data_1XVN # _entry.id 1XVN # _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 1XVN NDB DD0067 RCSB RCSB030816 WWPDB D_1000030816 # 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 1XVR unspecified 'CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21' 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 1XVN _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 1XVN _cell.length_a 39.928 _cell.length_b 39.928 _cell.length_c 80.098 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 1XVN _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _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(*AP*CP*GP*TP*AP*CP*GP*T)-3'" 2426.617 1 ? ? ? ? 2 polymer nat ECHINOMYCIN 809.008 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 non-polymer syn 2-CARBOXYQUINOXALINE 174.156 2 ? ? ? ? 5 water nat water 18.015 41 ? ? ? ? # _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 '(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DT)' ACGTACGT A ? 2 'polypeptide(L)' no yes '(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)' SAXVSAXV B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DT n 2 1 DSN n 2 2 ALA n 2 3 N2C y 2 3 NCY y 2 4 MVA n 2 5 DSN n 2 6 ALA n 2 7 NCY y 2 7 N2C y 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 1XVN 1 ? ? 1XVN ? 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 1XVN A 1 ? 8 ? 1XVN 1 ? 8 ? 1 8 2 2 1XVN B 1 ? 8 ? NOR01126 1 ? 8 ? 1 8 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 2 1XVN N2C B 3 ? NOR NOR01126 NCY 3 MICROHETEROGENEITY 3 1 2 1XVN NCY B 7 ? NOR NOR01126 N2C 7 MICROHETEROGENEITY 7 2 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 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 1XVN _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.19 _exptl_crystal.density_percent_sol 43.32 _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 'PEG 200, PEG 3350, MGCL2, MES, SPERMINE-HCL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K' # 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 'PEG 200' ? ? ? 1 2 1 'PEG 3350' ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 MES ? ? ? 1 5 1 spermine-HCl ? ? ? 1 6 1 H2O ? ? ? 1 7 2 'PEG 200' ? ? ? 1 8 2 'PEG 3350' ? ? ? 1 9 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 1XVN _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 26.200 _reflns.d_resolution_high 1.500 _reflns.number_obs 6499 _reflns.number_all ? _reflns.percent_possible_obs 99.0 _reflns.pdbx_Rmerge_I_obs 0.04240 _reflns.pdbx_Rsym_value 0.04240 _reflns.pdbx_netI_over_sigmaI 39.1100 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 21.270 _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 1.50 _reflns_shell.d_res_low 1.60 _reflns_shell.percent_possible_all 98.4 _reflns_shell.Rmerge_I_obs 0.42250 _reflns_shell.pdbx_Rsym_value 0.42250 _reflns_shell.meanI_over_sigI_obs 9.030 _reflns_shell.pdbx_redundancy 20.44 _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 1XVN _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 6499 _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 26.20 _refine.ls_d_res_high 1.50 _refine.ls_percent_reflns_obs 99.0 _refine.ls_R_factor_obs 0.202 _refine.ls_R_factor_all 0.202 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.237 _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 571 _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 ;THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED AND ARE MODELLED AS DISORDERED/MICROHETE. ; _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 1XVN _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 7 _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 66 _refine_hist.pdbx_number_atoms_nucleic_acid 161 _refine_hist.pdbx_number_atoms_ligand 25 _refine_hist.number_atoms_solvent 41 _refine_hist.number_atoms_total 293 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 26.20 # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1XVN _pdbx_refine.R_factor_all_no_cutoff 0.202 _pdbx_refine.R_factor_obs_no_cutoff 0.202 _pdbx_refine.free_R_factor_no_cutoff 0.237 _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 571 _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 1XVN _struct.title 'echinomycin (ACGTACGT)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 1XVN _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 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 5 ? G 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 ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2016 1_555 ? ? ? ? ? ? ? 2.035 ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2016 2_665 ? ? ? ? ? ? ? 2.034 ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2016 3_565 ? ? ? ? ? ? ? 2.035 ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2017 1_555 ? ? ? ? ? ? ? 2.234 ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2017 2_665 ? ? ? ? ? ? ? 2.235 ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 21 A HOH 2017 3_565 ? ? ? ? ? ? ? 2.235 ? covale1 covale ? ? D QUI . C ? ? ? 1_555 B DSN 1 N ? ? B QUI 0 B DSN 1 1_555 ? ? ? ? ? ? ? 1.361 ? covale2 covale ? ? B DSN 1 C ? ? ? 1_555 B ALA 2 N ? ? B DSN 1 B ALA 2 1_555 ? ? ? ? ? ? ? 1.333 ? covale3 covale ? ? B DSN 1 OG ? ? ? 1_555 B MVA 8 C ? ? B DSN 1 B MVA 8 1_555 ? ? ? ? ? ? ? 1.325 ? covale4 covale ? ? B ALA 2 C ? ? ? 1_555 B NCY 3 N B ? B ALA 2 B NCY 3 1_555 ? ? ? ? ? ? ? 1.322 ? covale5 covale ? ? B ALA 2 C ? ? ? 1_555 B N2C 3 N A ? B ALA 2 B N2C 3 1_555 ? ? ? ? ? ? ? 1.322 ? covale6 covale ? ? B NCY 3 C B ? ? 1_555 B MVA 4 N ? ? B NCY 3 B MVA 4 1_555 ? ? ? ? ? ? ? 1.323 ? covale7 covale ? ? B N2C 3 CB A ? ? 1_555 B NCY 7 SG A ? B N2C 3 B NCY 7 1_555 ? ? ? ? ? ? ? 1.807 ? covale8 covale ? ? B N2C 3 C A ? ? 1_555 B MVA 4 N ? ? B N2C 3 B MVA 4 1_555 ? ? ? ? ? ? ? 1.323 ? covale9 covale ? ? B NCY 3 SG B ? ? 1_555 B N2C 7 CB B ? B NCY 3 B N2C 7 1_555 ? ? ? ? ? ? ? 1.801 ? covale10 covale ? ? B MVA 4 C ? ? ? 1_555 B DSN 5 OG ? ? B MVA 4 B DSN 5 1_555 ? ? ? ? ? ? ? 1.304 ? covale11 covale ? ? B DSN 5 C ? ? ? 1_555 B ALA 6 N ? ? B DSN 5 B ALA 6 1_555 ? ? ? ? ? ? ? 1.331 ? covale12 covale ? ? B DSN 5 N ? ? ? 1_555 E QUI . C ? ? B DSN 5 B QUI 9 1_555 ? ? ? ? ? ? ? 1.372 ? covale13 covale ? ? B ALA 6 C ? ? ? 1_555 B NCY 7 N A ? B ALA 6 B NCY 7 1_555 ? ? ? ? ? ? ? 1.330 ? covale14 covale ? ? B ALA 6 C ? ? ? 1_555 B N2C 7 N B ? B ALA 6 B N2C 7 1_555 ? ? ? ? ? ? ? 1.330 ? covale15 covale ? ? B NCY 7 C A ? ? 1_555 B MVA 8 N ? ? B NCY 7 B MVA 8 1_555 ? ? ? ? ? ? ? 1.324 ? covale16 covale ? ? B N2C 7 C B ? ? 1_555 B MVA 8 N ? ? B N2C 7 B MVA 8 1_555 ? ? ? ? ? ? ? 1.324 ? hydrog1 hydrog ? ? A DA 1 N6 A ? ? 1_555 A DT 8 O4 A ? A DA 1 A DT 8 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog2 hydrog ? ? A DA 1 N7 A ? ? 1_555 A DT 8 N3 A ? A DA 1 A DT 8 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 7 N1 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 7 O6 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 7 N2 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 5 N7 ? ? A DT 4 A DA 5 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 4 A DA 5 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 4 O4 ? ? A DA 5 A DT 4 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog12 hydrog ? ? A DA 5 N7 ? ? ? 1_555 A DT 4 N3 ? ? A DA 5 A DT 4 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DT 8 N3 A ? ? 1_555 A DA 1 N7 A ? A DT 8 A DA 1 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? hydrog20 hydrog ? ? A DT 8 O4 A ? ? 1_555 A DA 1 N6 A ? A DT 8 A DA 1 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? # 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 ? ? ? ? 2 'BINDING SITE FOR RESIDUE MG A 21' AC2 Software ? ? ? ? 11 'BINDING SITE FOR CHAIN B 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 2 HOH F . ? HOH A 2016 . ? 1_555 ? 2 AC1 2 HOH F . ? HOH A 2017 . ? 1_555 ? 3 AC2 11 DA A 1 ? DA A 1 . ? 1_555 ? 4 AC2 11 DC A 2 ? DC A 2 . ? 1_555 ? 5 AC2 11 DG A 3 ? DG A 3 . ? 1_555 ? 6 AC2 11 DT A 4 ? DT A 4 . ? 1_555 ? 7 AC2 11 DA A 5 ? DA A 5 . ? 1_555 ? 8 AC2 11 DC A 6 ? DC A 6 . ? 1_555 ? 9 AC2 11 DG A 7 ? DG A 7 . ? 1_555 ? 10 AC2 11 DT A 8 ? DT A 8 . ? 1_555 ? 11 AC2 11 HOH G . ? HOH B 2001 . ? 1_555 ? 12 AC2 11 HOH G . ? HOH B 2005 . ? 1_555 ? 13 AC2 11 HOH G . ? HOH B 2006 . ? 1_555 ? # _database_PDB_matrix.entry_id 1XVN _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 1XVN _atom_sites.fract_transf_matrix[1][1] 0.025045 _atom_sites.fract_transf_matrix[1][2] 0.014460 _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] 0.028920 _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] 0.012485 _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 DA 1 1 1 DA DA A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DT 4 4 4 DT DT A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DT 8 8 8 DT DT A . n B 2 1 DSN 1 1 1 DSN DSN B . n B 2 2 ALA 2 2 2 ALA ALA B . n B 2 3 N2C 3 3 3 N2C N2C B . y B 2 3 NCY 3 3 3 NCY NCY B . y B 2 4 MVA 4 4 4 MVA MVA B . n B 2 5 DSN 5 5 5 DSN DSN B . n B 2 6 ALA 6 6 6 ALA ALA B . n B 2 7 NCY 7 7 7 NCY NCY B . y B 2 7 N2C 7 7 7 N2C N2C B . y B 2 8 MVA 8 8 8 MVA MVA B . 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 B 1 PRD_000491 D 1 PRD_000491 E # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # 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)' 740 ? 1 MORE -6.2 ? 1 'SSA (A^2)' 3910 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 9_555 -x,-x+y,-z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 21 ? C MG . 2 1 A HOH 2007 ? F HOH . 3 1 A HOH 2009 ? F 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 ? F HOH . ? A HOH 2016 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2016 ? 2_665 91.8 ? 2 O ? F HOH . ? A HOH 2016 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2016 ? 3_565 91.8 ? 3 O ? F HOH . ? A HOH 2016 ? 2_665 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2016 ? 3_565 91.8 ? 4 O ? F HOH . ? A HOH 2016 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 1_555 97.7 ? 5 O ? F HOH . ? A HOH 2016 ? 2_665 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 1_555 80.8 ? 6 O ? F HOH . ? A HOH 2016 ? 3_565 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 1_555 168.1 ? 7 O ? F HOH . ? A HOH 2016 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 2_665 168.1 ? 8 O ? F HOH . ? A HOH 2016 ? 2_665 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 2_665 97.7 ? 9 O ? F HOH . ? A HOH 2016 ? 3_565 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 2_665 80.8 ? 10 O ? F HOH . ? A HOH 2017 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 2_665 90.9 ? 11 O ? F HOH . ? A HOH 2016 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 3_565 80.8 ? 12 O ? F HOH . ? A HOH 2016 ? 2_665 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 3_565 168.1 ? 13 O ? F HOH . ? A HOH 2016 ? 3_565 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 3_565 97.7 ? 14 O ? F HOH . ? A HOH 2017 ? 1_555 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 3_565 90.9 ? 15 O ? F HOH . ? A HOH 2017 ? 2_665 MG ? C MG . ? A MG 21 ? 1_555 O ? F HOH . ? A HOH 2017 ? 3_565 90.9 ? # 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 1XVN _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 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OG _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DSN _pdbx_validate_close_contact.auth_seq_id_1 1 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 MVA _pdbx_validate_close_contact.auth_seq_id_2 8 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # 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 "O5'" A DA 1 ? A "C5'" A DA 1 ? A "C4'" A DA 1 ? A 104.43 109.40 -4.97 0.80 N 2 1 "O4'" A DA 1 ? B "C1'" A DA 1 ? B N9 A DA 1 ? B 102.56 108.00 -5.44 0.70 N 3 1 "O4'" A DC 2 ? A "C1'" A DC 2 ? A N1 A DC 2 ? ? 101.37 108.00 -6.63 0.70 N 4 1 "O4'" A DC 2 ? B "C1'" A DC 2 ? B N1 A DC 2 ? ? 103.02 108.00 -4.98 0.70 N 5 1 "C3'" A DC 2 ? B "O3'" A DC 2 ? B P A DG 3 ? ? 130.42 119.70 10.72 1.20 Y 6 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 113.00 108.30 4.70 0.30 N 7 1 C2 A DG 3 ? ? N3 A DG 3 ? ? C4 A DG 3 ? ? 108.14 111.90 -3.76 0.50 N 8 1 N1 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 124.26 119.90 4.36 0.60 N 9 1 C5 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 124.78 128.60 -3.82 0.60 N 10 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 101.28 108.00 -6.72 0.70 N 11 1 N3 A DT 4 ? ? C2 A DT 4 ? ? O2 A DT 4 ? ? 118.49 122.30 -3.81 0.60 N 12 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 100.56 108.00 -7.44 0.70 N 13 1 "O5'" A DG 7 ? A "C5'" A DG 7 ? A "C4'" A DG 7 ? A 103.82 109.40 -5.58 0.80 N 14 1 "O4'" A DG 7 ? B "C1'" A DG 7 ? B N9 A DG 7 ? ? 110.55 108.30 2.25 0.30 N 15 1 N1 A DG 7 ? ? C6 A DG 7 ? ? O6 A DG 7 ? ? 116.19 119.90 -3.71 0.60 N 16 1 "O4'" A DT 8 ? A "C1'" A DT 8 ? A N1 A DT 8 ? A 112.09 108.30 3.79 0.30 N 17 1 N3 A DT 8 ? B C4 A DT 8 ? B O4 A DT 8 ? B 115.92 119.90 -3.98 0.60 N 18 1 C4 A DT 8 ? B C5 A DT 8 ? B C7 A DT 8 ? B 122.92 119.00 3.92 0.60 N 19 1 C6 A DT 8 ? B C5 A DT 8 ? B C7 A DT 8 ? B 119.22 122.90 -3.68 0.60 N # _pdbx_validate_polymer_linkage.id 1 _pdbx_validate_polymer_linkage.PDB_model_num 1 _pdbx_validate_polymer_linkage.auth_atom_id_1 C _pdbx_validate_polymer_linkage.auth_asym_id_1 B _pdbx_validate_polymer_linkage.auth_comp_id_1 MVA _pdbx_validate_polymer_linkage.auth_seq_id_1 4 _pdbx_validate_polymer_linkage.PDB_ins_code_1 ? _pdbx_validate_polymer_linkage.label_alt_id_1 ? _pdbx_validate_polymer_linkage.auth_atom_id_2 N _pdbx_validate_polymer_linkage.auth_asym_id_2 B _pdbx_validate_polymer_linkage.auth_comp_id_2 DSN _pdbx_validate_polymer_linkage.auth_seq_id_2 5 _pdbx_validate_polymer_linkage.PDB_ins_code_2 ? _pdbx_validate_polymer_linkage.label_alt_id_2 ? _pdbx_validate_polymer_linkage.dist 3.33 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B N2C 3 ? CD ? B N2C 3 CD 2 1 Y 1 B NCY 7 ? CD ? B NCY 7 CD # _ndb_struct_conf_na.entry_id 1XVN _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 DA 1 1_555 A DT 8 9_555 0.535 -3.453 -0.472 2.263 -6.515 67.043 1 A_DA1:DT8_A A 1 ? A 8 ? 23 3 1 A DC 2 1_555 A DG 7 9_555 0.323 -0.097 0.284 -22.101 0.000 -1.342 2 A_DC2:DG7_A A 2 ? A 7 ? 19 1 1 A DG 3 1_555 A DC 6 9_555 -0.302 -0.157 0.388 20.879 -0.272 -0.146 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A DT 4 1_555 A DA 5 9_555 -0.621 3.581 0.358 -3.707 7.860 -69.788 4 A_DT4:DA5_A A 4 ? A 5 ? 23 3 1 A DA 5 1_555 A DT 4 9_555 0.621 -3.581 -0.358 3.707 -7.860 69.788 5 A_DA5:DT4_A A 5 ? A 4 ? 23 3 1 A DC 6 1_555 A DG 3 9_555 0.302 -0.157 0.388 -20.879 -0.272 -0.146 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DG 7 1_555 A DC 2 9_555 -0.323 -0.097 0.284 22.101 0.000 -1.342 7 A_DG7:DC2_A A 7 ? A 2 ? 19 1 1 A DT 8 1_555 A DA 1 9_555 -0.535 3.453 0.472 -2.263 6.515 -67.043 8 A_DT8:DA1_A A 8 ? A 1 ? 23 3 # 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 DA 1 1_555 A DT 8 9_555 A DC 2 1_555 A DG 7 9_555 2.461 6.828 1.010 -149.521 76.549 -45.961 -3.514 1.071 -0.451 -39.941 -78.016 -168.934 1 AA_DA1DC2:DG7DT8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A DC 2 1_555 A DG 7 9_555 A DG 3 1_555 A DC 6 9_555 -0.154 1.591 2.472 -0.917 2.667 1.778 -18.425 -13.091 2.634 54.637 18.778 3.334 2 AA_DC2DG3:DC6DG7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 9_555 A DT 4 1_555 A DA 5 9_555 0.465 0.456 7.201 -8.748 6.887 67.514 -0.164 -1.137 7.115 6.154 7.817 68.319 3 AA_DG3DT4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DT 4 1_555 A DA 5 9_555 A DA 5 1_555 A DT 4 9_555 2.778 -5.022 0.000 -152.479 82.594 180.000 -2.511 -1.389 0.000 41.297 76.239 180.000 4 AA_DT4DA5:DT4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A DT 4 9_555 A DC 6 1_555 A DG 3 9_555 3.932 6.034 -0.646 -140.395 93.835 -76.419 -2.876 2.196 -0.466 -48.094 -71.958 -171.257 5 AA_DA5DC6:DG3DT4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 9_555 A DG 7 1_555 A DC 2 9_555 0.154 1.591 2.472 0.917 2.667 1.778 -18.425 13.092 2.634 54.636 -18.778 3.334 6 AA_DC6DG7:DC2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DG 7 1_555 A DC 2 9_555 A DT 8 1_555 A DA 1 9_555 0.453 -1.289 7.199 -11.069 4.694 54.221 -1.983 -1.897 6.868 5.080 11.979 55.439 7 AA_DG7DT8:DA1DC2_AA A 7 ? A 2 ? A 8 ? A 1 ? # 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 C 3 MG 1 21 21 MG MG A . D 4 QUI 1 0 0 QUI QUI B . E 4 QUI 1 9 9 QUI QUI B . F 5 HOH 1 2001 2001 HOH HOH A . F 5 HOH 2 2002 2002 HOH HOH A . F 5 HOH 3 2003 2003 HOH HOH A . F 5 HOH 4 2004 2004 HOH HOH A . F 5 HOH 5 2005 2005 HOH HOH A . F 5 HOH 6 2006 2006 HOH HOH A . F 5 HOH 7 2007 2007 HOH HOH A . F 5 HOH 8 2008 2008 HOH HOH A . F 5 HOH 9 2009 2009 HOH HOH A . F 5 HOH 10 2010 2010 HOH HOH A . F 5 HOH 11 2011 2011 HOH HOH A . F 5 HOH 12 2012 2012 HOH HOH A . F 5 HOH 13 2013 2013 HOH HOH A . F 5 HOH 14 2014 2014 HOH HOH A . F 5 HOH 15 2015 2015 HOH HOH A . F 5 HOH 16 2016 2016 HOH HOH A . F 5 HOH 17 2017 2017 HOH HOH A . F 5 HOH 18 2018 2018 HOH HOH A . F 5 HOH 19 2019 2019 HOH HOH A . F 5 HOH 20 2020 2020 HOH HOH A . F 5 HOH 21 2021 2021 HOH HOH A . F 5 HOH 22 2022 2022 HOH HOH A . F 5 HOH 23 2023 2023 HOH HOH A . F 5 HOH 24 2024 2024 HOH HOH A . F 5 HOH 25 2025 2025 HOH HOH A . F 5 HOH 26 2026 2026 HOH HOH A . F 5 HOH 27 2027 2027 HOH HOH A . F 5 HOH 28 2028 2028 HOH HOH A . F 5 HOH 29 2029 2029 HOH HOH A . F 5 HOH 30 2030 2030 HOH HOH A . F 5 HOH 31 2031 2031 HOH HOH A . F 5 HOH 32 2032 2032 HOH HOH A . F 5 HOH 33 2033 2033 HOH HOH A . F 5 HOH 34 2034 2034 HOH HOH A . F 5 HOH 35 2035 2035 HOH HOH A . G 5 HOH 1 2001 2001 HOH HOH B . G 5 HOH 2 2002 2002 HOH HOH B . G 5 HOH 3 2003 2003 HOH HOH B . G 5 HOH 4 2004 2004 HOH HOH B . G 5 HOH 5 2005 2005 HOH HOH B . G 5 HOH 6 2006 2006 HOH HOH B . #