data_2B3E # _entry.id 2B3E # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 2B3E pdb_00002b3e 10.2210/pdb2b3e/pdb NDB DD0076 ? ? RCSB RCSB034625 ? ? WWPDB D_1000034625 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type NDB GDL009 'DNA COMPONENT.' unspecified PDB 2DBE 'DNA COMPONENT.' unspecified NDB DD0069 . unspecified PDB 1VZK . unspecified PDB 2B0k . unspecified PDB 2B2B . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2B3E _pdbx_database_status.recvd_initial_deposition_date 2005-09-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Campbell, N.H.' 1 'Evans, D.A.' 2 'Lee, M.P.' 3 'Parkinson, G.N.' 4 'Neidle, S.' 5 # _citation.id primary _citation.title ;Targeting the DNA minor groove with fused ring dicationic compounds: Comparison of in silico screening and a high-resolution crystal structure. ; _citation.journal_abbrev Bioorg.Med.Chem.Lett. _citation.journal_volume 16 _citation.page_first 15 _citation.page_last 19 _citation.year 2006 _citation.journal_id_ASTM BMCLE8 _citation.country UK _citation.journal_id_ISSN 0960-894X _citation.journal_id_CSD 1127 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16263285 _citation.pdbx_database_id_DOI 10.1016/j.bmcl.2005.10.036 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Campbell, N.H.' 1 ? primary 'Evans, D.A.' 2 ? primary 'Lee, M.P.' 3 ? primary 'Parkinson, G.N.' 4 ? primary 'Neidle, S.' 5 ? # _cell.entry_id 2B3E _cell.length_a 24.196 _cell.length_b 39.960 _cell.length_c 65.525 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2B3E _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 19 _symmetry.cell_setting ? _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*TP*CP*GP*CP*G)-3'" 3663.392 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn '6-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)-2-{5-[4-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENYL]THIEN-2-YL}-1H-BENZIMIDAZOLE' 412.510 1 ? ? ? ? 4 water nat water 18.015 107 ? ? ? ? # _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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'AT-RICH REGION IN THE GENOME OF ORGANISMS.' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2B3E _struct_ref.pdbx_db_accession 2B3E _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 2B3E A 1 ? 12 ? 2B3E 1 ? 12 ? 1 12 2 1 2B3E B 1 ? 12 ? 2B3E 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DBN non-polymer . '6-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)-2-{5-[4-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENYL]THIEN-2-YL}-1H-BENZIMIDAZOLE' DB819 'C23 H20 N6 S' 412.510 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.entry_id 2B3E _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.65 _exptl_crystal.density_percent_sol 53.64 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'MAGNESIUM CHLORIDE, DNA, COMPOUND DB819, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'MAGNESIUM CHLORIDE' ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'SODIUM CACODYLATE' ? ? ? 1 4 1 H2O ? ? ? 1 5 2 'MAGNESIUM CHLORIDE' ? ? ? 1 6 2 MPD ? ? ? 1 7 2 'SODIUM CACODYLATE' ? ? ? 1 8 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 105.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2005-05-23 _diffrn_detector.details 'OSMIC FOCUSING MIRROR SYSTEM' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'NI FILTER' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54178 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.54178 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 2B3E _reflns.observed_criterion_sigma_I -2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.000 _reflns.d_resolution_high 1.360 _reflns.number_obs 13180 _reflns.number_all ? _reflns.percent_possible_obs 92.2 _reflns.pdbx_Rmerge_I_obs 0.037 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 56.8200 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.380 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.36 _reflns_shell.d_res_low 1.41 _reflns_shell.percent_possible_all 60.7 _reflns_shell.Rmerge_I_obs 0.285 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.030 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2B3E _refine.ls_number_reflns_obs 13073 _refine.ls_number_reflns_all 13073 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 1.36 _refine.ls_percent_reflns_obs 83.0 _refine.ls_R_factor_obs 0.208 _refine.ls_R_factor_all 0.21 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.254 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.005 _refine.ls_number_reflns_R_free 1308 _refine.ls_number_parameters 2511 _refine.ls_number_restraints 2558 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ; _refine.pdbx_starting_model 'DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _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 ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 2B3E _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 624.00 _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 486 _refine_hist.pdbx_number_atoms_ligand 37 _refine_hist.number_atoms_solvent 101 _refine_hist.number_atoms_total 624 _refine_hist.d_res_high 1.36 _refine_hist.d_res_low 8.00 # 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 s_bond_d 0.011 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.032 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.036 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.046 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 2B3E _pdbx_refine.R_factor_all_no_cutoff 0.21 _pdbx_refine.R_factor_obs_no_cutoff 0.208 _pdbx_refine.free_R_factor_no_cutoff 0.254 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 10.005 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1308 _pdbx_refine.R_factor_all_4sig_cutoff 0.199 _pdbx_refine.R_factor_obs_4sig_cutoff 0.196 _pdbx_refine.free_R_factor_4sig_cutoff 0.244 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 10.048 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1147 _pdbx_refine.number_reflns_obs_4sig_cutoff 11415 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 2B3E _struct.title 'Crystal structure of DB819-D(CGCGAATTCGCG)2 complex.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2B3E _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;NUCLEIC ACIDS, DNA, DOUBLE HELIX, MINOR GROOVE, DNA MINOR, GROOVE BINDER, DNA MINOR GROOVE-LIGAND COMPLEX, DB819, A2T2, DICKERSON AND DREW DODECAMER, CRYSTAL STRUCTURE OF B-DNA, DNA-DRUG COMPLEX, MAGNESIUM-WATER COMPLEX, HYDRATED MAGNESIUM, DNA HYDRATION. ; # 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 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 129 1_555 ? ? ? ? ? ? ? 2.126 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 130 1_555 ? ? ? ? ? ? ? 2.110 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 132 1_555 ? ? ? ? ? ? ? 2.120 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 133 1_555 ? ? ? ? ? ? ? 2.130 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 26 B HOH 128 1_555 ? ? ? ? ? ? ? 2.106 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 26 B HOH 131 1_555 ? ? ? ? ? ? ? 2.110 ? ? 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 ? ? # 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 A MG 26 ? 6 'BINDING SITE FOR RESIDUE MG A 26' AC2 Software A DBN 25 ? 12 'BINDING SITE FOR RESIDUE DBN A 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 6 HOH E . ? HOH A 129 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 130 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 132 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 133 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH B 128 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH B 131 . ? 1_555 ? 7 AC2 12 DA A 6 ? DA A 6 . ? 1_555 ? 8 AC2 12 DT A 7 ? DT A 7 . ? 1_555 ? 9 AC2 12 DT A 8 ? DT A 8 . ? 1_555 ? 10 AC2 12 DC A 9 ? DC A 9 . ? 1_555 ? 11 AC2 12 HOH E . ? HOH A 43 . ? 1_555 ? 12 AC2 12 HOH E . ? HOH A 80 . ? 1_555 ? 13 AC2 12 HOH E . ? HOH A 95 . ? 1_555 ? 14 AC2 12 DA B 6 ? DA B 18 . ? 1_555 ? 15 AC2 12 DT B 7 ? DT B 19 . ? 1_555 ? 16 AC2 12 DT B 8 ? DT B 20 . ? 1_555 ? 17 AC2 12 DC B 9 ? DC B 21 . ? 1_555 ? 18 AC2 12 HOH F . ? HOH B 79 . ? 1_555 ? # _database_PDB_matrix.entry_id 2B3E _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 2B3E _atom_sites.fract_transf_matrix[1][1] 0.041329 _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] 0.025025 _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] 0.015261 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G 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 MG 1 26 26 MG MO6 A . D 3 DBN 1 25 25 DBN DBN A . E 4 HOH 1 28 28 HOH HOH A . E 4 HOH 2 30 30 HOH HOH A . E 4 HOH 3 31 31 HOH HOH A . E 4 HOH 4 33 33 HOH HOH A . E 4 HOH 5 35 35 HOH HOH A . E 4 HOH 6 37 37 HOH HOH A . E 4 HOH 7 38 38 HOH HOH A . E 4 HOH 8 39 39 HOH HOH A . E 4 HOH 9 41 41 HOH HOH A . E 4 HOH 10 42 42 HOH HOH A . E 4 HOH 11 43 43 HOH HOH A . E 4 HOH 12 44 44 HOH HOH A . E 4 HOH 13 45 45 HOH HOH A . E 4 HOH 14 46 46 HOH HOH A . E 4 HOH 15 47 47 HOH HOH A . E 4 HOH 16 48 48 HOH HOH A . E 4 HOH 17 49 49 HOH HOH A . E 4 HOH 18 52 52 HOH HOH A . E 4 HOH 19 53 53 HOH HOH A . E 4 HOH 20 54 54 HOH HOH A . E 4 HOH 21 55 55 HOH HOH A . E 4 HOH 22 57 57 HOH HOH A . E 4 HOH 23 59 59 HOH HOH A . E 4 HOH 24 60 60 HOH HOH A . E 4 HOH 25 61 61 HOH HOH A . E 4 HOH 26 62 62 HOH HOH A . E 4 HOH 27 64 64 HOH HOH A . E 4 HOH 28 66 66 HOH HOH A . E 4 HOH 29 67 67 HOH HOH A . E 4 HOH 30 68 68 HOH HOH A . E 4 HOH 31 71 71 HOH HOH A . E 4 HOH 32 72 72 HOH HOH A . E 4 HOH 33 75 75 HOH HOH A . E 4 HOH 34 76 76 HOH HOH A . E 4 HOH 35 77 77 HOH HOH A . E 4 HOH 36 78 78 HOH HOH A . E 4 HOH 37 80 80 HOH HOH A . E 4 HOH 38 81 81 HOH HOH A . E 4 HOH 39 86 86 HOH HOH A . E 4 HOH 40 91 91 HOH HOH A . E 4 HOH 41 92 92 HOH HOH A . E 4 HOH 42 95 95 HOH HOH A . E 4 HOH 43 96 96 HOH HOH A . E 4 HOH 44 102 102 HOH HOH A . E 4 HOH 45 103 103 HOH HOH A . E 4 HOH 46 104 104 HOH HOH A . E 4 HOH 47 106 106 HOH HOH A . E 4 HOH 48 108 108 HOH HOH A . E 4 HOH 49 113 113 HOH HOH A . E 4 HOH 50 115 115 HOH HOH A . E 4 HOH 51 119 119 HOH HOH A . E 4 HOH 52 120 120 HOH HOH A . E 4 HOH 53 122 122 HOH HOH A . E 4 HOH 54 124 124 HOH HOH A . E 4 HOH 55 125 125 HOH HOH A . E 4 HOH 56 129 26 HOH MO6 A . E 4 HOH 57 130 26 HOH MO6 A . E 4 HOH 58 132 26 HOH MO6 A . E 4 HOH 59 133 26 HOH MO6 A . F 4 HOH 1 27 27 HOH HOH B . F 4 HOH 2 29 29 HOH HOH B . F 4 HOH 3 32 32 HOH HOH B . F 4 HOH 4 34 34 HOH HOH B . F 4 HOH 5 36 36 HOH HOH B . F 4 HOH 6 40 40 HOH HOH B . F 4 HOH 7 50 50 HOH HOH B . F 4 HOH 8 51 51 HOH HOH B . F 4 HOH 9 56 56 HOH HOH B . F 4 HOH 10 58 58 HOH HOH B . F 4 HOH 11 63 63 HOH HOH B . F 4 HOH 12 65 65 HOH HOH B . F 4 HOH 13 69 69 HOH HOH B . F 4 HOH 14 70 70 HOH HOH B . F 4 HOH 15 73 73 HOH HOH B . F 4 HOH 16 74 74 HOH HOH B . F 4 HOH 17 79 79 HOH HOH B . F 4 HOH 18 82 82 HOH HOH B . F 4 HOH 19 83 83 HOH HOH B . F 4 HOH 20 84 84 HOH HOH B . F 4 HOH 21 85 85 HOH HOH B . F 4 HOH 22 87 87 HOH HOH B . F 4 HOH 23 88 88 HOH HOH B . F 4 HOH 24 89 89 HOH HOH B . F 4 HOH 25 90 90 HOH HOH B . F 4 HOH 26 93 93 HOH HOH B . F 4 HOH 27 94 94 HOH HOH B . F 4 HOH 28 97 97 HOH HOH B . F 4 HOH 29 98 98 HOH HOH B . F 4 HOH 30 99 99 HOH HOH B . F 4 HOH 31 100 100 HOH HOH B . F 4 HOH 32 101 101 HOH HOH B . F 4 HOH 33 105 105 HOH HOH B . F 4 HOH 34 107 107 HOH HOH B . F 4 HOH 35 109 109 HOH HOH B . F 4 HOH 36 110 110 HOH HOH B . F 4 HOH 37 111 111 HOH HOH B . F 4 HOH 38 112 112 HOH HOH B . F 4 HOH 39 114 114 HOH HOH B . F 4 HOH 40 116 116 HOH HOH B . F 4 HOH 41 117 117 HOH HOH B . F 4 HOH 42 118 118 HOH HOH B . F 4 HOH 43 121 121 HOH HOH B . F 4 HOH 44 123 123 HOH HOH B . F 4 HOH 45 126 126 HOH HOH B . F 4 HOH 46 127 127 HOH HOH B . F 4 HOH 47 128 26 HOH MO6 B . F 4 HOH 48 131 26 HOH MO6 B . # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'minor groove binder' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 129 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 130 ? 1_555 88.6 ? 2 O ? E HOH . ? A HOH 129 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 89.9 ? 3 O ? E HOH . ? A HOH 130 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 132 ? 1_555 89.0 ? 4 O ? E HOH . ? A HOH 129 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 133 ? 1_555 90.3 ? 5 O ? E HOH . ? A HOH 130 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 133 ? 1_555 91.9 ? 6 O ? E HOH . ? A HOH 132 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 133 ? 1_555 179.0 ? 7 O ? E HOH . ? A HOH 129 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 128 ? 1_555 91.8 ? 8 O ? E HOH . ? A HOH 130 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 128 ? 1_555 179.6 ? 9 O ? E HOH . ? A HOH 132 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 128 ? 1_555 90.9 ? 10 O ? E HOH . ? A HOH 133 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 128 ? 1_555 88.1 ? 11 O ? E HOH . ? A HOH 129 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 179.2 ? 12 O ? E HOH . ? A HOH 130 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 90.6 ? 13 O ? E HOH . ? A HOH 132 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 90.1 ? 14 O ? E HOH . ? A HOH 133 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 89.7 ? 15 O ? F HOH . ? B HOH 128 ? 1_555 MG ? C MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 89.0 ? # 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 2005-11-22 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2023-08-23 # _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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 5 '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 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_initial_refinement_model 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 5 '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 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.value' 12 5 'Structure model' '_struct_conn.pdbx_dist_value' 13 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 17 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 18 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 CNS phasing . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N26 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DBN _pdbx_validate_close_contact.auth_seq_id_1 25 _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 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 43 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.10 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 103.70 108.00 -4.30 0.70 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 102.91 108.00 -5.09 0.70 N 3 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 124.66 128.60 -3.94 0.60 N 4 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 102.54 108.00 -5.46 0.70 N 5 1 "C3'" A DA 6 ? ? "O3'" A DA 6 ? ? P A DT 7 ? ? 127.15 119.70 7.45 1.20 Y 6 1 N1 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 126.40 119.90 6.50 0.60 N 7 1 C5 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 123.56 128.60 -5.04 0.60 N 8 1 "O4'" A DC 11 ? ? "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? 101.96 104.50 -2.54 0.40 N 9 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 101.53 108.00 -6.47 0.70 N 10 1 "C1'" A DG 12 ? ? "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? 103.74 110.10 -6.36 1.00 N 11 1 N3 B DC 13 ? ? C4 B DC 13 ? ? C5 B DC 13 ? ? 118.71 121.90 -3.19 0.40 N 12 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 100.83 108.00 -7.17 0.70 N 13 1 C2 B DC 15 ? ? N3 B DC 15 ? ? C4 B DC 15 ? ? 123.38 119.90 3.48 0.50 N 14 1 C5 B DC 15 ? ? C4 B DC 15 ? ? N4 B DC 15 ? ? 124.47 120.20 4.27 0.70 N 15 1 C6 B DA 17 ? ? N1 B DA 17 ? ? C2 B DA 17 ? ? 123.17 118.60 4.57 0.60 N 16 1 N1 B DA 17 ? ? C2 B DA 17 ? ? N3 B DA 17 ? ? 124.25 129.30 -5.05 0.50 N 17 1 C6 B DA 18 ? ? N1 B DA 18 ? ? C2 B DA 18 ? ? 122.28 118.60 3.68 0.60 N 18 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 101.08 108.00 -6.92 0.70 N 19 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 99.18 108.00 -8.82 0.70 N 20 1 "C3'" B DG 22 ? ? "C2'" B DG 22 ? ? "C1'" B DG 22 ? ? 96.08 102.40 -6.32 0.80 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DBN C27 C N N 37 DBN C28 C N N 38 DBN C29 C N N 39 DBN C30 C N N 40 DBN C1 C Y N 41 DBN S2 S Y N 42 DBN C3 C Y N 43 DBN C4 C Y N 44 DBN C5 C Y N 45 DBN C6 C Y N 46 DBN N7 N Y N 47 DBN C8 C Y N 48 DBN C9 C Y N 49 DBN N10 N Y N 50 DBN C11 C Y N 51 DBN C12 C Y N 52 DBN C13 C Y N 53 DBN C14 C Y N 54 DBN C15 C Y N 55 DBN C16 C Y N 56 DBN C17 C Y N 57 DBN C18 C Y N 58 DBN C19 C Y N 59 DBN C20 C Y N 60 DBN C21 C N N 61 DBN N22 N N N 62 DBN N23 N N N 63 DBN C24 C N N 64 DBN N25 N N N 65 DBN N26 N N N 66 DBN H271 H N N 67 DBN H272 H N N 68 DBN H281 H N N 69 DBN H282 H N N 70 DBN H291 H N N 71 DBN H292 H N N 72 DBN H301 H N N 73 DBN H302 H N N 74 DBN H4 H N N 75 DBN H5 H N N 76 DBN H10 H N N 77 DBN H11 H N N 78 DBN H12 H N N 79 DBN H14 H N N 80 DBN H16 H N N 81 DBN H17 H N N 82 DBN H19 H N N 83 DBN H20 H N N 84 DBN H22 H N N 85 DBN H25 H N N 86 DC OP3 O N N 87 DC P P N N 88 DC OP1 O N N 89 DC OP2 O N N 90 DC "O5'" O N N 91 DC "C5'" C N N 92 DC "C4'" C N R 93 DC "O4'" O N N 94 DC "C3'" C N S 95 DC "O3'" O N N 96 DC "C2'" C N N 97 DC "C1'" C N R 98 DC N1 N N N 99 DC C2 C N N 100 DC O2 O N N 101 DC N3 N N N 102 DC C4 C N N 103 DC N4 N N N 104 DC C5 C N N 105 DC C6 C N N 106 DC HOP3 H N N 107 DC HOP2 H N N 108 DC "H5'" H N N 109 DC "H5''" H N N 110 DC "H4'" H N N 111 DC "H3'" H N N 112 DC "HO3'" H N N 113 DC "H2'" H N N 114 DC "H2''" H N N 115 DC "H1'" H N N 116 DC H41 H N N 117 DC H42 H N N 118 DC H5 H N N 119 DC H6 H N N 120 DG OP3 O N N 121 DG P P N N 122 DG OP1 O N N 123 DG OP2 O N N 124 DG "O5'" O N N 125 DG "C5'" C N N 126 DG "C4'" C N R 127 DG "O4'" O N N 128 DG "C3'" C N S 129 DG "O3'" O N N 130 DG "C2'" C N N 131 DG "C1'" C N R 132 DG N9 N Y N 133 DG C8 C Y N 134 DG N7 N Y N 135 DG C5 C Y N 136 DG C6 C N N 137 DG O6 O N N 138 DG N1 N N N 139 DG C2 C N N 140 DG N2 N N N 141 DG N3 N N N 142 DG C4 C Y N 143 DG HOP3 H N N 144 DG HOP2 H N N 145 DG "H5'" H N N 146 DG "H5''" H N N 147 DG "H4'" H N N 148 DG "H3'" H N N 149 DG "HO3'" H N N 150 DG "H2'" H N N 151 DG "H2''" H N N 152 DG "H1'" H N N 153 DG H8 H N N 154 DG H1 H N N 155 DG H21 H N N 156 DG H22 H N N 157 DT OP3 O N N 158 DT P P N N 159 DT OP1 O N N 160 DT OP2 O N N 161 DT "O5'" O N N 162 DT "C5'" C N N 163 DT "C4'" C N R 164 DT "O4'" O N N 165 DT "C3'" C N S 166 DT "O3'" O N N 167 DT "C2'" C N N 168 DT "C1'" C N R 169 DT N1 N N N 170 DT C2 C N N 171 DT O2 O N N 172 DT N3 N N N 173 DT C4 C N N 174 DT O4 O N N 175 DT C5 C N N 176 DT C7 C N N 177 DT C6 C N N 178 DT HOP3 H N N 179 DT HOP2 H N N 180 DT "H5'" H N N 181 DT "H5''" H N N 182 DT "H4'" H N N 183 DT "H3'" H N N 184 DT "HO3'" H N N 185 DT "H2'" H N N 186 DT "H2''" H N N 187 DT "H1'" H N N 188 DT H3 H N N 189 DT H71 H N N 190 DT H72 H N N 191 DT H73 H N N 192 DT H6 H N N 193 HOH O O N N 194 HOH H1 H N N 195 HOH H2 H N N 196 MG MG MG N N 197 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DBN C27 C28 sing N N 39 DBN C27 N22 sing N N 40 DBN C27 H271 sing N N 41 DBN C27 H272 sing N N 42 DBN C28 N23 sing N N 43 DBN C28 H281 sing N N 44 DBN C28 H282 sing N N 45 DBN C29 C30 sing N N 46 DBN C29 N25 sing N N 47 DBN C29 H291 sing N N 48 DBN C29 H292 sing N N 49 DBN C30 N26 sing N N 50 DBN C30 H301 sing N N 51 DBN C30 H302 sing N N 52 DBN C1 S2 sing Y N 53 DBN C1 C5 doub Y N 54 DBN C1 C15 sing Y N 55 DBN S2 C3 sing Y N 56 DBN C3 C4 doub Y N 57 DBN C3 C6 sing Y N 58 DBN C4 C5 sing Y N 59 DBN C4 H4 sing N N 60 DBN C5 H5 sing N N 61 DBN C6 N7 doub Y N 62 DBN C6 N10 sing Y N 63 DBN N7 C8 sing Y N 64 DBN C8 C9 doub Y N 65 DBN C8 C11 sing Y N 66 DBN C9 N10 sing Y N 67 DBN C9 C14 sing Y N 68 DBN N10 H10 sing N N 69 DBN C11 C12 doub Y N 70 DBN C11 H11 sing N N 71 DBN C12 C13 sing Y N 72 DBN C12 H12 sing N N 73 DBN C13 C14 doub Y N 74 DBN C13 C21 sing N N 75 DBN C14 H14 sing N N 76 DBN C15 C16 sing Y N 77 DBN C15 C20 doub Y N 78 DBN C16 C17 doub Y N 79 DBN C16 H16 sing N N 80 DBN C17 C18 sing Y N 81 DBN C17 H17 sing N N 82 DBN C18 C19 doub Y N 83 DBN C18 C24 sing N N 84 DBN C19 C20 sing Y N 85 DBN C19 H19 sing N N 86 DBN C20 H20 sing N N 87 DBN C21 N22 sing N N 88 DBN C21 N23 doub N N 89 DBN N22 H22 sing N N 90 DBN C24 N25 sing N N 91 DBN C24 N26 doub N N 92 DBN N25 H25 sing N N 93 DC OP3 P sing N N 94 DC OP3 HOP3 sing N N 95 DC P OP1 doub N N 96 DC P OP2 sing N N 97 DC P "O5'" sing N N 98 DC OP2 HOP2 sing N N 99 DC "O5'" "C5'" sing N N 100 DC "C5'" "C4'" sing N N 101 DC "C5'" "H5'" sing N N 102 DC "C5'" "H5''" sing N N 103 DC "C4'" "O4'" sing N N 104 DC "C4'" "C3'" sing N N 105 DC "C4'" "H4'" sing N N 106 DC "O4'" "C1'" sing N N 107 DC "C3'" "O3'" sing N N 108 DC "C3'" "C2'" sing N N 109 DC "C3'" "H3'" sing N N 110 DC "O3'" "HO3'" sing N N 111 DC "C2'" "C1'" sing N N 112 DC "C2'" "H2'" sing N N 113 DC "C2'" "H2''" sing N N 114 DC "C1'" N1 sing N N 115 DC "C1'" "H1'" sing N N 116 DC N1 C2 sing N N 117 DC N1 C6 sing N N 118 DC C2 O2 doub N N 119 DC C2 N3 sing N N 120 DC N3 C4 doub N N 121 DC C4 N4 sing N N 122 DC C4 C5 sing N N 123 DC N4 H41 sing N N 124 DC N4 H42 sing N N 125 DC C5 C6 doub N N 126 DC C5 H5 sing N N 127 DC C6 H6 sing N N 128 DG OP3 P sing N N 129 DG OP3 HOP3 sing N N 130 DG P OP1 doub N N 131 DG P OP2 sing N N 132 DG P "O5'" sing N N 133 DG OP2 HOP2 sing N N 134 DG "O5'" "C5'" sing N N 135 DG "C5'" "C4'" sing N N 136 DG "C5'" "H5'" sing N N 137 DG "C5'" "H5''" sing N N 138 DG "C4'" "O4'" sing N N 139 DG "C4'" "C3'" sing N N 140 DG "C4'" "H4'" sing N N 141 DG "O4'" "C1'" sing N N 142 DG "C3'" "O3'" sing N N 143 DG "C3'" "C2'" sing N N 144 DG "C3'" "H3'" sing N N 145 DG "O3'" "HO3'" sing N N 146 DG "C2'" "C1'" sing N N 147 DG "C2'" "H2'" sing N N 148 DG "C2'" "H2''" sing N N 149 DG "C1'" N9 sing N N 150 DG "C1'" "H1'" sing N N 151 DG N9 C8 sing Y N 152 DG N9 C4 sing Y N 153 DG C8 N7 doub Y N 154 DG C8 H8 sing N N 155 DG N7 C5 sing Y N 156 DG C5 C6 sing N N 157 DG C5 C4 doub Y N 158 DG C6 O6 doub N N 159 DG C6 N1 sing N N 160 DG N1 C2 sing N N 161 DG N1 H1 sing N N 162 DG C2 N2 sing N N 163 DG C2 N3 doub N N 164 DG N2 H21 sing N N 165 DG N2 H22 sing N N 166 DG N3 C4 sing N N 167 DT OP3 P sing N N 168 DT OP3 HOP3 sing N N 169 DT P OP1 doub N N 170 DT P OP2 sing N N 171 DT P "O5'" sing N N 172 DT OP2 HOP2 sing N N 173 DT "O5'" "C5'" sing N N 174 DT "C5'" "C4'" sing N N 175 DT "C5'" "H5'" sing N N 176 DT "C5'" "H5''" sing N N 177 DT "C4'" "O4'" sing N N 178 DT "C4'" "C3'" sing N N 179 DT "C4'" "H4'" sing N N 180 DT "O4'" "C1'" sing N N 181 DT "C3'" "O3'" sing N N 182 DT "C3'" "C2'" sing N N 183 DT "C3'" "H3'" sing N N 184 DT "O3'" "HO3'" sing N N 185 DT "C2'" "C1'" sing N N 186 DT "C2'" "H2'" sing N N 187 DT "C2'" "H2''" sing N N 188 DT "C1'" N1 sing N N 189 DT "C1'" "H1'" sing N N 190 DT N1 C2 sing N N 191 DT N1 C6 sing N N 192 DT C2 O2 doub N N 193 DT C2 N3 sing N N 194 DT N3 C4 sing N N 195 DT N3 H3 sing N N 196 DT C4 O4 doub N N 197 DT C4 C5 sing N N 198 DT C5 C7 sing N N 199 DT C5 C6 doub N N 200 DT C7 H71 sing N N 201 DT C7 H72 sing N N 202 DT C7 H73 sing N N 203 DT C6 H6 sing N N 204 HOH O H1 sing N N 205 HOH O H2 sing N N 206 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2B3E 'double helix' 2B3E '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 0.223 -0.160 0.234 0.405 -19.005 -0.625 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.294 -0.176 0.273 3.145 -5.539 -2.189 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.268 -0.099 0.178 -3.677 -6.041 -0.369 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.207 -0.079 0.018 12.096 -8.220 -1.835 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.054 -0.149 -0.160 6.706 -18.437 2.162 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.091 -0.153 -0.051 2.819 -20.625 7.071 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.132 -0.098 -0.026 -3.021 -18.608 5.750 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.004 -0.176 -0.164 -3.453 -16.655 3.246 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.265 -0.127 0.102 -9.045 -9.582 1.554 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.299 -0.101 0.176 10.324 -2.527 1.885 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.204 -0.143 0.321 6.144 -23.613 -3.013 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.405 -0.121 -0.188 8.081 18.740 -1.355 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 -0.264 0.025 3.247 -0.916 6.596 31.937 -1.096 0.312 3.194 11.828 1.643 32.606 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 0.804 0.575 3.449 1.695 -2.841 43.055 1.075 -0.918 3.434 -3.864 -2.306 43.176 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 -0.494 0.593 3.084 2.813 10.087 26.493 -1.036 1.631 3.034 20.997 -5.856 28.453 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 -0.012 0.094 3.414 1.426 3.107 37.024 -0.284 0.217 3.408 4.880 -2.239 37.176 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 0.265 -0.252 3.285 -1.093 4.559 36.720 -1.009 -0.564 3.223 7.201 1.726 37.008 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 0.039 -0.504 3.292 0.318 -0.047 31.562 -0.918 -0.012 3.293 -0.087 -0.585 31.563 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 -0.098 -0.158 3.212 2.403 1.051 37.275 -0.382 0.464 3.194 1.641 -3.754 37.364 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 0.149 0.282 3.410 -0.156 -0.568 40.486 0.474 -0.234 3.405 -0.821 0.226 40.490 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 0.398 1.298 3.095 -1.839 7.876 23.688 0.642 -1.469 3.308 18.509 4.322 25.013 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 -1.060 0.939 3.497 -2.760 -12.405 45.733 2.220 1.085 3.208 -15.609 3.473 47.374 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 1.496 0.702 3.559 4.824 -12.171 34.430 2.916 -1.658 3.305 -19.702 -7.809 36.764 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 '6-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)-2-{5-[4-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENYL]THIEN-2-YL}-1H-BENZIMIDAZOLE' DBN 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 2DBE _pdbx_initial_refinement_model.details 'DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE' #