data_3N4O # _entry.id 3N4O # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3N4O pdb_00003n4o 10.2210/pdb3n4o/pdb NDB NA0581 ? ? RCSB RCSB059375 ? ? WWPDB D_1000059375 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3GJJ . unspecified PDB 3N4N . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3N4O _pdbx_database_status.recvd_initial_deposition_date 2010-05-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Takenaka, A.' 1 'Juan, E.C.M.' 2 'Shimizu, S.' 3 # _citation.id primary _citation.title ;Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year 2010 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 1362-4962 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20554855 _citation.pdbx_database_id_DOI 10.1093/nar/gkq519 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Juan, E.C.M.' 1 ? primary 'Shimizu, S.' 2 ? primary 'Ma, X.' 3 ? primary 'Kurose, T.' 4 ? primary 'Haraguchi, T.' 5 ? primary 'Zhang, F.' 6 ? primary 'Tsunoda, M.' 7 ? primary 'Ohkubo, A.' 8 ? primary 'Sekine, M.' 9 ? primary 'Shibata, T.' 10 ? primary 'Millington, C.L.' 11 ? primary 'Williams, D.M.' 12 ? primary 'Takenaka, A.' 13 ? # _cell.entry_id 3N4O _cell.length_a 25.030 _cell.length_b 41.659 _cell.length_c 64.569 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _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 3N4O _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3'" 3686.429 2 ? ? ? ? 2 non-polymer syn "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 424.498 1 ? ? ? ? 3 water nat water 18.015 30 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(B7C)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATXCGCG _entity_poly.pdbx_strand_id D,E _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 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 B7C n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3N4O _struct_ref.pdbx_db_accession 3N4O _struct_ref.entity_id 1 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 3N4O D 1 ? 12 ? 3N4O 1 ? 12 ? 1 12 2 1 3N4O E 1 ? 12 ? 3N4O 13 ? 24 ? 13 24 # 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 B7C 'DNA linking' n '3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one' ? 'C12 H16 N3 O7 P' 345.245 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 HT non-polymer . "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 'HOECHST 33258' 'C25 H24 N6 O' 424.498 # _exptl.entry_id 3N4O _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.28 _exptl_crystal.density_percent_sol 46.12 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_details ;0.60mM ssDNA, 20mM Sodium cacodylate (pH6.0), 6mM Spermine tetrahydrochloride, 40mM Potassium chloride, 6mM Sodium chloride, 0.2% CHAPS, 0.30mM Hoechst33258, 5% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # _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 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2008-01-26 _diffrn_detector.details mirrors # _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 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-6A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-6A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.978 # _reflns.entry_id 3N4O _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.9 _reflns.number_obs 1714 _reflns.number_all ? _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.035 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 69.6 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 13.1 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.90 _reflns_shell.d_res_low 3.00 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.298 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 10.8 _reflns_shell.pdbx_redundancy 13.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 169 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3N4O _refine.ls_number_reflns_obs 1635 _refine.ls_number_reflns_all 1693 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1235175.42 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 9.89 _refine.ls_d_res_high 2.90 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.254 _refine.ls_R_factor_all 0.259 _refine.ls_R_factor_R_work 0.232 _refine.ls_R_factor_R_free 0.297 _refine.ls_R_factor_R_free_error 0.023 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 161 _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 44.4 _refine.aniso_B[1][1] 0.00 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.35 _refine.solvent_model_param_bsol 63.8396 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'Used weighted full matrix least squares procedure' _refine.pdbx_starting_model 1DNH _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3N4O _refine_analyze.Luzzati_coordinate_error_obs 0.39 _refine_analyze.Luzzati_sigma_a_obs 0.47 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.47 _refine_analyze.Luzzati_sigma_a_free 0.67 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 490 _refine_hist.pdbx_number_atoms_ligand 32 _refine_hist.number_atoms_solvent 30 _refine_hist.number_atoms_total 552 _refine_hist.d_res_high 2.90 _refine_hist.d_res_low 9.89 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 28.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.52 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.90 _refine_ls_shell.d_res_low 3.08 _refine_ls_shell.number_reflns_R_work 246 _refine_ls_shell.R_factor_R_work 0.406 _refine_ls_shell.percent_reflns_obs 100.0 _refine_ls_shell.R_factor_R_free 0.673 _refine_ls_shell.R_factor_R_free_error 0.132 _refine_ls_shell.percent_reflns_R_free 9.6 _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 246 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 water.param water.top 'X-RAY DIFFRACTION' 2 dna-rna_repBIC.param dna-rnaBIC.top 'X-RAY DIFFRACTION' 3 ht_xplor_param ht_xplor_top # _struct_ncs_dom.id 1 _struct_ncs_dom.details ? _struct_ncs_dom.pdbx_ens_id 1 # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 3N4O _struct.title ;Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3N4O _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'bicyclic cytosine, DNA' # 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 3 ? E N N 3 ? # _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 _struct_conn.pdbx_role covale1 covale both ? A DT 7 "O3'" ? ? ? 1_555 A B7C 8 P A ? D DT 7 D B7C 8 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale2 covale both ? A DT 7 "O3'" ? ? ? 1_555 A B7C 8 P B ? D DT 7 D B7C 8 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? A B7C 8 "O3'" A ? ? 1_555 A DC 9 P ? ? D B7C 8 D DC 9 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale4 covale both ? A B7C 8 "O3'" B ? ? 1_555 A DC 9 P ? ? D B7C 8 D DC 9 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale5 covale both ? B DT 7 "O3'" ? ? ? 1_555 B B7C 8 P A ? E DT 19 E B7C 20 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale6 covale both ? B DT 7 "O3'" ? ? ? 1_555 B B7C 8 P B ? E DT 19 E B7C 20 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale7 covale both ? B B7C 8 "O3'" A ? ? 1_555 B DC 9 P ? ? E B7C 20 E DC 21 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale8 covale both ? B B7C 8 "O3'" B ? ? 1_555 B DC 9 P ? ? E B7C 20 E DC 21 1_555 ? ? ? ? ? ? ? 1.602 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? D DC 1 E DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? D DC 1 E DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? D DC 1 E DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? D DG 2 E DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? D DG 2 E DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? D DG 2 E DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? D DC 3 E DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? D DC 3 E DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? D DC 3 E DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? D DG 4 E DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? D DG 4 E DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? D DG 4 E DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? D DA 6 E DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? D DA 6 E DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? D DT 7 E DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? D DT 7 E DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? D DC 9 E DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? D DC 9 E DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? D DC 9 E DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? D DG 10 E DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? D DG 10 E DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? D DG 10 E DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? D DC 11 E DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? D DC 11 E DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? D DC 11 E DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? D DG 12 E DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? D DG 12 E DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? D DG 12 E DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 E HT 25 ? 10 'BINDING SITE FOR RESIDUE HT E 25' 1 ? ? ? ? ? ? ? # 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 10 DA A 5 ? DA D 5 . ? 1_555 ? 2 AC1 10 DA A 6 ? DA D 6 . ? 1_555 ? 3 AC1 10 DT A 7 ? DT D 7 . ? 1_555 ? 4 AC1 10 B7C A 8 ? B7C D 8 . ? 1_555 ? 5 AC1 10 DC A 9 ? DC D 9 . ? 1_555 ? 6 AC1 10 DA B 5 ? DA E 17 . ? 1_555 ? 7 AC1 10 DA B 6 ? DA E 18 . ? 1_555 ? 8 AC1 10 DT B 7 ? DT E 19 . ? 1_555 ? 9 AC1 10 B7C B 8 ? B7C E 20 . ? 1_555 ? 10 AC1 10 DC B 9 ? DC E 21 . ? 1_555 ? # _database_PDB_matrix.entry_id 3N4O _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 3N4O _atom_sites.fract_transf_matrix[1][1] 0.039952 _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] 0.024004 _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] 0.015487 _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 N O P # 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 1 1 DC CYT D . n A 1 2 DG 2 2 2 DG GUA D . n A 1 3 DC 3 3 3 DC CYT D . n A 1 4 DG 4 4 4 DG GUA D . n A 1 5 DA 5 5 5 DA ADX D . n A 1 6 DA 6 6 6 DA ADE D . n A 1 7 DT 7 7 7 DT THY D . n A 1 8 B7C 8 8 8 B7C BIC D . n A 1 9 DC 9 9 9 DC CYT D . n A 1 10 DG 10 10 10 DG GUA D . n A 1 11 DC 11 11 11 DC CYT D . n A 1 12 DG 12 12 12 DG GUA D . n B 1 1 DC 1 13 13 DC CYT E . n B 1 2 DG 2 14 14 DG GUA E . n B 1 3 DC 3 15 15 DC CYT E . n B 1 4 DG 4 16 16 DG GUA E . n B 1 5 DA 5 17 17 DA ADX E . n B 1 6 DA 6 18 18 DA ADE E . n B 1 7 DT 7 19 19 DT THY E . n B 1 8 B7C 8 20 20 B7C BIC E . n B 1 9 DC 9 21 21 DC CYT E . n B 1 10 DG 10 22 22 DG GUA E . n B 1 11 DC 11 23 23 DC CYT E . n B 1 12 DG 12 24 24 DG GUA E . n # 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 2 HT 1 25 25 HT HT E . D 3 HOH 1 13 1 HOH TIP D . D 3 HOH 2 14 4 HOH TIP D . D 3 HOH 3 15 6 HOH TIP D . D 3 HOH 4 16 7 HOH TIP D . D 3 HOH 5 17 17 HOH TIP D . D 3 HOH 6 18 8 HOH TIP D . D 3 HOH 7 19 19 HOH TIP D . D 3 HOH 8 20 10 HOH TIP D . D 3 HOH 9 21 21 HOH TIP D . D 3 HOH 10 22 11 HOH TIP D . D 3 HOH 11 23 2 HOH TIP D . D 3 HOH 12 24 24 HOH TIP D . D 3 HOH 13 27 27 HOH TIP D . D 3 HOH 14 28 28 HOH TIP D . D 3 HOH 15 30 30 HOH TIP D . E 3 HOH 1 3 3 HOH TIP E . E 3 HOH 2 5 5 HOH TIP E . E 3 HOH 3 9 9 HOH TIP E . E 3 HOH 4 12 12 HOH TIP E . E 3 HOH 5 26 26 HOH TIP E . E 3 HOH 6 27 13 HOH TIP E . E 3 HOH 7 28 14 HOH TIP E . E 3 HOH 8 29 29 HOH TIP E . E 3 HOH 9 30 15 HOH TIP E . E 3 HOH 10 31 16 HOH TIP E . E 3 HOH 11 32 18 HOH TIP E . E 3 HOH 12 33 20 HOH TIP E . E 3 HOH 13 34 22 HOH TIP E . E 3 HOH 14 35 25 HOH TIP E . E 3 HOH 15 36 23 HOH TIP E . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A B7C 8 D B7C 8 ? DC ? 2 B B7C 8 E B7C 20 ? DC ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 1130 ? 1 MORE -2 ? 1 'SSA (A^2)' 4510 ? # _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 2010-08-11 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_ref_seq 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq.db_align_beg' 5 3 'Structure model' '_struct_ref_seq.db_align_end' 6 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 7 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 8 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.2 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 AMoRE phasing . ? 5 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal B7C OP3 O N N 1 B7C P P N N 2 B7C OP1 O N N 3 B7C OP2 O N N 4 B7C "O5'" O N N 5 B7C N1 N N N 6 B7C C6 C N N 7 B7C C2 C N N 8 B7C O2 O N N 9 B7C N3 N N N 10 B7C C4 C N N 11 B7C N4 N N N 12 B7C C5 C N N 13 B7C C7 C N N 14 B7C C8 C N N 15 B7C C9 C N N 16 B7C "C2'" C N N 17 B7C "C5'" C N N 18 B7C "C4'" C N R 19 B7C "O4'" O N N 20 B7C "C1'" C N R 21 B7C "C3'" C N S 22 B7C "O3'" O N N 23 B7C HOP3 H N N 24 B7C HOP1 H N N 25 B7C H6 H N N 26 B7C HN4 H N N 27 B7C H7 H N N 28 B7C H8 H N N 29 B7C H9 H N N 30 B7C H9A H N N 31 B7C "H2'" H N N 32 B7C "H2'A" H N N 33 B7C "H5'" H N N 34 B7C "H5'A" H N N 35 B7C "H4'" H N N 36 B7C "H1'" H N N 37 B7C "H3'" H N N 38 B7C "HO3'" H N N 39 DA OP3 O N N 40 DA P P N N 41 DA OP1 O N N 42 DA OP2 O N N 43 DA "O5'" O N N 44 DA "C5'" C N N 45 DA "C4'" C N R 46 DA "O4'" O N N 47 DA "C3'" C N S 48 DA "O3'" O N N 49 DA "C2'" C N N 50 DA "C1'" C N R 51 DA N9 N Y N 52 DA C8 C Y N 53 DA N7 N Y N 54 DA C5 C Y N 55 DA C6 C Y N 56 DA N6 N N N 57 DA N1 N Y N 58 DA C2 C Y N 59 DA N3 N Y N 60 DA C4 C Y N 61 DA HOP3 H N N 62 DA HOP2 H N N 63 DA "H5'" H N N 64 DA "H5''" H N N 65 DA "H4'" H N N 66 DA "H3'" H N N 67 DA "HO3'" H N N 68 DA "H2'" H N N 69 DA "H2''" H N N 70 DA "H1'" H N N 71 DA H8 H N N 72 DA H61 H N N 73 DA H62 H N N 74 DA H2 H N N 75 DC OP3 O N N 76 DC P P N N 77 DC OP1 O N N 78 DC OP2 O N N 79 DC "O5'" O N N 80 DC "C5'" C N N 81 DC "C4'" C N R 82 DC "O4'" O N N 83 DC "C3'" C N S 84 DC "O3'" O N N 85 DC "C2'" C N N 86 DC "C1'" C N R 87 DC N1 N N N 88 DC C2 C N N 89 DC O2 O N N 90 DC N3 N N N 91 DC C4 C N N 92 DC N4 N N N 93 DC C5 C N N 94 DC C6 C N N 95 DC HOP3 H N N 96 DC HOP2 H N N 97 DC "H5'" H N N 98 DC "H5''" H N N 99 DC "H4'" H N N 100 DC "H3'" H N N 101 DC "HO3'" H N N 102 DC "H2'" H N N 103 DC "H2''" H N N 104 DC "H1'" H N N 105 DC H41 H N N 106 DC H42 H N N 107 DC H5 H N N 108 DC H6 H N N 109 DG OP3 O N N 110 DG P P N N 111 DG OP1 O N N 112 DG OP2 O N N 113 DG "O5'" O N N 114 DG "C5'" C N N 115 DG "C4'" C N R 116 DG "O4'" O N N 117 DG "C3'" C N S 118 DG "O3'" O N N 119 DG "C2'" C N N 120 DG "C1'" C N R 121 DG N9 N Y N 122 DG C8 C Y N 123 DG N7 N Y N 124 DG C5 C Y N 125 DG C6 C N N 126 DG O6 O N N 127 DG N1 N N N 128 DG C2 C N N 129 DG N2 N N N 130 DG N3 N N N 131 DG C4 C Y N 132 DG HOP3 H N N 133 DG HOP2 H N N 134 DG "H5'" H N N 135 DG "H5''" H N N 136 DG "H4'" H N N 137 DG "H3'" H N N 138 DG "HO3'" H N N 139 DG "H2'" H N N 140 DG "H2''" H N N 141 DG "H1'" H N N 142 DG H8 H N N 143 DG H1 H N N 144 DG H21 H N N 145 DG H22 H N N 146 DT OP3 O N N 147 DT P P N N 148 DT OP1 O N N 149 DT OP2 O N N 150 DT "O5'" O N N 151 DT "C5'" C N N 152 DT "C4'" C N R 153 DT "O4'" O N N 154 DT "C3'" C N S 155 DT "O3'" O N N 156 DT "C2'" C N N 157 DT "C1'" C N R 158 DT N1 N N N 159 DT C2 C N N 160 DT O2 O N N 161 DT N3 N N N 162 DT C4 C N N 163 DT O4 O N N 164 DT C5 C N N 165 DT C7 C N N 166 DT C6 C N N 167 DT HOP3 H N N 168 DT HOP2 H N N 169 DT "H5'" H N N 170 DT "H5''" H N N 171 DT "H4'" H N N 172 DT "H3'" H N N 173 DT "HO3'" H N N 174 DT "H2'" H N N 175 DT "H2''" H N N 176 DT "H1'" H N N 177 DT H3 H N N 178 DT H71 H N N 179 DT H72 H N N 180 DT H73 H N N 181 DT H6 H N N 182 HOH O O N N 183 HOH H1 H N N 184 HOH H2 H N N 185 HT O1 O N N 186 HT C1 C Y N 187 HT C4 C Y N 188 HT C2 C Y N 189 HT C3 C Y N 190 HT C6 C Y N 191 HT C5 C Y N 192 HT C7 C Y N 193 HT N1 N Y N 194 HT C8 C Y N 195 HT C9 C Y N 196 HT N2 N Y N 197 HT C10 C Y N 198 HT C11 C Y N 199 HT C12 C Y N 200 HT C13 C Y N 201 HT C14 C Y N 202 HT N3 N Y N 203 HT C15 C Y N 204 HT C16 C Y N 205 HT N4 N Y N 206 HT C17 C Y N 207 HT C18 C Y N 208 HT C19 C Y N 209 HT C20 C Y N 210 HT N5 N N N 211 HT C21 C N N 212 HT C22 C N N 213 HT N6 N N N 214 HT C23 C N N 215 HT C24 C N N 216 HT C25 C N N 217 HT HO1 H N N 218 HT H2 H N N 219 HT H3 H N N 220 HT H5 H N N 221 HT H6 H N N 222 HT HN1 H N N 223 HT H10 H N N 224 HT H11 H N N 225 HT H13 H N N 226 HT HN3 H N N 227 HT H17 H N N 228 HT H18 H N N 229 HT H20 H N N 230 HT H211 H N N 231 HT H212 H N N 232 HT H221 H N N 233 HT H222 H N N 234 HT H231 H N N 235 HT H232 H N N 236 HT H241 H N N 237 HT H242 H N N 238 HT H253 H N N 239 HT H252 H N N 240 HT H251 H N N 241 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal B7C OP3 P sing N N 1 B7C P OP1 sing N N 2 B7C P OP2 doub N N 3 B7C P "O5'" sing N N 4 B7C "O5'" "C5'" sing N N 5 B7C N1 C6 sing N N 6 B7C N1 C2 sing N N 7 B7C N1 "C1'" sing N N 8 B7C C6 C5 doub N N 9 B7C C2 O2 doub N N 10 B7C C2 N3 sing N N 11 B7C N3 C4 doub N N 12 B7C C4 N4 sing N N 13 B7C C4 C5 sing N N 14 B7C N4 C9 sing N N 15 B7C C5 C7 sing N N 16 B7C C7 C8 doub N N 17 B7C C8 C9 sing N N 18 B7C "C2'" "C1'" sing N N 19 B7C "C2'" "C3'" sing N N 20 B7C "C5'" "C4'" sing N N 21 B7C "C4'" "O4'" sing N N 22 B7C "C4'" "C3'" sing N N 23 B7C "O4'" "C1'" sing N N 24 B7C "C3'" "O3'" sing N N 25 B7C OP3 HOP3 sing N N 26 B7C OP1 HOP1 sing N N 27 B7C C6 H6 sing N N 28 B7C N4 HN4 sing N N 29 B7C C7 H7 sing N N 30 B7C C8 H8 sing N N 31 B7C C9 H9 sing N N 32 B7C C9 H9A sing N N 33 B7C "C2'" "H2'" sing N N 34 B7C "C2'" "H2'A" sing N N 35 B7C "C5'" "H5'" sing N N 36 B7C "C5'" "H5'A" sing N N 37 B7C "C4'" "H4'" sing N N 38 B7C "C1'" "H1'" sing N N 39 B7C "C3'" "H3'" sing N N 40 B7C "O3'" "HO3'" sing N N 41 DA OP3 P sing N N 42 DA OP3 HOP3 sing N N 43 DA P OP1 doub N N 44 DA P OP2 sing N N 45 DA P "O5'" sing N N 46 DA OP2 HOP2 sing N N 47 DA "O5'" "C5'" sing N N 48 DA "C5'" "C4'" sing N N 49 DA "C5'" "H5'" sing N N 50 DA "C5'" "H5''" sing N N 51 DA "C4'" "O4'" sing N N 52 DA "C4'" "C3'" sing N N 53 DA "C4'" "H4'" sing N N 54 DA "O4'" "C1'" sing N N 55 DA "C3'" "O3'" sing N N 56 DA "C3'" "C2'" sing N N 57 DA "C3'" "H3'" sing N N 58 DA "O3'" "HO3'" sing N N 59 DA "C2'" "C1'" sing N N 60 DA "C2'" "H2'" sing N N 61 DA "C2'" "H2''" sing N N 62 DA "C1'" N9 sing N N 63 DA "C1'" "H1'" sing N N 64 DA N9 C8 sing Y N 65 DA N9 C4 sing Y N 66 DA C8 N7 doub Y N 67 DA C8 H8 sing N N 68 DA N7 C5 sing Y N 69 DA C5 C6 sing Y N 70 DA C5 C4 doub Y N 71 DA C6 N6 sing N N 72 DA C6 N1 doub Y N 73 DA N6 H61 sing N N 74 DA N6 H62 sing N N 75 DA N1 C2 sing Y N 76 DA C2 N3 doub Y N 77 DA C2 H2 sing N N 78 DA N3 C4 sing Y N 79 DC OP3 P sing N N 80 DC OP3 HOP3 sing N N 81 DC P OP1 doub N N 82 DC P OP2 sing N N 83 DC P "O5'" sing N N 84 DC OP2 HOP2 sing N N 85 DC "O5'" "C5'" sing N N 86 DC "C5'" "C4'" sing N N 87 DC "C5'" "H5'" sing N N 88 DC "C5'" "H5''" sing N N 89 DC "C4'" "O4'" sing N N 90 DC "C4'" "C3'" sing N N 91 DC "C4'" "H4'" sing N N 92 DC "O4'" "C1'" sing N N 93 DC "C3'" "O3'" sing N N 94 DC "C3'" "C2'" sing N N 95 DC "C3'" "H3'" sing N N 96 DC "O3'" "HO3'" sing N N 97 DC "C2'" "C1'" sing N N 98 DC "C2'" "H2'" sing N N 99 DC "C2'" "H2''" sing N N 100 DC "C1'" N1 sing N N 101 DC "C1'" "H1'" sing N N 102 DC N1 C2 sing N N 103 DC N1 C6 sing N N 104 DC C2 O2 doub N N 105 DC C2 N3 sing N N 106 DC N3 C4 doub N N 107 DC C4 N4 sing N N 108 DC C4 C5 sing N N 109 DC N4 H41 sing N N 110 DC N4 H42 sing N N 111 DC C5 C6 doub N N 112 DC C5 H5 sing N N 113 DC C6 H6 sing N N 114 DG OP3 P sing N N 115 DG OP3 HOP3 sing N N 116 DG P OP1 doub N N 117 DG P OP2 sing N N 118 DG P "O5'" sing N N 119 DG OP2 HOP2 sing N N 120 DG "O5'" "C5'" sing N N 121 DG "C5'" "C4'" sing N N 122 DG "C5'" "H5'" sing N N 123 DG "C5'" "H5''" sing N N 124 DG "C4'" "O4'" sing N N 125 DG "C4'" "C3'" sing N N 126 DG "C4'" "H4'" sing N N 127 DG "O4'" "C1'" sing N N 128 DG "C3'" "O3'" sing N N 129 DG "C3'" "C2'" sing N N 130 DG "C3'" "H3'" sing N N 131 DG "O3'" "HO3'" sing N N 132 DG "C2'" "C1'" sing N N 133 DG "C2'" "H2'" sing N N 134 DG "C2'" "H2''" sing N N 135 DG "C1'" N9 sing N N 136 DG "C1'" "H1'" sing N N 137 DG N9 C8 sing Y N 138 DG N9 C4 sing Y N 139 DG C8 N7 doub Y N 140 DG C8 H8 sing N N 141 DG N7 C5 sing Y N 142 DG C5 C6 sing N N 143 DG C5 C4 doub Y N 144 DG C6 O6 doub N N 145 DG C6 N1 sing N N 146 DG N1 C2 sing N N 147 DG N1 H1 sing N N 148 DG C2 N2 sing N N 149 DG C2 N3 doub N N 150 DG N2 H21 sing N N 151 DG N2 H22 sing N N 152 DG N3 C4 sing N N 153 DT OP3 P sing N N 154 DT OP3 HOP3 sing N N 155 DT P OP1 doub N N 156 DT P OP2 sing N N 157 DT P "O5'" sing N N 158 DT OP2 HOP2 sing N N 159 DT "O5'" "C5'" sing N N 160 DT "C5'" "C4'" sing N N 161 DT "C5'" "H5'" sing N N 162 DT "C5'" "H5''" sing N N 163 DT "C4'" "O4'" sing N N 164 DT "C4'" "C3'" sing N N 165 DT "C4'" "H4'" sing N N 166 DT "O4'" "C1'" sing N N 167 DT "C3'" "O3'" sing N N 168 DT "C3'" "C2'" sing N N 169 DT "C3'" "H3'" sing N N 170 DT "O3'" "HO3'" sing N N 171 DT "C2'" "C1'" sing N N 172 DT "C2'" "H2'" sing N N 173 DT "C2'" "H2''" sing N N 174 DT "C1'" N1 sing N N 175 DT "C1'" "H1'" sing N N 176 DT N1 C2 sing N N 177 DT N1 C6 sing N N 178 DT C2 O2 doub N N 179 DT C2 N3 sing N N 180 DT N3 C4 sing N N 181 DT N3 H3 sing N N 182 DT C4 O4 doub N N 183 DT C4 C5 sing N N 184 DT C5 C7 sing N N 185 DT C5 C6 doub N N 186 DT C7 H71 sing N N 187 DT C7 H72 sing N N 188 DT C7 H73 sing N N 189 DT C6 H6 sing N N 190 HOH O H1 sing N N 191 HOH O H2 sing N N 192 HT O1 C1 sing N N 193 HT O1 HO1 sing N N 194 HT C1 C2 doub Y N 195 HT C1 C6 sing Y N 196 HT C2 C3 sing Y N 197 HT C2 H2 sing N N 198 HT C3 C4 doub Y N 199 HT C3 H3 sing N N 200 HT C4 C5 sing Y N 201 HT C4 C7 sing Y N 202 HT C5 C6 doub Y N 203 HT C5 H5 sing N N 204 HT C6 H6 sing N N 205 HT C7 N1 sing Y N 206 HT C7 N2 doub Y N 207 HT N1 C8 sing Y N 208 HT N1 HN1 sing N N 209 HT C8 C9 doub Y N 210 HT C8 C13 sing Y N 211 HT C9 N2 sing Y N 212 HT C9 C10 sing Y N 213 HT C10 C11 doub Y N 214 HT C10 H10 sing N N 215 HT C11 C12 sing Y N 216 HT C11 H11 sing N N 217 HT C12 C13 doub Y N 218 HT C12 C14 sing Y N 219 HT C13 H13 sing N N 220 HT C14 N3 sing Y N 221 HT C14 N4 doub Y N 222 HT N3 C15 sing Y N 223 HT N3 HN3 sing N N 224 HT C15 C16 doub Y N 225 HT C15 C20 sing Y N 226 HT C16 N4 sing Y N 227 HT C16 C17 sing Y N 228 HT C17 C18 doub Y N 229 HT C17 H17 sing N N 230 HT C18 C19 sing Y N 231 HT C18 H18 sing N N 232 HT C19 C20 doub Y N 233 HT C19 N5 sing N N 234 HT C20 H20 sing N N 235 HT N5 C21 sing N N 236 HT N5 C24 sing N N 237 HT C21 C22 sing N N 238 HT C21 H211 sing N N 239 HT C21 H212 sing N N 240 HT C22 N6 sing N N 241 HT C22 H221 sing N N 242 HT C22 H222 sing N N 243 HT N6 C23 sing N N 244 HT N6 C25 sing N N 245 HT C23 C24 sing N N 246 HT C23 H231 sing N N 247 HT C23 H232 sing N N 248 HT C24 H241 sing N N 249 HT C24 H242 sing N N 250 HT C25 H253 sing N N 251 HT C25 H252 sing N N 252 HT C25 H251 sing N N 253 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3N4O 'double helix' 3N4O 'b-form double helix' 3N4O 'mismatched base pair' # 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 12 1_555 0.142 -0.166 -0.045 -3.081 -1.728 -2.722 1 D_DC1:DG24_E D 1 ? E 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.024 -0.282 0.084 -1.866 -11.094 -6.598 2 D_DG2:DC23_E D 2 ? E 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.027 -0.143 0.288 -2.603 -0.652 -2.444 3 D_DC3:DG22_E D 3 ? E 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.255 -0.194 0.113 8.578 -1.951 -2.780 4 D_DG4:DC21_E D 4 ? E 21 ? 19 1 1 A DA 6 1_555 B DT 7 1_555 -0.139 -0.135 -0.136 1.596 -18.110 5.261 5 D_DA6:DT19_E D 6 ? E 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.016 -0.148 0.384 -3.106 -16.755 0.654 6 D_DT7:DA18_E D 7 ? E 18 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.021 -0.143 -0.339 -7.445 -1.109 -3.049 7 D_DC9:DG16_E D 9 ? E 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.107 -0.263 -0.061 2.179 1.254 -1.059 8 D_DG10:DC15_E D 10 ? E 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.007 -0.233 0.584 -5.027 -13.017 -8.654 9 D_DC11:DG14_E D 11 ? E 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.024 -0.019 0.259 15.574 7.892 -2.873 10 D_DG12:DC13_E D 12 ? E 13 ? 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 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.486 0.173 3.277 0.086 4.564 39.052 -0.287 0.733 3.275 6.798 -0.127 39.308 1 DD_DC1DG2:DC23DG24_EE D 1 ? E 24 ? D 2 ? E 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.829 0.286 3.436 0.140 -4.739 35.329 1.187 -1.333 3.374 -7.765 -0.229 35.635 2 DD_DG2DC3:DG22DC23_EE D 2 ? E 23 ? D 3 ? E 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 0.038 0.839 3.052 3.134 4.603 28.191 0.704 0.596 3.132 9.334 -6.355 28.724 3 DD_DC3DG4:DC21DG22_EE D 3 ? E 22 ? D 4 ? E 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 6 1_555 B DT 7 1_555 -0.332 -0.200 6.695 -0.012 7.884 75.246 -0.648 0.270 6.651 6.440 0.010 75.597 4 DD_DG4DA6:DT19DC21_EE D 4 ? E 21 ? D 6 ? E 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.215 -0.635 3.381 -3.294 -2.396 34.630 -0.683 -0.877 3.382 -4.008 5.509 34.861 5 DD_DA6DT7:DA18DT19_EE D 6 ? E 19 ? D 7 ? E 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DC 9 1_555 B DG 4 1_555 -0.082 0.018 6.473 8.971 3.290 74.128 -0.187 0.616 6.426 2.718 -7.413 74.654 6 DD_DT7DC9:DG16DA18_EE D 7 ? E 18 ? D 9 ? E 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.100 1.152 3.243 -3.070 1.708 30.998 1.818 -0.769 3.276 3.183 5.721 31.192 7 DD_DC9DG10:DC15DG16_EE D 9 ? E 16 ? D 10 ? E 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.240 0.404 3.520 -5.961 -3.048 36.359 1.090 1.071 3.627 -4.833 9.454 36.950 8 DD_DG10DC11:DG14DC15_EE D 10 ? E 15 ? D 11 ? E 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.851 0.417 2.922 0.491 -3.117 37.922 0.992 -1.249 2.890 -4.786 -0.754 38.048 9 DD_DC11DG12:DC13DG14_EE D 11 ? E 14 ? D 12 ? E 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" HT 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1DNH _pdbx_initial_refinement_model.details ? #