data_3TVB # _entry.id 3TVB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3TVB pdb_00003tvb 10.2210/pdb3tvb/pdb NDB NA1314 ? ? RCSB RCSB067964 ? ? WWPDB D_1000067964 ? ? # 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 2012-03-14 2 'Structure model' 1 1 2012-07-11 3 'Structure model' 1 2 2020-01-29 4 'Structure model' 1 3 2024-02-28 # _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' Advisory 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' ndb_struct_na_base_pair 2 3 'Structure model' ndb_struct_na_base_pair_step 3 3 'Structure model' pdbx_distant_solvent_atoms 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_assembly_gen 6 3 'Structure model' pdbx_struct_assembly_prop 7 3 'Structure model' struct_biol 8 3 'Structure model' struct_conn 9 3 'Structure model' struct_conn_type 10 4 'Structure model' chem_comp_atom 11 4 'Structure model' chem_comp_bond 12 4 'Structure model' database_2 13 4 'Structure model' pdbx_struct_conn_angle 14 4 'Structure model' struct_conn 15 4 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3TVB _pdbx_database_status.recvd_initial_deposition_date 2011-09-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Clark, G.R.' 1 'Pytel, P.D.' 2 'Squire, C.J.' 3 # _citation.id primary _citation.title 'The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 40 _citation.page_first 5731 _citation.page_last 5738 _citation.year 2012 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22373921 _citation.pdbx_database_id_DOI 10.1093/nar/gks193 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Clark, G.R.' 1 ? primary 'Pytel, P.D.' 2 ? primary 'Squire, C.J.' 3 ? # 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 ;DNA (5'-D(*GP*GP*GP*G)-3') ; 1271.866 2 ? ? ? ? 2 non-polymer syn DAUNOMYCIN 527.520 4 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 8 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 water nat water 18.015 110 ? ? ? ? # _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 '(DG)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 DAUNOMYCIN DM1 3 'SODIUM ION' NA 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DG n 1 4 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 'Synthetic oligomer' # 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 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DM1 non-polymer . DAUNOMYCIN DAUNORUBICIN 'C27 H29 N O10' 527.520 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # 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 DG 1 1 1 DG DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n B 1 1 DG 1 5 5 DG DG B . n B 1 2 DG 2 6 6 DG DG B . n B 1 3 DG 3 7 7 DG DG B . n B 1 4 DG 4 8 8 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 DM1 1 9 9 DM1 DM1 A . D 2 DM1 1 10 10 DM1 DM1 A . E 3 NA 1 13 13 NA NA A . F 3 NA 1 14 14 NA NA A . G 3 NA 1 15 15 NA NA A . H 2 DM1 1 11 11 DM1 DM1 B . I 2 DM1 1 12 12 DM1 DM1 B . J 3 NA 1 16 16 NA NA B . K 3 NA 1 17 17 NA NA B . L 3 NA 1 18 18 NA NA B . M 3 NA 1 19 19 NA NA B . N 3 NA 1 20 20 NA NA B . O 4 MG 1 21 21 MG MG B . P 4 MG 1 22 22 MG MG B . Q 5 HOH 1 101 101 HOH HOH A . Q 5 HOH 2 103 103 HOH HOH A . Q 5 HOH 3 107 107 HOH HOH A . Q 5 HOH 4 108 108 HOH HOH A . Q 5 HOH 5 115 115 HOH HOH A . Q 5 HOH 6 116 116 HOH HOH A . Q 5 HOH 7 120 120 HOH HOH A . Q 5 HOH 8 122 122 HOH HOH A . Q 5 HOH 9 123 123 HOH HOH A . Q 5 HOH 10 124 124 HOH HOH A . Q 5 HOH 11 127 127 HOH HOH A . Q 5 HOH 12 128 128 HOH HOH A . Q 5 HOH 13 129 129 HOH HOH A . Q 5 HOH 14 130 130 HOH HOH A . Q 5 HOH 15 133 133 HOH HOH A . Q 5 HOH 16 135 135 HOH HOH A . Q 5 HOH 17 137 137 HOH HOH A . Q 5 HOH 18 138 138 HOH HOH A . Q 5 HOH 19 139 139 HOH HOH A . Q 5 HOH 20 146 146 HOH HOH A . Q 5 HOH 21 148 148 HOH HOH A . Q 5 HOH 22 149 149 HOH HOH A . Q 5 HOH 23 151 151 HOH HOH A . Q 5 HOH 24 152 152 HOH HOH A . Q 5 HOH 25 153 153 HOH HOH A . Q 5 HOH 26 155 155 HOH HOH A . Q 5 HOH 27 156 156 HOH HOH A . Q 5 HOH 28 158 158 HOH HOH A . Q 5 HOH 29 164 164 HOH HOH A . Q 5 HOH 30 168 168 HOH HOH A . Q 5 HOH 31 169 169 HOH HOH A . Q 5 HOH 32 173 173 HOH HOH A . Q 5 HOH 33 175 175 HOH HOH A . Q 5 HOH 34 179 179 HOH HOH A . Q 5 HOH 35 183 183 HOH HOH A . Q 5 HOH 36 184 184 HOH HOH A . Q 5 HOH 37 186 186 HOH HOH A . Q 5 HOH 38 187 187 HOH HOH A . Q 5 HOH 39 190 190 HOH HOH A . Q 5 HOH 40 192 192 HOH HOH A . Q 5 HOH 41 195 195 HOH HOH A . Q 5 HOH 42 200 200 HOH HOH A . Q 5 HOH 43 201 201 HOH HOH A . Q 5 HOH 44 202 202 HOH HOH A . Q 5 HOH 45 207 207 HOH HOH A . Q 5 HOH 46 208 208 HOH HOH A . Q 5 HOH 47 209 209 HOH HOH A . Q 5 HOH 48 210 210 HOH HOH A . Q 5 HOH 49 211 211 HOH HOH A . Q 5 HOH 50 212 212 HOH HOH A . R 5 HOH 1 102 102 HOH HOH B . R 5 HOH 2 106 106 HOH HOH B . R 5 HOH 3 109 109 HOH HOH B . R 5 HOH 4 110 110 HOH HOH B . R 5 HOH 5 111 111 HOH HOH B . R 5 HOH 6 112 112 HOH HOH B . R 5 HOH 7 113 113 HOH HOH B . R 5 HOH 8 114 114 HOH HOH B . R 5 HOH 9 117 117 HOH HOH B . R 5 HOH 10 118 118 HOH HOH B . R 5 HOH 11 119 119 HOH HOH B . R 5 HOH 12 121 121 HOH HOH B . R 5 HOH 13 125 125 HOH HOH B . R 5 HOH 14 126 126 HOH HOH B . R 5 HOH 15 131 131 HOH HOH B . R 5 HOH 16 132 132 HOH HOH B . R 5 HOH 17 134 134 HOH HOH B . R 5 HOH 18 136 136 HOH HOH B . R 5 HOH 19 140 140 HOH HOH B . R 5 HOH 20 141 141 HOH HOH B . R 5 HOH 21 142 142 HOH HOH B . R 5 HOH 22 143 143 HOH HOH B . R 5 HOH 23 144 144 HOH HOH B . R 5 HOH 24 145 145 HOH HOH B . R 5 HOH 25 147 147 HOH HOH B . R 5 HOH 26 150 150 HOH HOH B . R 5 HOH 27 154 154 HOH HOH B . R 5 HOH 28 157 157 HOH HOH B . R 5 HOH 29 159 159 HOH HOH B . R 5 HOH 30 160 160 HOH HOH B . R 5 HOH 31 161 161 HOH HOH B . R 5 HOH 32 162 162 HOH HOH B . R 5 HOH 33 163 163 HOH HOH B . R 5 HOH 34 165 165 HOH HOH B . R 5 HOH 35 166 166 HOH HOH B . R 5 HOH 36 167 167 HOH HOH B . R 5 HOH 37 170 170 HOH HOH B . R 5 HOH 38 171 171 HOH HOH B . R 5 HOH 39 172 172 HOH HOH B . R 5 HOH 40 174 174 HOH HOH B . R 5 HOH 41 176 176 HOH HOH B . R 5 HOH 42 177 177 HOH HOH B . R 5 HOH 43 178 178 HOH HOH B . R 5 HOH 44 180 180 HOH HOH B . R 5 HOH 45 181 181 HOH HOH B . R 5 HOH 46 182 182 HOH HOH B . R 5 HOH 47 185 185 HOH HOH B . R 5 HOH 48 188 188 HOH HOH B . R 5 HOH 49 189 189 HOH HOH B . R 5 HOH 50 191 191 HOH HOH B . R 5 HOH 51 193 193 HOH HOH B . R 5 HOH 52 194 194 HOH HOH B . R 5 HOH 53 196 196 HOH HOH B . R 5 HOH 54 197 197 HOH HOH B . R 5 HOH 55 198 198 HOH HOH B . R 5 HOH 56 199 199 HOH HOH B . R 5 HOH 57 203 203 HOH HOH B . R 5 HOH 58 204 204 HOH HOH B . R 5 HOH 59 205 205 HOH HOH B . R 5 HOH 60 206 206 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 SHELXL-97 refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 SHELX phasing . ? 5 # _cell.entry_id 3TVB _cell.length_a 40.209 _cell.length_b 40.209 _cell.length_c 49.831 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3TVB _symmetry.space_group_name_H-M 'I 4' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3TVB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.96 _exptl_crystal.density_percent_sol 68.93 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'Sitting drop' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;NATRIX NR46 droplets 0.005 M Magnesium sulfate, 0.05 M Tris HCl buffer at pH 8.5, 35% w/v 1,6-hexane diol, Sitting drop, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2004-07-10 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.006 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL9-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL9-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.006 # _reflns.entry_id 3TVB _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 10.0 _reflns.d_resolution_high 1.08 _reflns.number_obs 21428 _reflns.number_all 21428 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.072 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 81.79 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 66.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.08 _reflns_shell.d_res_low 1.13 _reflns_shell.percent_possible_all 99.2 _reflns_shell.Rmerge_I_obs 0.273 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 15.14 _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3TVB _refine.ls_number_reflns_obs 14501 _refine.ls_number_reflns_all 15269 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 4.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.08 _refine.ls_percent_reflns_obs 89.8 _refine.ls_R_factor_obs 0.1618 _refine.ls_R_factor_all 0.1640 _refine.ls_R_factor_R_work 0.1591 _refine.ls_R_factor_R_free 0.2023 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 11.0 _refine.ls_number_reflns_R_free 1677 _refine.ls_number_parameters 2579 _refine.ls_number_restraints 2250 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct 'AB INITIO' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH AND HUBER' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3TVB _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 430.19 _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 170 _refine_hist.pdbx_number_atoms_ligand 162 _refine_hist.number_atoms_solvent 110 _refine_hist.number_atoms_total 442 _refine_hist.d_res_high 1.08 _refine_hist.d_res_low 10.00 # 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_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.014 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.024 ? ? ? ? 'X-RAY DIFFRACTION' s_similar_dist 0.000 ? ? ? ? 'X-RAY DIFFRACTION' s_from_restr_planes 0.000 ? ? ? ? 'X-RAY DIFFRACTION' s_zero_chiral_vol 0.000 ? ? ? ? 'X-RAY DIFFRACTION' s_non_zero_chiral_vol 0.000 ? ? ? ? 'X-RAY DIFFRACTION' s_anti_bump_dis_restr 0.072 ? ? ? ? 'X-RAY DIFFRACTION' s_rigid_bond_adp_cmpnt 0.005 ? ? ? ? 'X-RAY DIFFRACTION' s_similar_adp_cmpnt 0.019 ? ? ? ? 'X-RAY DIFFRACTION' s_approx_iso_adps 0.000 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 3TVB _pdbx_refine.R_factor_all_no_cutoff 0.1640 _pdbx_refine.R_factor_obs_no_cutoff 0.1618 _pdbx_refine.free_R_factor_no_cutoff 0.2023 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 11.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1677 _pdbx_refine.R_factor_all_4sig_cutoff 0.1614 _pdbx_refine.R_factor_obs_4sig_cutoff 0.1591 _pdbx_refine.free_R_factor_4sig_cutoff 0.1985 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 11.0 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1598 _pdbx_refine.number_reflns_obs_4sig_cutoff 14501 # _database_PDB_matrix.entry_id 3TVB _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 3TVB _struct.title 'A Highly Symmetric DNA G-4 Quadruplex/drug Complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3TVB _struct_keywords.pdbx_keywords DNA/antibiotic _struct_keywords.text 'G-4 Quadruplex, Daunomycin, DNA-Drug Complex, DNA-antibiotic complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 2 ? I N N 2 ? J N N 3 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? O N N 4 ? P N N 4 ? Q N N 5 ? R N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3TVB _struct_ref.pdbx_db_accession 3TVB _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGGG _struct_ref.pdbx_db_isoform ? # 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 3TVB A 1 ? 4 ? 3TVB 1 ? 4 ? 1 4 2 1 3TVB B 1 ? 4 ? 3TVB 5 ? 8 ? 5 8 # _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 octameric _pdbx_struct_assembly.oligomeric_count 8 # 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)' 9450 ? 1 MORE -265 ? 1 'SSA (A^2)' 11500 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 40.2090000000 0.0000000000 -1.0000000000 0.0000000000 40.2090000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_655 -y+1,x,z 0.0000000000 -1.0000000000 0.0000000000 40.2090000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_565 y,-x+1,z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 40.2090000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # 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 ? ? A DG 1 O6 ? ? ? 1_555 E NA . NA ? ? A DG 1 A NA 13 1_555 ? ? ? ? ? ? ? 2.771 ? ? metalc2 metalc ? ? A DG 2 O6 ? ? ? 1_555 E NA . NA ? ? A DG 2 A NA 13 1_555 ? ? ? ? ? ? ? 2.858 ? ? metalc3 metalc ? ? A DG 2 O6 ? ? ? 1_555 F NA . NA ? ? A DG 2 A NA 14 1_555 ? ? ? ? ? ? ? 2.804 ? ? metalc4 metalc ? ? A DG 3 O6 ? ? ? 1_555 F NA . NA ? ? A DG 3 A NA 14 1_555 ? ? ? ? ? ? ? 2.633 ? ? metalc5 metalc ? ? A DG 3 O6 ? ? ? 1_555 G NA . NA ? ? A DG 3 A NA 15 1_555 ? ? ? ? ? ? ? 3.200 ? ? metalc6 metalc ? ? A DG 4 O6 ? ? ? 1_555 G NA . NA ? ? A DG 4 A NA 15 1_555 ? ? ? ? ? ? ? 2.379 ? ? metalc7 metalc ? ? B DG 1 O6 ? ? ? 1_555 J NA . NA ? ? B DG 5 B NA 16 1_555 ? ? ? ? ? ? ? 2.784 ? ? metalc8 metalc ? ? B DG 2 O6 ? ? ? 1_555 J NA . NA ? ? B DG 6 B NA 16 1_555 ? ? ? ? ? ? ? 2.884 ? ? metalc9 metalc ? ? B DG 2 O6 ? ? ? 1_555 K NA . NA ? ? B DG 6 B NA 17 1_555 ? ? ? ? ? ? ? 2.781 ? ? metalc10 metalc ? ? B DG 3 O6 ? ? ? 1_555 K NA . NA ? ? B DG 7 B NA 17 1_555 ? ? ? ? ? ? ? 2.648 ? ? metalc11 metalc ? ? B DG 3 O6 ? ? ? 1_555 L NA . NA ? ? B DG 7 B NA 18 1_555 ? ? ? ? ? ? ? 3.120 ? ? metalc12 metalc ? ? B DG 4 O6 ? ? ? 1_555 L NA . NA ? ? B DG 8 B NA 18 1_555 ? ? ? ? ? ? ? 2.458 ? ? metalc13 metalc ? ? M NA . NA ? ? ? 1_555 R HOH . O ? ? B NA 19 B HOH 109 1_555 ? ? ? ? ? ? ? 2.441 ? ? metalc14 metalc ? ? M NA . NA ? ? ? 1_555 R HOH . O ? ? B NA 19 B HOH 110 1_555 ? ? ? ? ? ? ? 2.437 ? ? metalc15 metalc ? ? O MG . MG ? ? ? 1_555 R HOH . O ? ? B MG 21 B HOH 111 1_555 ? ? ? ? ? ? ? 1.979 ? ? metalc16 metalc ? ? P MG . MG ? ? ? 1_555 R HOH . O ? ? B MG 22 B HOH 102 1_555 ? ? ? ? ? ? ? 2.148 ? ? metalc17 metalc ? ? P MG . MG ? ? ? 1_555 R HOH . O ? ? B MG 22 B HOH 106 1_555 ? ? ? ? ? ? ? 2.384 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DG 1 O6 ? ? A DG 1 A DG 1 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DG 1 N7 ? ? A DG 1 A DG 1 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N7 ? ? ? 1_555 A DG 1 N2 ? ? A DG 1 A DG 1 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DG 1 N1 ? ? A DG 1 A DG 1 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DG 2 O6 ? ? A DG 2 A DG 2 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 2 N7 ? ? A DG 2 A DG 2 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 2 N7 ? ? ? 1_555 A DG 2 N2 ? ? A DG 2 A DG 2 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DG 2 N1 ? ? A DG 2 A DG 2 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DG 3 O6 ? ? A DG 3 A DG 3 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 3 N7 ? ? A DG 3 A DG 3 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 3 N7 ? ? ? 1_555 A DG 3 N2 ? ? A DG 3 A DG 3 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DG 3 N1 ? ? A DG 3 A DG 3 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 4 O6 ? ? A DG 4 A DG 4 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 4 N7 ? ? A DG 4 A DG 4 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 4 N7 ? ? ? 1_555 A DG 4 N2 ? ? A DG 4 A DG 4 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DG 4 N1 ? ? A DG 4 A DG 4 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? B DG 1 N1 ? ? ? 1_555 B DG 1 O6 ? ? B DG 5 B DG 5 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? B DG 1 N2 ? ? ? 1_555 B DG 1 N7 ? ? B DG 5 B DG 5 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? B DG 1 N7 ? ? ? 1_555 B DG 1 N2 ? ? B DG 5 B DG 5 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? B DG 1 O6 ? ? ? 1_555 B DG 1 N1 ? ? B DG 5 B DG 5 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? B DG 2 N1 ? ? ? 1_555 B DG 2 O6 ? ? B DG 6 B DG 6 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? B DG 2 N2 ? ? ? 1_555 B DG 2 N7 ? ? B DG 6 B DG 6 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? B DG 2 N7 ? ? ? 1_555 B DG 2 N2 ? ? B DG 6 B DG 6 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? B DG 2 O6 ? ? ? 1_555 B DG 2 N1 ? ? B DG 6 B DG 6 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? B DG 3 N1 ? ? ? 1_555 B DG 3 O6 ? ? B DG 7 B DG 7 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? B DG 3 N2 ? ? ? 1_555 B DG 3 N7 ? ? B DG 7 B DG 7 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? B DG 3 N7 ? ? ? 1_555 B DG 3 N2 ? ? B DG 7 B DG 7 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog28 hydrog ? ? B DG 3 O6 ? ? ? 1_555 B DG 3 N1 ? ? B DG 7 B DG 7 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog29 hydrog ? ? B DG 4 N1 ? ? ? 1_555 B DG 4 O6 ? ? B DG 8 B DG 8 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? B DG 4 N2 ? ? ? 1_555 B DG 4 N7 ? ? B DG 8 B DG 8 3_655 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? B DG 4 N7 ? ? ? 1_555 B DG 4 N2 ? ? B DG 8 B DG 8 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? B DG 4 O6 ? ? ? 1_555 B DG 4 N1 ? ? B DG 8 B DG 8 4_565 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 O6 ? A DG 1 ? A DG 1 ? 1_555 NA ? E NA . ? A NA 13 ? 1_555 O6 ? A DG 2 ? A DG 2 ? 1_555 72.3 ? 2 O6 ? A DG 2 ? A DG 2 ? 1_555 NA ? F NA . ? A NA 14 ? 1_555 O6 ? A DG 3 ? A DG 3 ? 1_555 75.8 ? 3 O6 ? A DG 3 ? A DG 3 ? 1_555 NA ? G NA . ? A NA 15 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 68.1 ? 4 O6 ? B DG 1 ? B DG 5 ? 1_555 NA ? J NA . ? B NA 16 ? 1_555 O6 ? B DG 2 ? B DG 6 ? 1_555 72.8 ? 5 O6 ? B DG 2 ? B DG 6 ? 1_555 NA ? K NA . ? B NA 17 ? 1_555 O6 ? B DG 3 ? B DG 7 ? 1_555 75.9 ? 6 O6 ? B DG 3 ? B DG 7 ? 1_555 NA ? L NA . ? B NA 18 ? 1_555 O6 ? B DG 4 ? B DG 8 ? 1_555 68.9 ? 7 O ? R HOH . ? B HOH 109 ? 1_555 NA ? M NA . ? B NA 19 ? 1_555 O ? R HOH . ? B HOH 110 ? 1_555 44.4 ? 8 O ? R HOH . ? B HOH 102 ? 1_555 MG ? P MG . ? B MG 22 ? 1_555 O ? R HOH . ? B HOH 106 ? 1_555 91.7 ? # 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 DM1 9 ? 6 'BINDING SITE FOR RESIDUE DM1 A 9' AC2 Software A DM1 10 ? 10 'BINDING SITE FOR RESIDUE DM1 A 10' AC3 Software A NA 13 ? 3 'BINDING SITE FOR RESIDUE NA A 13' AC4 Software A NA 14 ? 4 'BINDING SITE FOR RESIDUE NA A 14' AC5 Software A NA 15 ? 3 'BINDING SITE FOR RESIDUE NA A 15' AC6 Software B DM1 11 ? 8 'BINDING SITE FOR RESIDUE DM1 B 11' AC7 Software B DM1 12 ? 10 'BINDING SITE FOR RESIDUE DM1 B 12' AC8 Software B NA 16 ? 4 'BINDING SITE FOR RESIDUE NA B 16' AC9 Software B NA 17 ? 4 'BINDING SITE FOR RESIDUE NA B 17' BC1 Software B NA 18 ? 3 'BINDING SITE FOR RESIDUE NA B 18' BC2 Software B NA 19 ? 2 'BINDING SITE FOR RESIDUE NA B 19' BC4 Software B MG 21 ? 1 'BINDING SITE FOR RESIDUE MG B 21' BC5 Software B MG 22 ? 4 'BINDING SITE FOR RESIDUE MG B 22' 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 DG A 1 ? DG A 1 . ? 1_555 ? 2 AC1 6 DG A 2 ? DG A 2 . ? 1_555 ? 3 AC1 6 DM1 D . ? DM1 A 10 . ? 1_555 ? 4 AC1 6 HOH Q . ? HOH A 123 . ? 1_555 ? 5 AC1 6 HOH Q . ? HOH A 149 . ? 1_555 ? 6 AC1 6 HOH Q . ? HOH A 201 . ? 1_555 ? 7 AC2 10 DM1 C . ? DM1 A 9 . ? 1_555 ? 8 AC2 10 HOH Q . ? HOH A 123 . ? 1_555 ? 9 AC2 10 HOH Q . ? HOH A 127 . ? 1_555 ? 10 AC2 10 HOH Q . ? HOH A 128 . ? 1_555 ? 11 AC2 10 HOH Q . ? HOH A 151 . ? 1_555 ? 12 AC2 10 HOH Q . ? HOH A 179 . ? 1_555 ? 13 AC2 10 HOH Q . ? HOH A 187 . ? 1_555 ? 14 AC2 10 HOH Q . ? HOH A 200 . ? 1_555 ? 15 AC2 10 HOH Q . ? HOH A 201 . ? 1_555 ? 16 AC2 10 DM1 H . ? DM1 B 11 . ? 1_555 ? 17 AC3 3 DG A 1 ? DG A 1 . ? 1_555 ? 18 AC3 3 DG A 2 ? DG A 2 . ? 1_555 ? 19 AC3 3 NA F . ? NA A 14 . ? 1_555 ? 20 AC4 4 DG A 2 ? DG A 2 . ? 1_555 ? 21 AC4 4 DG A 3 ? DG A 3 . ? 1_555 ? 22 AC4 4 NA E . ? NA A 13 . ? 1_555 ? 23 AC4 4 NA G . ? NA A 15 . ? 1_555 ? 24 AC5 3 DG A 3 ? DG A 3 . ? 1_555 ? 25 AC5 3 DG A 4 ? DG A 4 . ? 1_555 ? 26 AC5 3 NA F . ? NA A 14 . ? 1_555 ? 27 AC6 8 DM1 D . ? DM1 A 10 . ? 1_555 ? 28 AC6 8 DM1 I . ? DM1 B 12 . ? 1_555 ? 29 AC6 8 HOH R . ? HOH B 113 . ? 1_555 ? 30 AC6 8 HOH R . ? HOH B 125 . ? 1_555 ? 31 AC6 8 HOH R . ? HOH B 126 . ? 1_555 ? 32 AC6 8 HOH R . ? HOH B 132 . ? 1_555 ? 33 AC6 8 HOH R . ? HOH B 140 . ? 1_555 ? 34 AC6 8 HOH R . ? HOH B 170 . ? 1_555 ? 35 AC7 10 DG B 1 ? DG B 5 . ? 1_555 ? 36 AC7 10 DG B 2 ? DG B 6 . ? 1_555 ? 37 AC7 10 DM1 H . ? DM1 B 11 . ? 1_555 ? 38 AC7 10 HOH R . ? HOH B 102 . ? 1_555 ? 39 AC7 10 HOH R . ? HOH B 113 . ? 1_555 ? 40 AC7 10 HOH R . ? HOH B 145 . ? 1_555 ? 41 AC7 10 HOH R . ? HOH B 150 . ? 1_555 ? 42 AC7 10 HOH R . ? HOH B 159 . ? 1_555 ? 43 AC7 10 HOH R . ? HOH B 162 . ? 1_555 ? 44 AC7 10 HOH R . ? HOH B 198 . ? 1_555 ? 45 AC8 4 DG B 1 ? DG B 5 . ? 1_555 ? 46 AC8 4 DG B 2 ? DG B 6 . ? 1_555 ? 47 AC8 4 NA K . ? NA B 17 . ? 1_555 ? 48 AC8 4 MG P . ? MG B 22 . ? 1_555 ? 49 AC9 4 DG B 2 ? DG B 6 . ? 1_555 ? 50 AC9 4 DG B 3 ? DG B 7 . ? 1_555 ? 51 AC9 4 NA J . ? NA B 16 . ? 1_555 ? 52 AC9 4 NA L . ? NA B 18 . ? 1_555 ? 53 BC1 3 DG B 3 ? DG B 7 . ? 1_555 ? 54 BC1 3 DG B 4 ? DG B 8 . ? 1_555 ? 55 BC1 3 NA K . ? NA B 17 . ? 1_555 ? 56 BC2 2 HOH R . ? HOH B 109 . ? 1_555 ? 57 BC2 2 HOH R . ? HOH B 110 . ? 1_555 ? 58 BC4 1 HOH R . ? HOH B 111 . ? 1_555 ? 59 BC5 4 DG B 1 ? DG B 5 . ? 1_555 ? 60 BC5 4 NA J . ? NA B 16 . ? 1_555 ? 61 BC5 4 HOH R . ? HOH B 102 . ? 1_555 ? 62 BC5 4 HOH R . ? HOH B 106 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 199 _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_2 203 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N1 A DG 1 ? ? C2 A DG 1 ? ? 1.422 1.373 0.049 0.008 N 2 1 C4 A DG 1 ? ? C5 A DG 1 ? ? 1.434 1.379 0.055 0.007 N 3 1 C5 A DG 1 ? ? C6 A DG 1 ? ? 1.343 1.419 -0.076 0.010 N 4 1 C5 A DG 1 ? ? N7 A DG 1 ? ? 1.347 1.388 -0.041 0.006 N 5 1 N7 A DG 1 ? ? C8 A DG 1 ? ? 1.395 1.305 0.090 0.006 N 6 1 N9 A DG 1 ? ? C4 A DG 1 ? ? 1.317 1.375 -0.058 0.008 N 7 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.574 1.512 0.062 0.007 N 8 1 N1 A DG 2 ? ? C2 A DG 2 ? ? 1.422 1.373 0.049 0.008 N 9 1 C6 A DG 2 ? ? N1 A DG 2 ? ? 1.346 1.391 -0.045 0.007 N 10 1 C8 A DG 2 ? ? N9 A DG 2 ? ? 1.319 1.374 -0.055 0.007 N 11 1 P A DG 3 ? ? OP2 A DG 3 ? ? 1.367 1.485 -0.118 0.017 N 12 1 P A DG 3 ? ? "O5'" A DG 3 ? ? 1.516 1.593 -0.077 0.010 N 13 1 "C5'" A DG 3 ? ? "C4'" A DG 3 ? ? 1.442 1.509 -0.067 0.011 N 14 1 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.594 1.435 0.159 0.013 N 15 1 N1 A DG 3 ? ? C2 A DG 3 ? ? 1.425 1.373 0.052 0.008 N 16 1 C5 A DG 3 ? ? C6 A DG 3 ? ? 1.491 1.419 0.072 0.010 N 17 1 C8 A DG 3 ? ? N9 A DG 3 ? ? 1.420 1.374 0.046 0.007 N 18 1 P A DG 4 ? ? OP1 A DG 4 ? ? 1.588 1.485 0.103 0.017 N 19 1 "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 1.446 1.521 -0.075 0.010 N 20 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 1.515 1.449 0.066 0.009 N 21 1 N1 A DG 4 ? ? C2 A DG 4 ? ? 1.436 1.373 0.063 0.008 N 22 1 C6 A DG 4 ? ? N1 A DG 4 ? ? 1.293 1.391 -0.098 0.007 N 23 1 C8 A DG 4 ? ? N9 A DG 4 ? ? 1.466 1.374 0.092 0.007 N 24 1 C2 A DG 4 ? ? N2 A DG 4 ? ? 1.271 1.341 -0.070 0.010 N 25 1 "C5'" B DG 5 ? ? "C4'" B DG 5 ? ? 1.442 1.509 -0.067 0.011 N 26 1 "C3'" B DG 6 ? ? "C2'" B DG 6 ? ? 1.455 1.516 -0.061 0.008 N 27 1 C2 B DG 7 ? ? N3 B DG 7 ? ? 1.402 1.323 0.079 0.008 N 28 1 C5 B DG 7 ? ? N7 B DG 7 ? ? 1.346 1.388 -0.042 0.006 N 29 1 N7 B DG 7 ? ? C8 B DG 7 ? ? 1.352 1.305 0.047 0.006 N 30 1 "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 1.366 1.509 -0.143 0.011 N 31 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? 1.596 1.518 0.078 0.012 N 32 1 N3 B DG 8 ? ? C4 B DG 8 ? ? 1.291 1.350 -0.059 0.007 N 33 1 C4 B DG 8 ? ? C5 B DG 8 ? ? 1.426 1.379 0.047 0.007 N 34 1 C2 B DG 8 ? ? N2 B DG 8 ? ? 1.232 1.341 -0.109 0.010 N # 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 N1 A DG 1 ? ? C2 A DG 1 ? ? N3 A DG 1 ? ? 119.73 123.90 -4.17 0.60 N 2 1 C2 A DG 1 ? ? N3 A DG 1 ? ? C4 A DG 1 ? ? 117.12 111.90 5.22 0.50 N 3 1 N3 A DG 1 ? ? C4 A DG 1 ? ? C5 A DG 1 ? ? 125.03 128.60 -3.57 0.50 N 4 1 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 109.71 113.10 -3.39 0.50 N 5 1 C8 A DG 1 ? ? N9 A DG 1 ? ? C4 A DG 1 ? ? 110.01 106.40 3.61 0.40 N 6 1 C4 A DG 2 ? ? C5 A DG 2 ? ? N7 A DG 2 ? ? 113.48 110.80 2.68 0.40 N 7 1 C5 A DG 2 ? ? N7 A DG 2 ? ? C8 A DG 2 ? ? 100.88 104.30 -3.42 0.50 N 8 1 N9 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 102.82 105.40 -2.58 0.40 N 9 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 124.06 128.60 -4.54 0.60 N 10 1 C2 A DG 3 ? ? N3 A DG 3 ? ? C4 A DG 3 ? ? 115.79 111.90 3.89 0.50 N 11 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 108.02 113.10 -5.08 0.50 N 12 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 109.42 106.40 3.02 0.40 N 13 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 100.49 109.40 -8.91 0.80 N 14 1 P A DG 4 ? ? "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? 110.68 120.90 -10.22 1.60 N 15 1 "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? "C2'" A DG 4 ? ? 110.33 103.10 7.23 0.90 N 16 1 "C3'" A DG 4 ? ? "C2'" A DG 4 ? ? "C1'" A DG 4 ? ? 95.32 102.40 -7.08 0.80 N 17 1 N1 A DG 4 ? ? C2 A DG 4 ? ? N3 A DG 4 ? ? 118.73 123.90 -5.17 0.60 N 18 1 C2 A DG 4 ? ? N3 A DG 4 ? ? C4 A DG 4 ? ? 115.09 111.90 3.19 0.50 N 19 1 N7 A DG 4 ? ? C8 A DG 4 ? ? N9 A DG 4 ? ? 109.45 113.10 -3.65 0.50 N 20 1 N3 A DG 4 ? ? C2 A DG 4 ? ? N2 A DG 4 ? ? 124.96 119.90 5.06 0.70 N 21 1 "C3'" B DG 5 ? ? "C2'" B DG 5 ? ? "C1'" B DG 5 ? ? 96.85 102.40 -5.55 0.80 N 22 1 N1 B DG 5 ? ? C2 B DG 5 ? ? N3 B DG 5 ? ? 120.27 123.90 -3.63 0.60 N 23 1 C2 B DG 5 ? ? N3 B DG 5 ? ? C4 B DG 5 ? ? 116.04 111.90 4.14 0.50 N 24 1 N3 B DG 5 ? ? C2 B DG 5 ? ? N2 B DG 5 ? ? 124.63 119.90 4.73 0.70 N 25 1 C4 B DG 6 ? ? C5 B DG 6 ? ? N7 B DG 6 ? ? 113.35 110.80 2.55 0.40 N 26 1 "O5'" B DG 7 ? ? "C5'" B DG 7 ? ? "C4'" B DG 7 ? ? 104.60 109.40 -4.80 0.80 N 27 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 97.32 102.40 -5.08 0.80 N 28 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 103.09 108.00 -4.91 0.70 N 29 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N3 B DG 8 ? ? 117.07 123.90 -6.83 0.60 N 30 1 C2 B DG 8 ? ? N3 B DG 8 ? ? C4 B DG 8 ? ? 118.43 111.90 6.53 0.50 N 31 1 C5 B DG 8 ? ? N7 B DG 8 ? ? C8 B DG 8 ? ? 107.43 104.30 3.13 0.50 N 32 1 C8 B DG 8 ? ? N9 B DG 8 ? ? C4 B DG 8 ? ? 109.20 106.40 2.80 0.40 N 33 1 N9 B DG 8 ? ? C4 B DG 8 ? ? C5 B DG 8 ? ? 102.58 105.40 -2.82 0.40 N 34 1 N3 B DG 8 ? ? C4 B DG 8 ? ? N9 B DG 8 ? ? 130.69 126.00 4.69 0.60 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'OUTSIDE BINDER' # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A NA 13 ? E NA . 2 1 A NA 14 ? F NA . 3 1 A NA 15 ? G NA . 4 1 B NA 16 ? J NA . 5 1 B NA 17 ? K NA . 6 1 B NA 18 ? L NA . 7 1 B NA 19 ? M NA . 8 1 B NA 20 ? N NA . 9 1 B MG 21 ? O MG . 10 1 B MG 22 ? P MG . 11 1 A HOH 101 ? Q HOH . 12 1 A HOH 103 ? Q HOH . 13 1 B HOH 106 ? R HOH . # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? B HOH 111 ? 7.01 . 2 1 O ? B HOH 178 ? . 6.45 3 1 O ? B HOH 196 ? 6.99 . 4 1 O ? B HOH 206 ? . 7.29 # 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 DG OP3 O N N 1 DG P P N N 2 DG OP1 O N N 3 DG OP2 O N N 4 DG "O5'" O N N 5 DG "C5'" C N N 6 DG "C4'" C N R 7 DG "O4'" O N N 8 DG "C3'" C N S 9 DG "O3'" O N N 10 DG "C2'" C N N 11 DG "C1'" C N R 12 DG N9 N Y N 13 DG C8 C Y N 14 DG N7 N Y N 15 DG C5 C Y N 16 DG C6 C N N 17 DG O6 O N N 18 DG N1 N N N 19 DG C2 C N N 20 DG N2 N N N 21 DG N3 N N N 22 DG C4 C Y N 23 DG HOP3 H N N 24 DG HOP2 H N N 25 DG "H5'" H N N 26 DG "H5''" H N N 27 DG "H4'" H N N 28 DG "H3'" H N N 29 DG "HO3'" H N N 30 DG "H2'" H N N 31 DG "H2''" H N N 32 DG "H1'" H N N 33 DG H8 H N N 34 DG H1 H N N 35 DG H21 H N N 36 DG H22 H N N 37 DM1 C1 C Y N 38 DM1 C2 C Y N 39 DM1 C3 C Y N 40 DM1 C4 C Y N 41 DM1 O4 O N N 42 DM1 C5 C Y N 43 DM1 C6 C N N 44 DM1 O6 O N N 45 DM1 C7 C Y N 46 DM1 C8 C Y N 47 DM1 O8 O N N 48 DM1 C9 C Y N 49 DM1 C10 C N S 50 DM1 O10 O N N 51 DM1 C11 C N N 52 DM1 C12 C N S 53 DM1 O12 O N N 54 DM1 C13 C N N 55 DM1 O13 O N N 56 DM1 C14 C N N 57 DM1 C15 C N N 58 DM1 C16 C Y N 59 DM1 C17 C Y N 60 DM1 O17 O N N 61 DM1 C18 C Y N 62 DM1 C19 C N N 63 DM1 O19 O N N 64 DM1 C20 C Y N 65 DM1 C21 C N N 66 DM1 "C1'" C N R 67 DM1 "C2'" C N N 68 DM1 "C3'" C N S 69 DM1 "N3'" N N N 70 DM1 "C4'" C N S 71 DM1 "O4'" O N N 72 DM1 "C5'" C N S 73 DM1 "O5'" O N N 74 DM1 "C6'" C N N 75 DM1 H1 H N N 76 DM1 H2 H N N 77 DM1 H3 H N N 78 DM1 HO8 H N N 79 DM1 H10 H N N 80 DM1 H111 H N N 81 DM1 H112 H N N 82 DM1 HO12 H N N 83 DM1 H141 H N N 84 DM1 H142 H N N 85 DM1 H143 H N N 86 DM1 H151 H N N 87 DM1 H152 H N N 88 DM1 HO17 H N N 89 DM1 H211 H N N 90 DM1 H212 H N N 91 DM1 H213 H N N 92 DM1 "H1'" H N N 93 DM1 "H2'1" H N N 94 DM1 "H2'2" H N N 95 DM1 "H3'" H N N 96 DM1 "HN'1" H N N 97 DM1 "HN'2" H N N 98 DM1 "H4'" H N N 99 DM1 "HO4'" H N N 100 DM1 "H5'" H N N 101 DM1 "H6'1" H N N 102 DM1 "H6'2" H N N 103 DM1 "H6'3" H N N 104 HOH O O N N 105 HOH H1 H N N 106 HOH H2 H N N 107 MG MG MG N N 108 NA NA NA N N 109 # 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 DG OP3 P sing N N 1 DG OP3 HOP3 sing N N 2 DG P OP1 doub N N 3 DG P OP2 sing N N 4 DG P "O5'" sing N N 5 DG OP2 HOP2 sing N N 6 DG "O5'" "C5'" sing N N 7 DG "C5'" "C4'" sing N N 8 DG "C5'" "H5'" sing N N 9 DG "C5'" "H5''" sing N N 10 DG "C4'" "O4'" sing N N 11 DG "C4'" "C3'" sing N N 12 DG "C4'" "H4'" sing N N 13 DG "O4'" "C1'" sing N N 14 DG "C3'" "O3'" sing N N 15 DG "C3'" "C2'" sing N N 16 DG "C3'" "H3'" sing N N 17 DG "O3'" "HO3'" sing N N 18 DG "C2'" "C1'" sing N N 19 DG "C2'" "H2'" sing N N 20 DG "C2'" "H2''" sing N N 21 DG "C1'" N9 sing N N 22 DG "C1'" "H1'" sing N N 23 DG N9 C8 sing Y N 24 DG N9 C4 sing Y N 25 DG C8 N7 doub Y N 26 DG C8 H8 sing N N 27 DG N7 C5 sing Y N 28 DG C5 C6 sing N N 29 DG C5 C4 doub Y N 30 DG C6 O6 doub N N 31 DG C6 N1 sing N N 32 DG N1 C2 sing N N 33 DG N1 H1 sing N N 34 DG C2 N2 sing N N 35 DG C2 N3 doub N N 36 DG N2 H21 sing N N 37 DG N2 H22 sing N N 38 DG N3 C4 sing N N 39 DM1 C1 C2 doub Y N 40 DM1 C1 C20 sing Y N 41 DM1 C1 H1 sing N N 42 DM1 C2 C3 sing Y N 43 DM1 C2 H2 sing N N 44 DM1 C3 C4 doub Y N 45 DM1 C3 H3 sing N N 46 DM1 C4 O4 sing N N 47 DM1 C4 C5 sing Y N 48 DM1 O4 C21 sing N N 49 DM1 C5 C6 sing N N 50 DM1 C5 C20 doub Y N 51 DM1 C6 O6 doub N N 52 DM1 C6 C7 sing N N 53 DM1 C7 C8 doub Y N 54 DM1 C7 C18 sing Y N 55 DM1 C8 O8 sing N N 56 DM1 C8 C9 sing Y N 57 DM1 O8 HO8 sing N N 58 DM1 C9 C10 sing N N 59 DM1 C9 C16 doub Y N 60 DM1 C10 O10 sing N N 61 DM1 C10 C11 sing N N 62 DM1 C10 H10 sing N N 63 DM1 O10 "C1'" sing N N 64 DM1 C11 C12 sing N N 65 DM1 C11 H111 sing N N 66 DM1 C11 H112 sing N N 67 DM1 C12 O12 sing N N 68 DM1 C12 C13 sing N N 69 DM1 C12 C15 sing N N 70 DM1 O12 HO12 sing N N 71 DM1 C13 O13 doub N N 72 DM1 C13 C14 sing N N 73 DM1 C14 H141 sing N N 74 DM1 C14 H142 sing N N 75 DM1 C14 H143 sing N N 76 DM1 C15 C16 sing N N 77 DM1 C15 H151 sing N N 78 DM1 C15 H152 sing N N 79 DM1 C16 C17 sing Y N 80 DM1 C17 O17 sing N N 81 DM1 C17 C18 doub Y N 82 DM1 O17 HO17 sing N N 83 DM1 C18 C19 sing N N 84 DM1 C19 O19 doub N N 85 DM1 C19 C20 sing N N 86 DM1 C21 H211 sing N N 87 DM1 C21 H212 sing N N 88 DM1 C21 H213 sing N N 89 DM1 "C1'" "C2'" sing N N 90 DM1 "C1'" "O5'" sing N N 91 DM1 "C1'" "H1'" sing N N 92 DM1 "C2'" "C3'" sing N N 93 DM1 "C2'" "H2'1" sing N N 94 DM1 "C2'" "H2'2" sing N N 95 DM1 "C3'" "N3'" sing N N 96 DM1 "C3'" "C4'" sing N N 97 DM1 "C3'" "H3'" sing N N 98 DM1 "N3'" "HN'1" sing N N 99 DM1 "N3'" "HN'2" sing N N 100 DM1 "C4'" "O4'" sing N N 101 DM1 "C4'" "C5'" sing N N 102 DM1 "C4'" "H4'" sing N N 103 DM1 "O4'" "HO4'" sing N N 104 DM1 "C5'" "O5'" sing N N 105 DM1 "C5'" "C6'" sing N N 106 DM1 "C5'" "H5'" sing N N 107 DM1 "C6'" "H6'1" sing N N 108 DM1 "C6'" "H6'2" sing N N 109 DM1 "C6'" "H6'3" sing N N 110 HOH O H1 sing N N 111 HOH O H2 sing N N 112 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3TVB 'double helix' 3TVB 'triple 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 DG 1 1_555 A DG 1 3_655 1.709 3.408 0.092 0.746 2.708 -89.966 1 A_DG1:DG1_A A 1 ? A 1 ? 6 3 1 A DG 2 1_555 A DG 2 3_655 -1.435 -3.520 0.281 0.637 8.849 89.655 2 A_DG2:DG2_A A 2 ? A 2 ? 6 3 1 A DG 3 1_555 A DG 3 3_655 -1.561 -3.477 0.049 -4.281 3.527 89.866 3 A_DG3:DG3_A A 3 ? A 3 ? 6 3 1 A DG 4 1_555 A DG 4 3_655 -1.525 -3.536 0.165 -12.664 10.713 88.782 4 A_DG4:DG4_A A 4 ? A 4 ? 6 3 1 A DG 1 1_555 A DG 1 4_565 -1.709 -3.408 -0.092 -0.746 -2.708 89.966 5 A_DG1:DG1_A A 1 ? A 1 ? 6 3 1 A DG 2 1_555 A DG 2 4_565 1.435 3.520 -0.281 -0.637 -8.849 -89.655 6 A_DG2:DG2_A A 2 ? A 2 ? 6 3 1 A DG 3 1_555 A DG 3 4_565 1.561 3.477 -0.049 4.281 -3.527 -89.866 7 A_DG3:DG3_A A 3 ? A 3 ? 6 3 1 A DG 4 1_555 A DG 4 4_565 1.525 3.536 -0.165 12.664 -10.713 -88.782 8 A_DG4:DG4_A A 4 ? A 4 ? 6 3 1 B DG 1 1_555 B DG 1 3_655 -1.666 -3.440 -0.069 -1.036 -1.804 89.981 9 B_DG5:DG5_B B 5 ? B 5 ? 6 3 1 B DG 2 1_555 B DG 2 3_655 1.450 3.511 -0.259 -1.290 -7.899 -89.720 10 B_DG6:DG6_B B 6 ? B 6 ? 6 3 1 B DG 3 1_555 B DG 3 3_655 1.479 3.517 -0.038 3.668 -2.795 -89.907 11 B_DG7:DG7_B B 7 ? B 7 ? 6 3 1 B DG 4 1_555 B DG 4 3_655 1.588 3.471 -0.160 12.354 -10.834 -88.805 12 B_DG8:DG8_B B 8 ? B 8 ? 6 3 1 B DG 1 1_555 B DG 1 4_565 1.666 3.440 0.069 1.036 1.804 -89.981 13 B_DG5:DG5_B B 5 ? B 5 ? 6 3 1 B DG 2 1_555 B DG 2 4_565 -1.450 -3.511 0.259 1.290 7.899 89.720 14 B_DG6:DG6_B B 6 ? B 6 ? 6 3 1 B DG 3 1_555 B DG 3 4_565 -1.479 -3.517 0.038 -3.668 2.795 89.907 15 B_DG7:DG7_B B 7 ? B 7 ? 6 3 1 B DG 4 1_555 B DG 4 4_565 -1.588 -3.471 0.160 -12.354 10.834 88.805 16 B_DG8:DG8_B B 8 ? B 8 ? 6 3 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 A DG 1 3_655 A DG 2 1_555 A DG 2 3_655 2.212 2.868 1.751 -79.620 156.662 -81.060 -1.785 0.928 -0.043 -78.996 -40.148 -176.757 1 AA_DG1DG2:DG2DG1_AA A 1 ? A 1 ? A 2 ? A 2 ? 1 A DG 2 1_555 A DG 2 3_655 A DG 3 1_555 A DG 3 3_655 -0.446 -0.828 3.354 -3.092 4.188 34.366 -2.037 0.266 3.260 7.038 5.196 34.746 2 AA_DG2DG3:DG3DG2_AA A 2 ? A 2 ? A 3 ? A 3 ? 1 A DG 3 1_555 A DG 3 3_655 A DG 4 1_555 A DG 4 3_655 -0.570 -0.522 3.078 1.956 5.544 21.882 -3.171 2.100 2.800 14.277 -5.038 22.649 3 AA_DG3DG4:DG4DG3_AA A 3 ? A 3 ? A 4 ? A 4 ? 1 A DG 1 1_555 A DG 1 4_565 A DG 2 1_555 A DG 2 4_565 2.212 2.868 1.751 -79.620 156.662 -81.060 -1.785 0.928 -0.043 -78.996 -40.148 -176.757 4 AA_DG1DG2:DG2DG1_AA A 1 ? A 1 ? A 2 ? A 2 ? 1 A DG 2 1_555 A DG 2 4_565 A DG 3 1_555 A DG 3 4_565 -0.446 -0.828 3.354 -3.092 4.188 34.366 -2.037 0.266 3.260 7.038 5.196 34.746 5 AA_DG2DG3:DG3DG2_AA A 2 ? A 2 ? A 3 ? A 3 ? 1 A DG 3 1_555 A DG 3 4_565 A DG 4 1_555 A DG 4 4_565 -0.570 -0.522 3.078 1.956 5.544 21.882 -3.171 2.100 2.800 14.277 -5.038 22.649 6 AA_DG3DG4:DG4DG3_AA A 3 ? A 3 ? A 4 ? A 4 ? 1 B DG 1 1_555 B DG 1 3_655 B DG 2 1_555 B DG 2 3_655 2.261 2.855 1.810 -77.622 157.767 -80.164 -1.800 0.948 -0.030 -79.550 -39.139 -176.809 7 BB_DG5DG6:DG6DG5_BB B 5 ? B 5 ? B 6 ? B 6 ? 1 B DG 2 1_555 B DG 2 3_655 B DG 3 1_555 B DG 3 3_655 -0.434 -0.874 3.353 -2.795 3.921 33.462 -2.147 0.287 3.257 6.767 4.823 33.797 8 BB_DG6DG7:DG7DG6_BB B 6 ? B 6 ? B 7 ? B 7 ? 1 B DG 3 1_555 B DG 3 3_655 B DG 4 1_555 B DG 4 3_655 -0.525 -0.505 3.067 2.351 5.709 23.376 -2.865 1.938 2.800 13.784 -5.678 24.167 9 BB_DG7DG8:DG8DG7_BB B 7 ? B 7 ? B 8 ? B 8 ? 1 B DG 1 1_555 B DG 1 4_565 B DG 2 1_555 B DG 2 4_565 2.261 2.855 1.810 -77.622 157.767 -80.164 -1.800 0.948 -0.030 -79.550 -39.139 -176.809 10 BB_DG5DG6:DG6DG5_BB B 5 ? B 5 ? B 6 ? B 6 ? 1 B DG 2 1_555 B DG 2 4_565 B DG 3 1_555 B DG 3 4_565 -0.434 -0.874 3.353 -2.795 3.921 33.462 -2.147 0.287 3.257 6.767 4.823 33.797 11 BB_DG6DG7:DG7DG6_BB B 6 ? B 6 ? B 7 ? B 7 ? 1 B DG 3 1_555 B DG 3 4_565 B DG 4 1_555 B DG 4 4_565 -0.525 -0.505 3.067 2.351 5.709 23.376 -2.865 1.938 2.800 13.784 -5.678 24.167 12 BB_DG7DG8:DG8DG7_BB B 7 ? B 7 ? B 8 ? B 8 ? # _atom_sites.entry_id 3TVB _atom_sites.fract_transf_matrix[1][1] 0.024870 _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] 0.024870 _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] 0.020068 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N NA O P # loop_