data_7KU4 # _entry.id 7KU4 # _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 7KU4 pdb_00007ku4 10.2210/pdb7ku4/pdb WWPDB D_1000253050 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7KU4 _pdbx_database_status.recvd_initial_deposition_date 2020-11-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ogbonna, E.' 1 0000-0002-0762-0603 'Fang, Z.' 2 0000-0001-8679-6633 'Wilson, W.D.' 3 0000-0001-5225-5089 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Bioorg.Med.Chem. _citation.journal_id_ASTM BMECEP _citation.journal_id_CSD 1200 _citation.journal_id_ISSN 1464-3391 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 68 _citation.language ? _citation.page_first 116861 _citation.page_last 116861 _citation.title ;Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. ; _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.bmc.2022.116861 _citation.pdbx_database_id_PubMed 35661929 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ogbonna, E.N.' 1 ? primary 'Paul, A.' 2 ? primary 'Ross Terrell, J.' 3 ? primary 'Fang, Z.' 4 ? primary 'Chen, C.' 5 ? primary 'Poon, G.M.K.' 6 ? primary 'Boykin, D.W.' 7 ? primary 'Wilson, W.D.' 8 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 7KU4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 25.335 _cell.length_a_esd ? _cell.length_b 40.127 _cell.length_b_esd ? _cell.length_c 65.451 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KU4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # 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 "1:(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')" 3663.392 2 ? ? ? ? 2 non-polymer syn '2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE' 360.436 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 73 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 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 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 12 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7KU4 _struct_ref.pdbx_db_accession 7KU4 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 7KU4 A 1 ? 12 ? 7KU4 1 ? 12 ? 1 12 2 1 7KU4 B 1 ? 12 ? 7KU4 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 D1B non-polymer . '2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE' ? 'C19 H16 N6 S' 360.436 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7KU4 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.31 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.79 _exptl_crystal.description 'Rod shaped crystal' _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas 0.717 _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details 'Temperature was kept constant' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10% MPD, 0.040M Sodium Cacodylate trihydrate, 0.012 Spermine Tetrahydrate, 0.080M Sodium Chloride, 0.020M Magnesium chloride hexahydrate ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 S 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2020-05-28 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'SINGLE CRYSTAL Si (200)' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.14 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 5.0.1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 5.0.1 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 7KU4 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.6 _reflns.d_resolution_low 50.000 _reflns.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.number_all ? _reflns.number_obs 9102 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 96.600 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.200 _reflns.pdbx_Rmerge_I_obs 0.070 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.600 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.981 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.073 _reflns.pdbx_Rpim_I_all 0.021 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split 1.600 1.630 ? ? ? ? ? ? 430 95.100 ? ? ? ? 0.493 ? ? ? ? ? ? ? ? 12.300 ? 0.983 ? ? 0.515 0.146 ? 1 1 0.980 ? ? 1.630 1.660 ? ? ? ? ? ? 430 95.300 ? ? ? ? 0.439 ? ? ? ? ? ? ? ? 12.500 ? 1.032 ? ? 0.458 0.129 ? 2 1 0.985 ? ? 1.660 1.690 ? ? ? ? ? ? 445 94.700 ? ? ? ? 0.365 ? ? ? ? ? ? ? ? 12.300 ? 1.037 ? ? 0.381 0.108 ? 3 1 0.985 ? ? 1.690 1.720 ? ? ? ? ? ? 426 95.300 ? ? ? ? 0.302 ? ? ? ? ? ? ? ? 12.000 ? 1.071 ? ? 0.316 0.092 ? 4 1 0.988 ? ? 1.720 1.760 ? ? ? ? ? ? 447 95.900 ? ? ? ? 0.277 ? ? ? ? ? ? ? ? 11.500 ? 1.109 ? ? 0.290 0.084 ? 5 1 0.988 ? ? 1.760 1.800 ? ? ? ? ? ? 444 96.100 ? ? ? ? 0.261 ? ? ? ? ? ? ? ? 12.600 ? 1.153 ? ? 0.272 0.076 ? 6 1 0.975 ? ? 1.800 1.850 ? ? ? ? ? ? 443 95.700 ? ? ? ? 0.233 ? ? ? ? ? ? ? ? 12.300 ? 1.173 ? ? 0.243 0.069 ? 7 1 0.985 ? ? 1.850 1.900 ? ? ? ? ? ? 430 95.800 ? ? ? ? 0.214 ? ? ? ? ? ? ? ? 11.700 ? 1.173 ? ? 0.224 0.066 ? 8 1 0.975 ? ? 1.900 1.950 ? ? ? ? ? ? 453 96.200 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 12.600 ? 1.184 ? ? 0.203 0.057 ? 9 1 0.988 ? ? 1.950 2.020 ? ? ? ? ? ? 452 96.600 ? ? ? ? 0.176 ? ? ? ? ? ? ? ? 12.700 ? 1.180 ? ? 0.184 0.051 ? 10 1 0.980 ? ? 2.020 2.090 ? ? ? ? ? ? 447 96.500 ? ? ? ? 0.159 ? ? ? ? ? ? ? ? 12.600 ? 1.195 ? ? 0.166 0.047 ? 11 1 0.989 ? ? 2.090 2.170 ? ? ? ? ? ? 445 96.700 ? ? ? ? 0.147 ? ? ? ? ? ? ? ? 12.400 ? 1.165 ? ? 0.153 0.042 ? 12 1 0.990 ? ? 2.170 2.270 ? ? ? ? ? ? 460 96.600 ? ? ? ? 0.130 ? ? ? ? ? ? ? ? 12.200 ? 1.139 ? ? 0.136 0.038 ? 13 1 0.985 ? ? 2.270 2.390 ? ? ? ? ? ? 455 97.400 ? ? ? ? 0.118 ? ? ? ? ? ? ? ? 12.300 ? 1.035 ? ? 0.123 0.034 ? 14 1 0.994 ? ? 2.390 2.540 ? ? ? ? ? ? 467 96.900 ? ? ? ? 0.108 ? ? ? ? ? ? ? ? 12.400 ? 0.942 ? ? 0.113 0.032 ? 15 1 0.989 ? ? 2.540 2.740 ? ? ? ? ? ? 457 97.600 ? ? ? ? 0.092 ? ? ? ? ? ? ? ? 12.800 ? 0.846 ? ? 0.095 0.026 ? 16 1 0.997 ? ? 2.740 3.010 ? ? ? ? ? ? 462 97.900 ? ? ? ? 0.079 ? ? ? ? ? ? ? ? 12.200 ? 0.750 ? ? 0.083 0.024 ? 17 1 0.997 ? ? 3.010 3.450 ? ? ? ? ? ? 481 98.200 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? 11.800 ? 0.598 ? ? 0.072 0.022 ? 18 1 0.997 ? ? 3.450 4.340 ? ? ? ? ? ? 498 98.600 ? ? ? ? 0.062 ? ? ? ? ? ? ? ? 12.100 ? 0.495 ? ? 0.065 0.019 ? 19 1 0.997 ? ? 4.340 50.000 ? ? ? ? ? ? 530 97.400 ? ? ? ? 0.052 ? ? ? ? ? ? ? ? 11.100 ? 0.469 ? ? 0.055 0.016 ? 20 1 0.999 ? ? # _refine.aniso_B[1][1] -0.0100 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] 0.0100 _refine.aniso_B[2][3] -0.0000 _refine.aniso_B[3][3] -0.0000 _refine.B_iso_max 33.980 _refine.B_iso_mean 12.1190 _refine.B_iso_min 4.920 _refine.correlation_coeff_Fo_to_Fc 0.9430 _refine.correlation_coeff_Fo_to_Fc_free 0.9300 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 7KU4 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.600 _refine.ls_d_res_low 34.2100 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 8046 _refine.ls_number_reflns_R_free 446 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 90.5000 _refine.ls_percent_reflns_R_free 5.3000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2176 _refine.ls_R_factor_R_free 0.2308 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2168 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 1BNA _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1170 _refine.pdbx_overall_ESU_R_Free 0.1050 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 1.7500 _refine.overall_SU_ML 0.0630 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 34.2100 _refine_hist.number_atoms_solvent 73 _refine_hist.number_atoms_total 586 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_ligand 19.61 _refine_hist.pdbx_B_iso_mean_solvent 20.73 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 486 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.014 0.011 573 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 288 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 2.057 1.251 878 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.668 3.030 670 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 0.072 0.200 72 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.031 0.020 326 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.005 0.021 146 ? r_gen_planes_other ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.6 _refine_ls_shell.d_res_low 1.6360 _refine_ls_shell.number_reflns_all 360 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 21 _refine_ls_shell.number_reflns_R_work 339 _refine_ls_shell.percent_reflns_obs 54.0500 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.1230 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.1920 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 7KU4 _struct.title ;DNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the heterocyclic small molecule (DB818). ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7KU4 _struct_keywords.text 'DNA-molecule complex, DNA' _struct_keywords.pdbx_keywords 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 4 ? F N N 4 ? # 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 metalc1 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 102 A HOH 212 1_555 ? ? ? ? ? ? ? 2.083 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 102 A HOH 214 3_645 ? ? ? ? ? ? ? 1.983 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 102 A HOH 216 1_555 ? ? ? ? ? ? ? 2.093 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 102 A HOH 217 3_645 ? ? ? ? ? ? ? 2.100 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 102 A HOH 225 1_555 ? ? ? ? ? ? ? 2.092 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 102 B HOH 116 3_645 ? ? ? ? ? ? ? 2.102 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _atom_sites.entry_id 7KU4 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.039471 _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] 0.024921 _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] 0.015279 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C MG N O P S # loop_ # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG B . 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 D1B 1 101 101 D1B LIG A . D 3 MG 1 102 1 MG MG A . E 4 HOH 1 201 26 HOH HOH A . E 4 HOH 2 202 19 HOH HOH A . E 4 HOH 3 203 62 HOH HOH A . E 4 HOH 4 204 53 HOH HOH A . E 4 HOH 5 205 56 HOH HOH A . E 4 HOH 6 206 36 HOH HOH A . E 4 HOH 7 207 55 HOH HOH A . E 4 HOH 8 208 13 HOH HOH A . E 4 HOH 9 209 14 HOH HOH A . E 4 HOH 10 210 27 HOH HOH A . E 4 HOH 11 211 73 HOH HOH A . E 4 HOH 12 212 2 HOH HOH A . E 4 HOH 13 213 38 HOH HOH A . E 4 HOH 14 214 3 HOH HOH A . E 4 HOH 15 215 39 HOH HOH A . E 4 HOH 16 216 6 HOH HOH A . E 4 HOH 17 217 4 HOH HOH A . E 4 HOH 18 218 48 HOH HOH A . E 4 HOH 19 219 44 HOH HOH A . E 4 HOH 20 220 18 HOH HOH A . E 4 HOH 21 221 69 HOH HOH A . E 4 HOH 22 222 11 HOH HOH A . E 4 HOH 23 223 8 HOH HOH A . E 4 HOH 24 224 24 HOH HOH A . E 4 HOH 25 225 1 HOH HOH A . E 4 HOH 26 226 29 HOH HOH A . E 4 HOH 27 227 45 HOH HOH A . E 4 HOH 28 228 37 HOH HOH A . E 4 HOH 29 229 35 HOH HOH A . E 4 HOH 30 230 71 HOH HOH A . E 4 HOH 31 231 22 HOH HOH A . E 4 HOH 32 232 75 HOH HOH A . E 4 HOH 33 233 42 HOH HOH A . E 4 HOH 34 234 59 HOH HOH A . E 4 HOH 35 235 40 HOH HOH A . E 4 HOH 36 236 7 HOH HOH A . E 4 HOH 37 237 10 HOH HOH A . E 4 HOH 38 238 30 HOH HOH A . E 4 HOH 39 239 9 HOH HOH A . E 4 HOH 40 240 60 HOH HOH A . E 4 HOH 41 241 65 HOH HOH A . E 4 HOH 42 242 52 HOH HOH A . F 4 HOH 1 101 28 HOH HOH B . F 4 HOH 2 102 46 HOH HOH B . F 4 HOH 3 103 74 HOH HOH B . F 4 HOH 4 104 51 HOH HOH B . F 4 HOH 5 105 70 HOH HOH B . F 4 HOH 6 106 20 HOH HOH B . F 4 HOH 7 107 15 HOH HOH B . F 4 HOH 8 108 54 HOH HOH B . F 4 HOH 9 109 43 HOH HOH B . F 4 HOH 10 110 47 HOH HOH B . F 4 HOH 11 111 32 HOH HOH B . F 4 HOH 12 112 68 HOH HOH B . F 4 HOH 13 113 17 HOH HOH B . F 4 HOH 14 114 67 HOH HOH B . F 4 HOH 15 115 12 HOH HOH B . F 4 HOH 16 116 5 HOH HOH B . F 4 HOH 17 117 64 HOH HOH B . F 4 HOH 18 118 58 HOH HOH B . F 4 HOH 19 119 25 HOH HOH B . F 4 HOH 20 120 21 HOH HOH B . F 4 HOH 21 121 41 HOH HOH B . F 4 HOH 22 122 50 HOH HOH B . F 4 HOH 23 123 57 HOH HOH B . F 4 HOH 24 124 49 HOH HOH B . F 4 HOH 25 125 34 HOH HOH B . F 4 HOH 26 126 72 HOH HOH B . F 4 HOH 27 127 31 HOH HOH B . F 4 HOH 28 128 23 HOH HOH B . F 4 HOH 29 129 16 HOH HOH B . F 4 HOH 30 130 63 HOH HOH B . F 4 HOH 31 131 33 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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,F # 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)' 2110 ? 1 MORE -7 ? 1 'SSA (A^2)' 4210 ? # _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_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 ? E HOH . ? A HOH 212 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 214 ? 3_645 91.5 ? 2 O ? E HOH . ? A HOH 212 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 91.3 ? 3 O ? E HOH . ? A HOH 214 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 216 ? 1_555 176.2 ? 4 O ? E HOH . ? A HOH 212 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 217 ? 3_645 87.9 ? 5 O ? E HOH . ? A HOH 214 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 217 ? 3_645 91.4 ? 6 O ? E HOH . ? A HOH 216 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 217 ? 3_645 91.2 ? 7 O ? E HOH . ? A HOH 212 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 225 ? 1_555 88.0 ? 8 O ? E HOH . ? A HOH 214 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 225 ? 1_555 90.2 ? 9 O ? E HOH . ? A HOH 216 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 225 ? 1_555 87.4 ? 10 O ? E HOH . ? A HOH 217 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? E HOH . ? A HOH 225 ? 1_555 175.6 ? 11 O ? E HOH . ? A HOH 212 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? F HOH . ? B HOH 116 ? 3_645 177.9 ? 12 O ? E HOH . ? A HOH 214 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? F HOH . ? B HOH 116 ? 3_645 89.2 ? 13 O ? E HOH . ? A HOH 216 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? F HOH . ? B HOH 116 ? 3_645 87.9 ? 14 O ? E HOH . ? A HOH 217 ? 3_645 MG ? D MG . ? A MG 102 ? 1_555 O ? F HOH . ? B HOH 116 ? 3_645 94.1 ? 15 O ? E HOH . ? A HOH 225 ? 1_555 MG ? D MG . ? A MG 102 ? 1_555 O ? F HOH . ? B HOH 116 ? 3_645 90.0 ? # 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 2021-12-01 2 'Structure model' 1 1 2022-06-15 3 'Structure model' 1 2 2023-10-18 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' pdbx_initial_refinement_model # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v721 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0267 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v721 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 7KU4 _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _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 OP2 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DA _pdbx_validate_close_contact.auth_seq_id_1 18 _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 HOH _pdbx_validate_close_contact.auth_seq_id_2 101 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.85 # 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 DG 10 ? ? P A DG 10 ? ? OP2 A DG 10 ? ? 97.09 105.70 -8.61 0.90 N 2 1 "O5'" A DG 12 ? ? P A DG 12 ? ? OP2 A DG 12 ? ? 99.36 105.70 -6.34 0.90 N # 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 D1B C1 C Y N 1 D1B S2 S Y N 2 D1B C3 C Y N 3 D1B C4 C Y N 4 D1B C5 C Y N 5 D1B C6 C Y N 6 D1B N7 N Y N 7 D1B C8 C Y N 8 D1B C9 C Y N 9 D1B N10 N Y N 10 D1B C11 C Y N 11 D1B C12 C Y N 12 D1B C13 C Y N 13 D1B C14 C Y N 14 D1B C15 C Y N 15 D1B C16 C Y N 16 D1B C17 C Y N 17 D1B C18 C Y N 18 D1B C19 C Y N 19 D1B C20 C Y N 20 D1B C21 C N N 21 D1B N22 N N N 22 D1B N23 N N N 23 D1B C24 C N N 24 D1B N25 N N N 25 D1B N26 N N N 26 D1B H4 H N N 27 D1B H5 H N N 28 D1B H10 H N N 29 D1B H11 H N N 30 D1B H12 H N N 31 D1B H14 H N N 32 D1B H16 H N N 33 D1B H17 H N N 34 D1B H19 H N N 35 D1B H20 H N N 36 D1B H221 H N N 37 D1B H222 H N N 38 D1B H23 H N N 39 D1B H25 H N N 40 D1B H261 H N N 41 D1B H262 H N N 42 DA OP3 O N N 43 DA P P N N 44 DA OP1 O N N 45 DA OP2 O N N 46 DA "O5'" O N N 47 DA "C5'" C N N 48 DA "C4'" C N R 49 DA "O4'" O N N 50 DA "C3'" C N S 51 DA "O3'" O N N 52 DA "C2'" C N N 53 DA "C1'" C N R 54 DA N9 N Y N 55 DA C8 C Y N 56 DA N7 N Y N 57 DA C5 C Y N 58 DA C6 C Y N 59 DA N6 N N N 60 DA N1 N Y N 61 DA C2 C Y N 62 DA N3 N Y N 63 DA C4 C Y N 64 DA HOP3 H N N 65 DA HOP2 H N N 66 DA "H5'" H N N 67 DA "H5''" H N N 68 DA "H4'" H N N 69 DA "H3'" H N N 70 DA "HO3'" H N N 71 DA "H2'" H N N 72 DA "H2''" H N N 73 DA "H1'" H N N 74 DA H8 H N N 75 DA H61 H N N 76 DA H62 H N N 77 DA H2 H N N 78 DC OP3 O N N 79 DC P P N N 80 DC OP1 O N N 81 DC OP2 O N N 82 DC "O5'" O N N 83 DC "C5'" C N N 84 DC "C4'" C N R 85 DC "O4'" O N N 86 DC "C3'" C N S 87 DC "O3'" O N N 88 DC "C2'" C N N 89 DC "C1'" C N R 90 DC N1 N N N 91 DC C2 C N N 92 DC O2 O N N 93 DC N3 N N N 94 DC C4 C N N 95 DC N4 N N N 96 DC C5 C N N 97 DC C6 C N N 98 DC HOP3 H N N 99 DC HOP2 H N N 100 DC "H5'" H N N 101 DC "H5''" H N N 102 DC "H4'" H N N 103 DC "H3'" H N N 104 DC "HO3'" H N N 105 DC "H2'" H N N 106 DC "H2''" H N N 107 DC "H1'" H N N 108 DC H41 H N N 109 DC H42 H N N 110 DC H5 H N N 111 DC H6 H N N 112 DG OP3 O N N 113 DG P P N N 114 DG OP1 O N N 115 DG OP2 O N N 116 DG "O5'" O N N 117 DG "C5'" C N N 118 DG "C4'" C N R 119 DG "O4'" O N N 120 DG "C3'" C N S 121 DG "O3'" O N N 122 DG "C2'" C N N 123 DG "C1'" C N R 124 DG N9 N Y N 125 DG C8 C Y N 126 DG N7 N Y N 127 DG C5 C Y N 128 DG C6 C N N 129 DG O6 O N N 130 DG N1 N N N 131 DG C2 C N N 132 DG N2 N N N 133 DG N3 N N N 134 DG C4 C Y N 135 DG HOP3 H N N 136 DG HOP2 H N N 137 DG "H5'" H N N 138 DG "H5''" H N N 139 DG "H4'" H N N 140 DG "H3'" H N N 141 DG "HO3'" H N N 142 DG "H2'" H N N 143 DG "H2''" H N N 144 DG "H1'" H N N 145 DG H8 H N N 146 DG H1 H N N 147 DG H21 H N N 148 DG H22 H N N 149 DT OP3 O N N 150 DT P P N N 151 DT OP1 O N N 152 DT OP2 O N N 153 DT "O5'" O N N 154 DT "C5'" C N N 155 DT "C4'" C N R 156 DT "O4'" O N N 157 DT "C3'" C N S 158 DT "O3'" O N N 159 DT "C2'" C N N 160 DT "C1'" C N R 161 DT N1 N N N 162 DT C2 C N N 163 DT O2 O N N 164 DT N3 N N N 165 DT C4 C N N 166 DT O4 O N N 167 DT C5 C N N 168 DT C7 C N N 169 DT C6 C N N 170 DT HOP3 H N N 171 DT HOP2 H N N 172 DT "H5'" H N N 173 DT "H5''" H N N 174 DT "H4'" H N N 175 DT "H3'" H N N 176 DT "HO3'" H N N 177 DT "H2'" H N N 178 DT "H2''" H N N 179 DT "H1'" H N N 180 DT H3 H N N 181 DT H71 H N N 182 DT H72 H N N 183 DT H73 H N N 184 DT H6 H N N 185 HOH O O N N 186 HOH H1 H N N 187 HOH H2 H N N 188 MG MG MG N N 189 # 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 D1B C1 S2 sing Y N 1 D1B C1 C5 doub Y N 2 D1B C1 C15 sing Y N 3 D1B S2 C3 sing Y N 4 D1B C3 C4 doub Y N 5 D1B C3 C6 sing Y N 6 D1B C4 C5 sing Y N 7 D1B C4 H4 sing N N 8 D1B C5 H5 sing N N 9 D1B C6 N7 doub Y N 10 D1B C6 N10 sing Y N 11 D1B N7 C8 sing Y N 12 D1B C8 C9 doub Y N 13 D1B C8 C11 sing Y N 14 D1B C9 N10 sing Y N 15 D1B C9 C14 sing Y N 16 D1B N10 H10 sing N N 17 D1B C11 C12 doub Y N 18 D1B C11 H11 sing N N 19 D1B C12 C13 sing Y N 20 D1B C12 H12 sing N N 21 D1B C13 C14 doub Y N 22 D1B C13 C21 sing N N 23 D1B C14 H14 sing N N 24 D1B C15 C16 sing Y N 25 D1B C15 C20 doub Y N 26 D1B C16 C17 doub Y N 27 D1B C16 H16 sing N N 28 D1B C17 C18 sing Y N 29 D1B C17 H17 sing N N 30 D1B C18 C19 doub Y N 31 D1B C18 C24 sing N N 32 D1B C19 C20 sing Y N 33 D1B C19 H19 sing N N 34 D1B C20 H20 sing N N 35 D1B C21 N22 sing N N 36 D1B C21 N23 doub N Z 37 D1B N22 H221 sing N N 38 D1B N22 H222 sing N N 39 D1B N23 H23 sing N N 40 D1B C24 N25 doub N N 41 D1B C24 N26 sing N N 42 D1B N25 H25 sing N N 43 D1B N26 H261 sing N N 44 D1B N26 H262 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 HOH O H1 sing N N 195 HOH O H2 sing N N 196 # _ndb_struct_conf_na.entry_id 7KU4 _ndb_struct_conf_na.feature 'b-form 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 12 1_555 0.230 -0.196 0.088 4.056 -14.207 -0.923 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.289 -0.238 0.403 8.201 -10.800 -2.269 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.143 -0.183 0.197 -3.067 -7.274 -0.510 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.256 -0.162 -0.163 7.322 -9.805 -0.529 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.008 -0.097 -0.026 5.932 -15.593 3.570 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.008 -0.123 -0.052 -2.345 -16.501 5.048 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.008 -0.172 0.007 0.605 -18.674 5.339 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.073 -0.199 -0.189 1.286 -13.948 3.963 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.197 -0.148 -0.166 -6.500 -12.061 -2.127 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.127 -0.193 0.231 6.229 -8.980 1.761 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.083 -0.210 0.166 4.110 -18.859 -2.604 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.126 -0.103 0.355 4.155 -6.651 -2.248 12 A_DG12:DC13_B A 12 ? B 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 -0.023 0.026 3.143 -2.675 6.461 33.276 -0.950 -0.372 3.086 11.130 4.608 33.983 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.518 0.514 3.611 2.307 -6.259 43.641 1.328 -0.452 3.530 -8.360 -3.082 44.123 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.290 0.741 3.125 3.291 10.406 26.348 -0.862 1.339 3.128 21.684 -6.858 28.482 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.052 -0.046 3.265 -1.570 2.715 37.336 -0.427 -0.125 3.254 4.231 2.446 37.463 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.108 -0.257 3.424 -0.473 2.284 35.682 -0.762 -0.247 3.400 3.723 0.771 35.756 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.098 -0.459 3.066 -0.257 -0.454 33.386 -0.728 -0.210 3.071 -0.790 0.447 33.390 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.203 -0.226 3.198 1.774 0.208 33.338 -0.426 0.639 3.181 0.363 -3.089 33.385 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.221 0.010 3.433 1.188 -1.316 41.401 0.162 0.445 3.424 -1.861 -1.679 41.438 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.620 0.903 3.106 -3.930 5.492 26.396 0.593 -2.266 3.104 11.782 8.431 27.232 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.192 0.567 3.345 -2.472 -8.261 42.544 1.585 1.368 3.246 -11.247 3.365 43.370 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.018 0.349 3.278 -1.809 4.886 33.325 -0.200 -0.328 3.289 8.456 3.130 33.719 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM111749 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id D1B _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id D1B _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE' D1B 3 'MAGNESIUM ION' MG 4 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 1BNA _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'surface plasmon resonance' _pdbx_struct_assembly_auth_evidence.details ? #