 5 1 H2O ? ? ? 1 6 2 MPD ? ? ? 1 7 2 MgCl2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2003-12-11 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI-111 CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.1' _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.1 _diffrn_source.pdbx_wavelength 0.9 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1XVR _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 16.500 _reflns.d_resolution_high 1.400 _reflns.number_obs 10857 _reflns.number_all ? _reflns.percent_possible_obs 97.8 _reflns.pdbx_Rmerge_I_obs 0.05460 _reflns.pdbx_Rsym_value 0.05460 _reflns.pdbx_netI_over_sigmaI 12.7200 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.820 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.50 _reflns_shell.percent_possible_all 94.3 _reflns_shell.Rmerge_I_obs 0.27500 _reflns_shell.pdbx_Rsym_value 0.27500 _reflns_shell.meanI_over_sigI_obs 4.870 _reflns_shell.pdbx_redundancy 3.53 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1XVR _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 10857 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 16.50 _refine.ls_d_res_high 1.40 _refine.ls_percent_reflns_obs 97.8 _refine.ls_R_factor_obs 0.189 _refine.ls_R_factor_all 0.189 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.235 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 1089 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MR _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH AND HUBER' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 1XVR _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 4 _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 106 _refine_hist.pdbx_number_atoms_nucleic_acid 240 _refine_hist.pdbx_number_atoms_ligand 50 _refine_hist.number_atoms_solvent 43 _refine_hist.number_atoms_total 439 _refine_hist.d_res_high 1.40 _refine_hist.d_res_low 16.50 # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1XVR _pdbx_refine.R_factor_all_no_cutoff 0.189 _pdbx_refine.R_factor_obs_no_cutoff 0.189 _pdbx_refine.free_R_factor_no_cutoff 0.235 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1089 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 1XVR _struct.title 'echinomycin (CGTACG)2 complex' _struct.pdbx_descriptor 'ECHINOMYCIN/DNA Complex, 2-CARBOXYQUINOXALINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XVR _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC _struct_keywords.text 'BISINTERCALATOR, HOOGSTEEN BASEPAIR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX' # 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 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 5 ? L N N 5 ? M N N 5 ? N N N 5 ? # _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 metalc1 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 201 A HOH 2005 1_555 ? ? ? ? ? ? ? 2.048 ? metalc2 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 201 A HOH 2005 2_657 ? ? ? ? ? ? ? 2.048 ? metalc3 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 201 A HOH 2006 1_555 ? ? ? ? ? ? ? 1.985 ? metalc4 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 201 A HOH 2006 2_657 ? ? ? ? ? ? ? 1.981 ? metalc5 metalc ? ? E MG . MG ? ? ? 1_555 M HOH . O ? ? A MG 201 D HOH 2001 1_555 ? ? ? ? ? ? ? 2.141 ? metalc6 metalc ? ? E MG . MG ? ? ? 1_555 M HOH . O ? ? A MG 201 D HOH 2001 2_657 ? ? ? ? ? ? ? 2.142 ? metalc7 metalc ? ? F MG . MG ? ? ? 1_555 N HOH . O ? ? C MG 211 E HOH 2001 1_555 ? ? ? ? ? ? ? 2.179 ? metalc8 metalc ? ? F MG . MG ? ? ? 1_555 N HOH . O ? ? C MG 211 E HOH 2001 2_657 ? ? ? ? ? ? ? 2.180 ? metalc9 metalc ? ? F MG . MG ? ? ? 1_555 L HOH . O ? ? C MG 211 C HOH 2002 1_555 ? ? ? ? ? ? ? 1.999 ? metalc10 metalc ? ? F MG . MG ? ? ? 1_555 L HOH . O ? ? C MG 211 C HOH 2002 2_657 ? ? ? ? ? ? ? 2.001 ? metalc11 metalc ? ? F MG . MG ? ? ? 1_555 L HOH . O ? ? C MG 211 C HOH 2003 1_555 ? ? ? ? ? ? ? 2.092 ? metalc12 metalc ? ? F MG . MG ? ? ? 1_555 L HOH . O ? ? C MG 211 C HOH 2003 2_657 ? ? ? ? ? ? ? 2.096 ? covale1 covale ? ? G QUI . C ? ? ? 1_555 C DSN 1 N ? ? D QUI 0 D DSN 1 1_555 ? ? ? ? ? ? ? 1.361 ? covale2 covale ? ? C DSN 1 C ? ? ? 1_555 C ALA 2 N ? ? D DSN 1 D ALA 2 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? C DSN 1 OG ? ? ? 1_555 C MVA 8 C ? ? D DSN 1 D MVA 8 1_555 ? ? ? ? ? ? ? 1.331 ? covale4 covale ? ? C ALA 2 C ? ? ? 1_555 C N2C 3 N ? ? D ALA 2 D N2C 3 1_555 ? ? ? ? ? ? ? 1.337 ? covale5 covale ? ? C N2C 3 C ? ? ? 1_555 C MVA 4 N ? ? D N2C 3 D MVA 4 1_555 ? ? ? ? ? ? ? 1.354 ? covale6 covale ? ? C N2C 3 CB ? ? ? 1_555 C NCY 7 SG ? ? D N2C 3 D NCY 7 1_555 ? ? ? ? ? ? ? 1.797 ? covale7 covale ? ? C MVA 4 C ? ? ? 1_555 C DSN 5 OG ? ? D MVA 4 D DSN 5 1_555 ? ? ? ? ? ? ? 1.313 ? covale8 covale ? ? C DSN 5 C ? ? ? 1_555 C ALA 6 N ? ? D DSN 5 D ALA 6 1_555 ? ? ? ? ? ? ? 1.322 ? covale9 covale ? ? C DSN 5 N ? ? ? 1_555 H QUI . C ? ? D DSN 5 D QUI 9 1_555 ? ? ? ? ? ? ? 1.360 ? covale10 covale ? ? C ALA 6 C ? ? ? 1_555 C NCY 7 N ? ? D ALA 6 D NCY 7 1_555 ? ? ? ? ? ? ? 1.327 ? covale11 covale ? ? C NCY 7 C ? ? ? 1_555 C MVA 8 N ? ? D NCY 7 D MVA 8 1_555 ? ? ? ? ? ? ? 1.334 ? covale12 covale ? ? I QUI . C ? ? ? 1_555 D DSN 1 N ? ? E QUI 0 E DSN 1 1_555 ? ? ? ? ? ? ? 1.366 ? covale13 covale ? ? D DSN 1 OG ? ? ? 1_555 D MVA 8 C ? ? E DSN 1 E MVA 8 1_555 ? ? ? ? ? ? ? 1.330 ? covale14 covale ? ? D DSN 1 C ? ? ? 1_555 D ALA 2 N ? ? E DSN 1 E ALA 2 1_555 ? ? ? ? ? ? ? 1.333 ? covale15 covale ? ? D ALA 2 C ? ? ? 1_555 D N2C 3 N ? ? E ALA 2 E N2C 3 1_555 ? ? ? ? ? ? ? 1.342 ? covale16 covale ? ? D N2C 3 CB ? ? ? 1_555 D NCY 7 SG ? ? E N2C 3 E NCY 7 1_555 ? ? ? ? ? ? ? 1.802 ? covale17 covale ? ? D N2C 3 C ? ? ? 1_555 D MVA 4 N ? ? E N2C 3 E MVA 4 1_555 ? ? ? ? ? ? ? 1.340 ? covale18 covale ? ? D MVA 4 C ? ? ? 1_555 D DSN 5 OG ? ? E MVA 4 E DSN 5 1_555 ? ? ? ? ? ? ? 1.308 ? covale19 covale ? ? D DSN 5 C ? ? ? 1_555 D ALA 6 N ? ? E DSN 5 E ALA 6 1_555 ? ? ? ? ? ? ? 1.326 ? covale20 covale ? ? D DSN 5 N ? ? ? 1_555 J QUI . C ? ? E DSN 5 E QUI 9 1_555 ? ? ? ? ? ? ? 1.377 ? covale21 covale ? ? D ALA 6 C ? ? ? 1_555 D NCY 7 N ? ? E ALA 6 E NCY 7 1_555 ? ? ? ? ? ? ? 1.320 ? covale22 covale ? ? D NCY 7 C ? ? ? 1_555 D MVA 8 N ? ? E NCY 7 E MVA 8 1_555 ? ? ? ? ? ? ? 1.327 ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 2 C DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 2 C DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 2 C DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 3 C DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 3 C DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 3 C DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N7 ? ? A DT 4 C DA 105 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 4 C DA 105 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 5 C DT 104 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog10 hydrog ? ? A DA 4 N7 ? ? ? 1_555 B DT 3 N3 ? ? A DA 5 C DT 104 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 6 C DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 6 C DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 6 C DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 7 C DC 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 7 C DC 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 7 C DC 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? hydrog ? ? # 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 RESIDUE MG A 201' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MG C 211' AC3 Software ? ? ? ? 13 'BINDING SITE FOR CHAIN D OF ECHINOMYCIN' AC4 Software ? ? ? ? 14 'BINDING SITE FOR CHAIN E OF ECHINOMYCIN' # 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 HOH K . ? HOH A 2005 . ? 1_555 ? 2 AC1 3 HOH K . ? HOH A 2006 . ? 1_555 ? 3 AC1 3 HOH M . ? HOH D 2001 . ? 1_555 ? 4 AC2 3 HOH L . ? HOH C 2002 . ? 1_555 ? 5 AC2 3 HOH L . ? HOH C 2003 . ? 1_555 ? 6 AC2 3 HOH N . ? HOH E 2001 . ? 1_555 ? 7 AC3 13 DC A 1 ? DC A 2 . ? 1_555 ? 8 AC3 13 DG A 2 ? DG A 3 . ? 1_555 ? 9 AC3 13 DT A 3 ? DT A 4 . ? 1_555 ? 10 AC3 13 DG A 6 ? DG A 7 . ? 1_555 ? 11 AC3 13 DA B 4 ? DA C 105 . ? 1_555 ? 12 AC3 13 DC B 5 ? DC C 106 . ? 1_555 ? 13 AC3 13 DG B 6 ? DG C 107 . ? 1_555 ? 14 AC3 13 HOH M . ? HOH D 2001 . ? 1_555 ? 15 AC3 13 HOH M . ? HOH D 2002 . ? 1_555 ? 16 AC3 13 HOH M . ? HOH D 2004 . ? 1_555 ? 17 AC3 13 HOH M . ? HOH D 2005 . ? 1_555 ? 18 AC3 13 DSN D 5 ? DSN E 5 . ? 1_555 ? 19 AC3 13 QUI J . ? QUI E 9 . ? 1_555 ? 20 AC4 14 DA A 4 ? DA A 5 . ? 1_555 ? 21 AC4 14 DC A 5 ? DC A 6 . ? 1_555 ? 22 AC4 14 DG A 6 ? DG A 7 . ? 1_555 ? 23 AC4 14 DC B 1 ? DC C 102 . ? 1_555 ? 24 AC4 14 DG B 2 ? DG C 103 . ? 1_555 ? 25 AC4 14 DT B 3 ? DT C 104 . ? 1_555 ? 26 AC4 14 DG B 6 ? DG C 107 . ? 1_555 ? 27 AC4 14 DSN C 5 ? DSN D 5 . ? 1_555 ? 28 AC4 14 QUI H . ? QUI D 9 . ? 1_555 ? 29 AC4 14 HOH N . ? HOH E 2001 . ? 1_555 ? 30 AC4 14 HOH N . ? HOH E 2002 . ? 1_555 ? 31 AC4 14 HOH N . ? HOH E 2005 . ? 1_555 ? 32 AC4 14 HOH N . ? HOH E 2006 . ? 1_555 ? 33 AC4 14 HOH N . ? HOH E 2007 . ? 1_555 ? # _database_PDB_matrix.entry_id 1XVR _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 1XVR _atom_sites.fract_transf_matrix[1][1] 0.033885 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.015793 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.015970 _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] 0.032314 _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 MG N O P 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 DC 1 2 2 DC DC A . n A 1 2 DG 2 3 3 DG DG A . n A 1 3 DT 3 4 4 DT DT A . n A 1 4 DA 4 5 5 DA DA A . n A 1 5 DC 5 6 6 DC DC A . n A 1 6 DG 6 7 7 DG DG A . n B 1 1 DC 1 102 102 DC DC C . n B 1 2 DG 2 103 103 DG DG C . n B 1 3 DT 3 104 104 DT DT C . n B 1 4 DA 4 105 105 DA DA C . n B 1 5 DC 5 106 106 DC DC C . n B 1 6 DG 6 107 107 DG DG C . n C 2 1 DSN 1 1 1 DSN DSN D . n C 2 2 ALA 2 2 2 ALA ALA D . n C 2 3 N2C 3 3 3 N2C N2C D . n C 2 4 MVA 4 4 4 MVA MVA D . n C 2 5 DSN 5 5 5 DSN DSN D . n C 2 6 ALA 6 6 6 ALA ALA D . n C 2 7 NCY 7 7 7 NCY NCY D . n C 2 8 MVA 8 8 8 MVA MVA D . n D 2 1 DSN 1 1 1 DSN DSN E . n D 2 2 ALA 2 2 2 ALA ALA E . n D 2 3 N2C 3 3 3 N2C N2C E . n D 2 4 MVA 4 4 4 MVA MVA E . n D 2 5 DSN 5 5 5 DSN DSN E . n D 2 6 ALA 6 6 6 ALA ALA E . n D 2 7 NCY 7 7 7 NCY NCY E . n D 2 8 MVA 8 8 8 MVA MVA E . n # _pdbx_molecule_features.prd_id PRD_000491 _pdbx_molecule_features.name Echinomycin _pdbx_molecule_features.type 'Cyclic depsipeptide' _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000491 C 1 PRD_000491 G 1 PRD_000491 H 2 PRD_000491 D 2 PRD_000491 I 2 PRD_000491 J # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,E,F,G,H,I,J,K,L,M,N # 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)' 560 ? 1 MORE -3.8 ? 1 'SSA (A^2)' 2840 ? # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A MG 201 ? E MG . 2 1 C MG 211 ? F MG . 3 1 E HOH 2005 ? N HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? K HOH . ? A HOH 2005 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2005 ? 2_657 94.2 ? 2 O ? K HOH . ? A HOH 2005 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2006 ? 1_555 91.9 ? 3 O ? K HOH . ? A HOH 2005 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2006 ? 1_555 91.2 ? 4 O ? K HOH . ? A HOH 2005 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2006 ? 2_657 91.4 ? 5 O ? K HOH . ? A HOH 2005 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2006 ? 2_657 92.0 ? 6 O ? K HOH . ? A HOH 2006 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? K HOH . ? A HOH 2006 ? 2_657 175.3 ? 7 O ? K HOH . ? A HOH 2005 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 1_555 88.0 ? 8 O ? K HOH . ? A HOH 2005 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 1_555 177.8 ? 9 O ? K HOH . ? A HOH 2006 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 1_555 88.9 ? 10 O ? K HOH . ? A HOH 2006 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 1_555 87.8 ? 11 O ? K HOH . ? A HOH 2005 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 2_657 177.8 ? 12 O ? K HOH . ? A HOH 2005 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 2_657 88.0 ? 13 O ? K HOH . ? A HOH 2006 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 2_657 87.7 ? 14 O ? K HOH . ? A HOH 2006 ? 2_657 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 2_657 89.0 ? 15 O ? M HOH . ? D HOH 2001 ? 1_555 MG ? E MG . ? A MG 201 ? 1_555 O ? M HOH . ? D HOH 2001 ? 2_657 89.8 ? 16 O ? N HOH . ? E HOH 2001 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? N HOH . ? E HOH 2001 ? 2_657 86.6 ? 17 O ? N HOH . ? E HOH 2001 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2002 ? 1_555 89.1 ? 18 O ? N HOH . ? E HOH 2001 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2002 ? 1_555 175.7 ? 19 O ? N HOH . ? E HOH 2001 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2002 ? 2_657 175.7 ? 20 O ? N HOH . ? E HOH 2001 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2002 ? 2_657 89.1 ? 21 O ? L HOH . ? C HOH 2002 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2002 ? 2_657 95.2 ? 22 O ? N HOH . ? E HOH 2001 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 1_555 88.4 ? 23 O ? N HOH . ? E HOH 2001 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 1_555 89.8 ? 24 O ? L HOH . ? C HOH 2002 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 1_555 89.8 ? 25 O ? L HOH . ? C HOH 2002 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 1_555 92.0 ? 26 O ? N HOH . ? E HOH 2001 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 2_657 89.8 ? 27 O ? N HOH . ? E HOH 2001 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 2_657 88.3 ? 28 O ? L HOH . ? C HOH 2002 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 2_657 92.0 ? 29 O ? L HOH . ? C HOH 2002 ? 2_657 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 2_657 89.6 ? 30 O ? L HOH . ? C HOH 2003 ? 1_555 MG ? F MG . ? C MG 211 ? 1_555 O ? L HOH . ? C HOH 2003 ? 2_657 177.5 ? # 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 2005-04-12 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 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal EPMR phasing . ? 1 SHELXL-97 refinement . ? 2 HKL-2000 'data reduction' . ? 3 XDS 'data scaling' . ? 4 # _pdbx_entry_details.entry_id 1XVR _pdbx_entry_details.compound_details ;THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. ; _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 "O4'" A DC 2 ? A "C4'" A DC 2 ? A "C3'" A DC 2 ? A 100.78 104.50 -3.72 0.40 N 2 1 "C1'" A DC 2 ? A "O4'" A DC 2 ? A "C4'" A DC 2 ? A 103.03 110.10 -7.07 1.00 N 3 1 "O4'" A DC 2 ? A "C1'" A DC 2 ? A N1 A DC 2 ? ? 112.14 108.30 3.84 0.30 N 4 1 P A DG 3 ? A "O5'" A DG 3 ? A "C5'" A DG 3 ? A 130.93 120.90 10.03 1.60 N 5 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 100.24 108.00 -7.76 0.70 N 6 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 103.30 108.00 -4.70 0.70 N 7 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 101.46 108.00 -6.54 0.70 N 8 1 "O5'" A DG 7 ? ? "C5'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.75 109.40 -5.65 0.80 N 9 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.10 108.30 2.80 0.30 N 10 1 "O4'" C DT 104 ? ? "C1'" C DT 104 ? ? N1 C DT 104 ? ? 101.59 108.00 -6.41 0.70 N 11 1 C6 C DT 104 ? ? N1 C DT 104 ? ? C2 C DT 104 ? ? 117.40 121.30 -3.90 0.50 N 12 1 C5 C DT 104 ? ? C6 C DT 104 ? ? N1 C DT 104 ? ? 127.91 123.70 4.21 0.60 N 13 1 N3 C DT 104 ? ? C2 C DT 104 ? ? O2 C DT 104 ? ? 118.05 122.30 -4.25 0.60 N 14 1 N3 C DT 104 ? ? C4 C DT 104 ? ? O4 C DT 104 ? ? 124.29 119.90 4.39 0.60 N 15 1 C4 C DT 104 ? ? C5 C DT 104 ? ? C7 C DT 104 ? ? 115.23 119.00 -3.77 0.60 N 16 1 C6 C DT 104 ? ? C5 C DT 104 ? ? C7 C DT 104 ? ? 128.40 122.90 5.50 0.60 N 17 1 N1 C DA 105 ? ? C6 C DA 105 ? ? N6 C DA 105 ? ? 122.77 118.60 4.17 0.60 N 18 1 "O4'" C DC 106 ? ? "C1'" C DC 106 ? ? N1 C DC 106 ? ? 103.02 108.00 -4.98 0.70 N 19 1 "O4'" C DG 107 ? ? "C1'" C DG 107 ? ? N9 C DG 107 ? ? 112.48 108.30 4.18 0.30 N # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C D MVA 4 ? ? N D DSN 5 ? ? 3.95 2 1 C E MVA 4 ? ? N E DSN 5 ? ? 3.83 # _ndb_struct_conf_na.entry_id 1XVR _ndb_struct_conf_na.feature 'double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 6 1_555 0.247 -0.149 0.305 -21.322 2.999 -2.409 1 A_DC2:DG107_C A 2 ? C 107 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 -0.364 -0.101 0.375 22.044 -0.009 -1.156 2 A_DG3:DC106_C A 3 ? C 106 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 -0.525 3.618 0.457 -6.349 10.239 -67.690 3 A_DT4:DA105_C A 4 ? C 105 ? 23 3 1 A DA 4 1_555 B DT 3 1_555 0.603 -3.567 -0.565 6.514 -11.427 67.592 4 A_DA5:DT104_C A 5 ? C 104 ? 23 3 1 A DC 5 1_555 B DG 2 1_555 0.373 -0.087 0.345 -19.748 0.134 -0.300 5 A_DC6:DG103_C A 6 ? C 103 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 -0.227 -0.157 0.319 21.896 2.879 -2.451 6 A_DG7:DC102_C A 7 ? C 102 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B DC 5 1_555 0.188 2.326 2.527 2.768 -0.176 6.209 20.161 7.112 2.324 -1.525 -24.034 6.800 1 AA_DC2DG3:DC106DG107_CC A 2 ? C 107 ? A 3 ? C 106 ? 1 A DG 2 1_555 B DC 5 1_555 A DT 3 1_555 B DA 4 1_555 0.529 0.599 7.402 -10.710 4.671 66.428 0.132 -1.415 7.277 4.230 9.698 67.332 2 AA_DG3DT4:DA105DC106_CC A 3 ? C 106 ? A 4 ? C 105 ? 1 A DT 3 1_555 B DA 4 1_555 A DA 4 1_555 B DT 3 1_555 -2.980 4.921 -1.297 157.138 -80.728 -150.293 -2.499 -1.565 0.001 40.390 78.619 -179.144 3 AA_DT4DA5:DT104DA105_CC A 4 ? C 105 ? A 5 ? C 104 ? 1 A DA 4 1_555 B DT 3 1_555 A DC 5 1_555 B DG 2 1_555 3.780 6.388 -0.710 -140.314 91.008 -39.939 -2.975 2.266 -0.530 -47.785 -73.674 -168.013 4 AA_DA5DC6:DG103DT104_CC A 5 ? C 104 ? A 6 ? C 103 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.251 2.405 2.579 -3.044 -0.247 6.783 19.201 -6.231 2.375 -1.965 24.179 7.439 5 AA_DC6DG7:DC102DG103_CC A 6 ? C 103 ? A 7 ? C 102 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 2-CARBOXYQUINOXALINE QUI 5 water HOH # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 MG 1 201 201 MG MG A . F 3 MG 1 211 211 MG MG C . G 4 QUI 1 0 0 QUI QUI D . H 4 QUI 1 9 9 QUI QUI D . I 4 QUI 1 0 0 QUI QUI E . J 4 QUI 1 9 9 QUI QUI E . K 5 HOH 1 2001 2001 HOH HOH A . K 5 HOH 2 2002 2002 HOH HOH A . K 5 HOH 3 2003 2003 HOH HOH A . K 5 HOH 4 2004 2004 HOH HOH A . K 5 HOH 5 2005 2005 HOH HOH A . K 5 HOH 6 2006 2006 HOH HOH A . K 5 HOH 7 2007 2007 HOH HOH A . K 5 HOH 8 2008 2008 HOH HOH A . K 5 HOH 9 2009 2009 HOH HOH A . K 5 HOH 10 2010 2010 HOH HOH A . K 5 HOH 11 2011 2011 HOH HOH A . K 5 HOH 12 2012 2012 HOH HOH A . K 5 HOH 13 2013 2013 HOH HOH A . K 5 HOH 14 2014 2014 HOH HOH A . K 5 HOH 15 2015 2015 HOH HOH A . K 5 HOH 16 2016 2016 HOH HOH A . K 5 HOH 17 2017 2017 HOH HOH A . L 5 HOH 1 2001 2001 HOH HOH C . L 5 HOH 2 2002 2002 HOH HOH C . L 5 HOH 3 2003 2003 HOH HOH C . L 5 HOH 4 2004 2004 HOH HOH C . L 5 HOH 5 2005 2005 HOH HOH C . L 5 HOH 6 2006 2006 HOH HOH C . L 5 HOH 7 2007 2007 HOH HOH C . L 5 HOH 8 2008 2008 HOH HOH C . L 5 HOH 9 2009 2009 HOH HOH C . L 5 HOH 10 2010 2010 HOH HOH C . L 5 HOH 11 2011 2011 HOH HOH C . L 5 HOH 12 2012 2012 HOH HOH C . L 5 HOH 13 2013 2013 HOH HOH C . L 5 HOH 14 2014 2014 HOH HOH C . M 5 HOH 1 2001 2001 HOH HOH D . M 5 HOH 2 2002 2002 HOH HOH D . M 5 HOH 3 2003 2003 HOH HOH D . M 5 HOH 4 2004 2004 HOH HOH D . M 5 HOH 5 2005 2005 HOH HOH D . N 5 HOH 1 2001 2001 HOH HOH E . N 5 HOH 2 2002 2002 HOH HOH E . N 5 HOH 3 2003 2003 HOH HOH E . N 5 HOH 4 2004 2004 HOH HOH E . N 5 HOH 5 2005 2005 HOH HOH E . N 5 HOH 6 2006 2006 HOH HOH E . N 5 HOH 7 2007 2007 HOH HOH E . #