data_3I5E # _entry.id 3I5E # _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 3I5E pdb_00003i5e 10.2210/pdb3i5e/pdb NDB NA0154 ? ? RCSB RCSB053985 ? ? WWPDB D_1000053985 ? ? # 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 2009-07-28 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.value' 8 3 'Structure model' '_struct_conn.pdbx_dist_value' 9 3 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 10 3 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 11 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3I5E _pdbx_database_status.recvd_initial_deposition_date 2009-07-05 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3I5L _pdbx_database_related.details 'Duplex DNA with Polyamide Bound' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chenoweth, D.M.' 1 'Dervan, P.B.' 2 # _citation.id primary _citation.title 'Allosteric modulation of DNA by small molecules' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 106 _citation.page_first 13175 _citation.page_last 13179 _citation.year 2009 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19666554 _citation.pdbx_database_id_DOI 10.1073/pnas.0906532106 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chenoweth, D.M.' 1 ? primary 'Dervan, P.B.' 2 ? # 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*CP*AP*GP*GP*CP*CP*TP*GP*G)-3'" 3045.992 1 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 3 water nat water 18.015 125 ? ? ? ? # _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)(DC)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAGGCCTGG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH # 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 DC n 1 3 DA n 1 4 DG n 1 5 DG n 1 6 DC n 1 7 DC n 1 8 DT n 1 9 DG n 1 10 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 YES # 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG A . 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 B 2 CA 1 51 51 CA CA A . C 2 CA 1 52 52 CA CA A . D 3 HOH 1 101 101 HOH HOH A . D 3 HOH 2 102 102 HOH HOH A . D 3 HOH 3 103 103 HOH HOH A . D 3 HOH 4 104 104 HOH HOH A . D 3 HOH 5 105 105 HOH HOH A . D 3 HOH 6 106 106 HOH HOH A . D 3 HOH 7 107 107 HOH HOH A . D 3 HOH 8 108 108 HOH HOH A . D 3 HOH 9 109 109 HOH HOH A . D 3 HOH 10 110 110 HOH HOH A . D 3 HOH 11 111 111 HOH HOH A . D 3 HOH 12 112 112 HOH HOH A . D 3 HOH 13 113 113 HOH HOH A . D 3 HOH 14 114 114 HOH HOH A . D 3 HOH 15 115 115 HOH HOH A . D 3 HOH 16 116 116 HOH HOH A . D 3 HOH 17 117 117 HOH HOH A . D 3 HOH 18 119 119 HOH HOH A . D 3 HOH 19 120 120 HOH HOH A . D 3 HOH 20 121 121 HOH HOH A . D 3 HOH 21 123 123 HOH HOH A . D 3 HOH 22 125 125 HOH HOH A . D 3 HOH 23 126 126 HOH HOH A . D 3 HOH 24 127 127 HOH HOH A . D 3 HOH 25 128 128 HOH HOH A . D 3 HOH 26 129 129 HOH HOH A . D 3 HOH 27 130 130 HOH HOH A . D 3 HOH 28 131 131 HOH HOH A . D 3 HOH 29 132 132 HOH HOH A . D 3 HOH 30 133 133 HOH HOH A . D 3 HOH 31 134 134 HOH HOH A . D 3 HOH 32 135 135 HOH HOH A . D 3 HOH 33 136 136 HOH HOH A . D 3 HOH 34 137 137 HOH HOH A . D 3 HOH 35 138 138 HOH HOH A . D 3 HOH 36 139 139 HOH HOH A . D 3 HOH 37 140 140 HOH HOH A . D 3 HOH 38 141 141 HOH HOH A . D 3 HOH 39 142 142 HOH HOH A . D 3 HOH 40 143 143 HOH HOH A . D 3 HOH 41 145 145 HOH HOH A . D 3 HOH 42 146 146 HOH HOH A . D 3 HOH 43 147 147 HOH HOH A . D 3 HOH 44 148 148 HOH HOH A . D 3 HOH 45 149 149 HOH HOH A . D 3 HOH 46 150 150 HOH HOH A . D 3 HOH 47 151 151 HOH HOH A . D 3 HOH 48 152 152 HOH HOH A . D 3 HOH 49 153 153 HOH HOH A . D 3 HOH 50 154 154 HOH HOH A . D 3 HOH 51 155 155 HOH HOH A . D 3 HOH 52 156 156 HOH HOH A . D 3 HOH 53 157 157 HOH HOH A . D 3 HOH 54 158 158 HOH HOH A . D 3 HOH 55 159 159 HOH HOH A . D 3 HOH 56 160 160 HOH HOH A . D 3 HOH 57 161 161 HOH HOH A . D 3 HOH 58 162 162 HOH HOH A . D 3 HOH 59 163 163 HOH HOH A . D 3 HOH 60 164 164 HOH HOH A . D 3 HOH 61 165 165 HOH HOH A . D 3 HOH 62 166 166 HOH HOH A . D 3 HOH 63 167 167 HOH HOH A . D 3 HOH 64 168 168 HOH HOH A . D 3 HOH 65 169 169 HOH HOH A . D 3 HOH 66 170 170 HOH HOH A . D 3 HOH 67 171 171 HOH HOH A . D 3 HOH 68 172 172 HOH HOH A . D 3 HOH 69 173 173 HOH HOH A . D 3 HOH 70 174 174 HOH HOH A . D 3 HOH 71 176 176 HOH HOH A . D 3 HOH 72 177 177 HOH HOH A . D 3 HOH 73 178 178 HOH HOH A . D 3 HOH 74 179 179 HOH HOH A . D 3 HOH 75 180 180 HOH HOH A . D 3 HOH 76 181 181 HOH HOH A . D 3 HOH 77 182 182 HOH HOH A . D 3 HOH 78 183 183 HOH HOH A . D 3 HOH 79 184 184 HOH HOH A . D 3 HOH 80 186 186 HOH HOH A . D 3 HOH 81 187 187 HOH HOH A . D 3 HOH 82 188 188 HOH HOH A . D 3 HOH 83 191 191 HOH HOH A . D 3 HOH 84 192 192 HOH HOH A . D 3 HOH 85 193 193 HOH HOH A . D 3 HOH 86 194 194 HOH HOH A . D 3 HOH 87 195 195 HOH HOH A . D 3 HOH 88 196 196 HOH HOH A . D 3 HOH 89 197 197 HOH HOH A . D 3 HOH 90 198 198 HOH HOH A . D 3 HOH 91 200 200 HOH HOH A . D 3 HOH 92 201 201 HOH HOH A . D 3 HOH 93 204 204 HOH HOH A . D 3 HOH 94 206 206 HOH HOH A . D 3 HOH 95 207 207 HOH HOH A . D 3 HOH 96 208 208 HOH HOH A . D 3 HOH 97 211 211 HOH HOH A . D 3 HOH 98 212 212 HOH HOH A . D 3 HOH 99 213 213 HOH HOH A . D 3 HOH 100 216 216 HOH HOH A . D 3 HOH 101 217 217 HOH HOH A . D 3 HOH 102 218 218 HOH HOH A . D 3 HOH 103 219 219 HOH HOH A . D 3 HOH 104 220 220 HOH HOH A . D 3 HOH 105 221 221 HOH HOH A . D 3 HOH 106 222 222 HOH HOH A . D 3 HOH 107 224 224 HOH HOH A . D 3 HOH 108 225 225 HOH HOH A . D 3 HOH 109 226 226 HOH HOH A . D 3 HOH 110 227 227 HOH HOH A . D 3 HOH 111 228 228 HOH HOH A . D 3 HOH 112 229 229 HOH HOH A . D 3 HOH 113 230 230 HOH HOH A . D 3 HOH 114 231 231 HOH HOH A . D 3 HOH 115 232 232 HOH HOH A . D 3 HOH 116 233 233 HOH HOH A . D 3 HOH 117 234 234 HOH HOH A . D 3 HOH 118 235 235 HOH HOH A . D 3 HOH 119 236 236 HOH HOH A . D 3 HOH 120 237 237 HOH HOH A . D 3 HOH 121 238 238 HOH HOH A . D 3 HOH 122 239 239 HOH HOH A . D 3 HOH 123 240 240 HOH HOH A . D 3 HOH 124 241 241 HOH HOH A . D 3 HOH 125 242 242 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 REFMAC refinement 5.2.0019 ? 2 MOSFLM 'data reduction' . ? 3 SCALA 'data scaling' . ? 4 SHELX phasing . ? 5 # _cell.entry_id 3I5E _cell.length_a 31.827 _cell.length_b 25.636 _cell.length_c 34.173 _cell.angle_alpha 90.00 _cell.angle_beta 116.72 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3I5E _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3I5E _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.04 _exptl_crystal.density_percent_sol 39.83 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details ;21% 2-methyl-2,4-pentanediol (MPD), 35 mM calcium acetate, 10 mM Tris pH 7.5 equilibrated in sitting drops against a reservoir of 35% MPD at 4 C., VAPOR DIFFUSION, SITTING DROP, temperature 277.15K ; _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 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date ? _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 0.999 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.999 # _reflns.entry_id 3I5E _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 15.91 _reflns.d_resolution_high 0.98 _reflns.number_obs 14260 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.050 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.5 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 0.98 _reflns_shell.d_res_low 2.63 _reflns_shell.percent_possible_all 84.8 _reflns_shell.Rmerge_I_obs 0.075 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.3 _reflns_shell.pdbx_redundancy 1.4 _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 3I5E _refine.ls_number_reflns_obs 12125 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.91 _refine.ls_d_res_high 0.98 _refine.ls_percent_reflns_obs 89.45 _refine.ls_R_factor_obs 0.11027 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.10849 _refine.ls_R_factor_R_free 0.14369 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 631 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.979 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.B_iso_mean 6.245 _refine.aniso_B[1][1] 0.02 _refine.aniso_B[2][2] -0.01 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.02 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL PARAMETERS FOR MASK CACLULATION' _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 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.026 _refine.pdbx_overall_ESU_R_Free 0.028 _refine.overall_SU_ML 0.014 _refine.overall_SU_B 0.562 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 297 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 137 _refine_hist.number_atoms_total 437 _refine_hist.d_res_high 0.98 _refine_hist.d_res_low 15.91 # 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 r_bond_refined_d 0.033 0.021 ? 333 'X-RAY DIFFRACTION' ? r_bond_other_d 0.004 0.020 ? 137 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.444 3.000 ? 514 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.543 3.000 ? 347 'X-RAY DIFFRACTION' ? r_chiral_restr 0.150 0.200 ? 58 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.046 0.020 ? 153 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 30 'X-RAY DIFFRACTION' ? r_nbd_refined 0.544 0.200 ? 61 'X-RAY DIFFRACTION' ? r_nbd_other 0.261 0.200 ? 148 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.254 0.200 ? 112 'X-RAY DIFFRACTION' ? r_nbtor_other 0.111 0.200 ? 79 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.361 0.200 ? 106 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.272 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.413 0.200 ? 42 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.385 0.200 ? 83 'X-RAY DIFFRACTION' ? r_scbond_it 2.932 3.000 ? 477 'X-RAY DIFFRACTION' ? r_scangle_it 3.525 4.500 ? 514 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 1.992 3.000 ? 717 'X-RAY DIFFRACTION' ? r_sphericity_free 13.357 3.000 ? 140 'X-RAY DIFFRACTION' ? r_sphericity_bonded 4.256 3.000 ? 434 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 0.980 _refine_ls_shell.d_res_low 1.005 _refine_ls_shell.number_reflns_R_work 840 _refine_ls_shell.R_factor_R_work 0.161 _refine_ls_shell.percent_reflns_obs 84.81 _refine_ls_shell.R_factor_R_free 0.231 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 42 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3I5E _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 # _struct.entry_id 3I5E _struct.title 'Allosteric Modulation of DNA by Small Molecules' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3I5E _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DOUBLE STRANDED DNA, POLYAMIDE, DOUBLE HELIX, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3I5E _struct_ref.pdbx_db_accession 3I5E _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code CCAGGCCTGG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3I5E _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3I5E _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # 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)' 1080 ? 1 MORE -20 ? 1 'SSA (A^2)' 3870 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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_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 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? B CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 51 A HOH 139 1_555 ? ? ? ? ? ? ? 2.440 ? ? metalc2 metalc ? ? B CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 51 A HOH 150 1_555 ? ? ? ? ? ? ? 2.671 ? ? metalc3 metalc ? ? B CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 51 A HOH 232 1_555 ? ? ? ? ? ? ? 2.487 ? ? metalc4 metalc ? ? C CA . CA A ? ? 1_555 D HOH . O ? ? A CA 52 A HOH 111 1_555 ? ? ? ? ? ? ? 2.524 ? ? metalc5 metalc ? ? C CA . CA A ? ? 1_555 D HOH . O A ? A CA 52 A HOH 123 1_555 ? ? ? ? ? ? ? 2.502 ? ? metalc6 metalc ? ? C CA . CA A ? ? 1_555 D HOH . O A ? A CA 52 A HOH 239 1_555 ? ? ? ? ? ? ? 2.347 ? ? metalc7 metalc ? ? C CA . CA B ? ? 1_555 D HOH . O B ? A CA 52 A HOH 239 1_555 ? ? ? ? ? ? ? 2.308 ? ? metalc8 metalc ? ? C CA . CA A ? ? 1_555 D HOH . O A ? A CA 52 A HOH 240 1_555 ? ? ? ? ? ? ? 2.387 ? ? metalc9 metalc ? ? C CA . CA B ? ? 1_555 D HOH . O B ? A CA 52 A HOH 240 1_555 ? ? ? ? ? ? ? 2.328 ? ? hydrog1 hydrog ? ? A DC 1 N3 A ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 A ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 A ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 A ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 A ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 A ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 8 N3 ? ? A DA 3 A DT 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 8 O4 ? ? A DA 3 A DT 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 6 N4 A ? A DG 4 A DC 6 2_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 A ? A DG 4 A DC 7 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 A ? A DG 4 A DC 7 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 A ? A DG 4 A DC 7 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N1 A ? ? 1_555 A DC 6 N3 A ? A DG 5 A DC 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 N2 A ? ? 1_555 A DC 6 O2 A ? A DG 5 A DC 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 5 O6 A ? ? 1_555 A DC 6 N4 A ? A DG 5 A DC 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 N4 A ? ? 1_555 A DG 4 O6 ? ? A DC 6 A DG 4 2_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog17 hydrog ? ? A DC 6 N3 A ? ? 1_555 A DG 5 N1 A ? A DC 6 A DG 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 6 N4 A ? ? 1_555 A DG 5 O6 A ? A DC 6 A DG 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 6 O2 A ? ? 1_555 A DG 5 N2 A ? A DC 6 A DG 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 7 N3 A ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 7 N4 A ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 7 O2 A ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 A ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 A ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 A ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 A ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 A ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 A ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 O ? D HOH . ? A HOH 139 ? 1_555 CA ? B CA . ? A CA 51 ? 1_555 O ? D HOH . ? A HOH 150 ? 1_555 140.5 ? 2 O ? D HOH . ? A HOH 139 ? 1_555 CA ? B CA . ? A CA 51 ? 1_555 O ? D HOH . ? A HOH 232 ? 1_555 101.9 ? 3 O ? D HOH . ? A HOH 150 ? 1_555 CA ? B CA . ? A CA 51 ? 1_555 O ? D HOH . ? A HOH 232 ? 1_555 93.4 ? 4 O ? D HOH . ? A HOH 111 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 123 ? 1_555 79.3 ? 5 O ? D HOH . ? A HOH 111 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 239 ? 1_555 80.3 ? 6 O A D HOH . ? A HOH 123 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 239 ? 1_555 81.2 ? 7 O ? D HOH . ? A HOH 111 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 240 ? 1_555 72.8 ? 8 O A D HOH . ? A HOH 123 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 240 ? 1_555 151.7 ? 9 O A D HOH . ? A HOH 239 ? 1_555 CA A C CA . ? A CA 52 ? 1_555 O A D HOH . ? A HOH 240 ? 1_555 98.3 ? 10 O B D HOH . ? A HOH 239 ? 1_555 CA B C CA . ? A CA 52 ? 1_555 O B D HOH . ? A HOH 240 ? 1_555 80.1 ? # 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 CA 51 ? 5 'BINDING SITE FOR RESIDUE CA A 51' AC2 Software A CA 52 ? 12 'BINDING SITE FOR RESIDUE CA A 52' # 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 5 DC A 6 ? DC A 6 . ? 1_555 ? 2 AC1 5 DC A 7 ? DC A 7 . ? 1_555 ? 3 AC1 5 HOH D . ? HOH A 139 . ? 1_555 ? 4 AC1 5 HOH D . ? HOH A 150 . ? 1_555 ? 5 AC1 5 HOH D . ? HOH A 232 . ? 1_555 ? 6 AC2 12 HOH D . ? HOH A 111 . ? 1_555 ? 7 AC2 12 HOH D . ? HOH A 111 . ? 2_554 ? 8 AC2 12 HOH D . ? HOH A 123 . ? 2_554 ? 9 AC2 12 HOH D . ? HOH A 123 . ? 1_555 ? 10 AC2 12 HOH D . ? HOH A 239 . ? 2_554 ? 11 AC2 12 HOH D . ? HOH A 239 . ? 1_555 ? 12 AC2 12 HOH D . ? HOH A 240 . ? 1_555 ? 13 AC2 12 HOH D . ? HOH A 240 . ? 2_554 ? 14 AC2 12 HOH D . ? HOH A 241 . ? 2_554 ? 15 AC2 12 HOH D . ? HOH A 241 . ? 1_555 ? 16 AC2 12 HOH D . ? HOH A 242 . ? 2_554 ? 17 AC2 12 HOH D . ? HOH A 242 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 201 ? ? O A HOH 221 ? ? 1.66 2 1 O A HOH 140 ? ? O A HOH 212 ? ? 1.91 3 1 O A HOH 220 ? ? O A HOH 236 ? ? 2.00 4 1 O A HOH 191 ? ? O A HOH 224 ? ? 2.04 5 1 O A HOH 198 ? ? O A HOH 213 ? ? 2.12 6 1 O A HOH 137 ? ? O A HOH 213 ? ? 2.16 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 179 ? ? 1_555 O A HOH 207 ? ? 2_656 1.62 2 1 O A HOH 207 ? ? 1_555 O A HOH 207 ? ? 2_656 1.69 3 1 O A HOH 158 ? ? 1_555 O A HOH 206 ? ? 3_545 1.73 4 1 O A HOH 159 ? ? 1_555 O A HOH 198 ? ? 4_555 1.85 5 1 O A HOH 182 ? ? 1_555 O A HOH 200 ? ? 2_555 1.97 6 1 O A HOH 193 ? ? 1_555 O A HOH 204 ? ? 3_455 2.03 7 1 O A HOH 201 ? ? 1_555 O A HOH 216 ? ? 3_555 2.06 8 1 O A HOH 211 ? ? 1_555 O A HOH 219 ? ? 2_555 2.07 9 1 O A HOH 224 ? ? 1_555 O A HOH 231 ? ? 2_555 2.10 # 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 "O5'" A DC 1 ? B "C5'" A DC 1 ? B 1.242 1.418 -0.176 0.025 N 2 1 "C5'" A DC 1 ? B "C4'" A DC 1 ? B 1.574 1.512 0.062 0.007 N 3 1 "C4'" A DC 1 ? B "C3'" A DC 1 ? B 1.437 1.521 -0.084 0.010 N 4 1 "O3'" A DC 1 ? B "C3'" A DC 1 ? B 1.514 1.435 0.079 0.013 N 5 1 "O3'" A DC 1 ? A P A DC 2 ? A 1.703 1.607 0.096 0.012 Y 6 1 "O5'" A DC 2 ? A "C5'" A DC 2 ? A 1.600 1.440 0.160 0.016 N 7 1 "O5'" A DC 2 ? B "C5'" A DC 2 ? B 1.557 1.440 0.117 0.016 N 8 1 C4 A DG 4 ? ? C5 A DG 4 ? ? 1.333 1.379 -0.046 0.007 N 9 1 "O3'" A DG 4 ? ? P A DG 5 ? B 1.418 1.607 -0.189 0.012 Y 10 1 C4 A DC 6 ? B C5 A DC 6 ? B 1.494 1.425 0.069 0.008 N 11 1 C2 A DC 7 ? B O2 A DC 7 ? B 1.182 1.240 -0.058 0.009 N 12 1 C8 A DG 9 ? ? N9 A DG 9 ? ? 1.419 1.374 0.045 0.007 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 "O4'" A DC 1 ? A "C1'" A DC 1 ? A N1 A DC 1 ? A 101.82 108.00 -6.18 0.70 N 2 1 "O4'" A DC 1 ? B "C1'" A DC 1 ? B N1 A DC 1 ? B 110.98 108.30 2.68 0.30 N 3 1 N3 A DC 1 ? A C4 A DC 1 ? A C5 A DC 1 ? A 118.90 121.90 -3.00 0.40 N 4 1 C4 A DC 1 ? A C5 A DC 1 ? A C6 A DC 1 ? A 120.98 117.40 3.58 0.50 N 5 1 C6 A DC 2 ? A N1 A DC 2 ? A C2 A DC 2 ? A 117.73 120.30 -2.57 0.40 N 6 1 N3 A DC 2 ? A C4 A DC 2 ? A C5 A DC 2 ? A 118.30 121.90 -3.60 0.40 N 7 1 C5 A DC 2 ? B C6 A DC 2 ? B N1 A DC 2 ? B 117.54 121.00 -3.46 0.50 N 8 1 OP1 A DG 5 ? A P A DG 5 ? A OP2 A DG 5 ? A 109.86 119.60 -9.74 1.50 N 9 1 "O5'" A DG 5 ? B "C5'" A DG 5 ? B "C4'" A DG 5 ? B 102.87 109.40 -6.53 0.80 N 10 1 "C5'" A DG 5 ? B "C4'" A DG 5 ? B "C3'" A DG 5 ? B 130.08 115.70 14.38 1.20 N 11 1 "C5'" A DG 5 ? B "C4'" A DG 5 ? B "O4'" A DG 5 ? B 96.40 109.30 -12.90 1.90 N 12 1 N1 A DG 5 ? B C6 A DG 5 ? B O6 A DG 5 ? B 115.60 119.90 -4.30 0.60 N 13 1 "C3'" A DG 5 ? A "O3'" A DG 5 ? A P A DC 6 ? A 128.64 119.70 8.94 1.20 Y 14 1 OP1 A DC 6 ? A P A DC 6 ? A OP2 A DC 6 ? A 98.68 119.60 -20.92 1.50 N 15 1 "O5'" A DC 6 ? A P A DC 6 ? A OP2 A DC 6 ? A 130.11 110.70 19.41 1.20 N 16 1 "O4'" A DC 6 ? A "C4'" A DC 6 ? A "C3'" A DC 6 ? A 109.83 106.00 3.83 0.60 N 17 1 C2 A DC 6 ? A N3 A DC 6 ? A C4 A DC 6 ? A 123.35 119.90 3.45 0.50 N 18 1 N3 A DC 6 ? A C4 A DC 6 ? A C5 A DC 6 ? A 119.46 121.90 -2.44 0.40 N 19 1 C5 A DC 6 ? A C6 A DC 6 ? A N1 A DC 6 ? A 124.32 121.00 3.32 0.50 N 20 1 N3 A DC 6 ? A C2 A DC 6 ? A O2 A DC 6 ? A 126.34 121.90 4.44 0.70 N 21 1 N3 A DC 6 ? B C4 A DC 6 ? B N4 A DC 6 ? B 122.21 118.00 4.21 0.70 N 22 1 C5 A DC 6 ? B C4 A DC 6 ? B N4 A DC 6 ? B 114.88 120.20 -5.32 0.70 N 23 1 C2 A DC 6 ? A N1 A DC 6 ? A "C1'" A DC 6 ? A 126.24 118.80 7.44 1.10 N 24 1 "C3'" A DC 6 ? A "O3'" A DC 6 ? A P A DC 7 ? A 133.27 119.70 13.57 1.20 Y 25 1 "O5'" A DC 7 ? A P A DC 7 ? A OP2 A DC 7 ? A 100.15 105.70 -5.55 0.90 N 26 1 "O5'" A DC 7 ? B "C5'" A DC 7 ? B "C4'" A DC 7 ? B 102.86 109.40 -6.54 0.80 N 27 1 "C1'" A DC 7 ? B "O4'" A DC 7 ? B "C4'" A DC 7 ? B 103.41 110.10 -6.69 1.00 N 28 1 "O4'" A DC 7 ? A "C1'" A DC 7 ? A N1 A DC 7 ? A 110.11 108.30 1.81 0.30 N 29 1 C6 A DC 7 ? A N1 A DC 7 ? A C2 A DC 7 ? A 117.18 120.30 -3.12 0.40 N 30 1 C2 A DC 7 ? A N3 A DC 7 ? A C4 A DC 7 ? A 124.72 119.90 4.82 0.50 N 31 1 C2 A DC 7 ? B N3 A DC 7 ? B C4 A DC 7 ? B 123.64 119.90 3.74 0.50 N 32 1 N3 A DC 7 ? A C4 A DC 7 ? A C5 A DC 7 ? A 118.95 121.90 -2.95 0.40 N 33 1 "O3'" A DC 7 ? A P A DT 8 ? ? OP2 A DT 8 ? ? 119.43 110.50 8.93 1.10 Y 34 1 N9 A DG 9 ? ? C4 A DG 9 ? ? C5 A DG 9 ? ? 107.89 105.40 2.49 0.40 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA A 3 ? ? 0.061 'SIDE CHAIN' 2 1 DC A 6 ? A 0.072 'SIDE CHAIN' 3 1 DC A 7 ? A 0.072 'SIDE CHAIN' 4 1 DG A 9 ? ? 0.064 'SIDE CHAIN' # 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 CA CA CA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # 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 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3I5E 'double helix' 3I5E '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 A DG 10 2_555 0.044 -0.206 0.065 -5.517 -16.318 2.094 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 2_555 0.158 -0.195 0.084 -2.642 -9.297 -2.603 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 2_555 0.018 -0.125 0.131 0.230 -4.008 1.174 3 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DG 4 1_555 A DC 7 2_555 -0.332 -0.192 0.311 13.520 -9.512 0.492 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DG 5 1_555 A DC 6 2_555 -0.322 0.021 0.859 22.433 -12.642 4.884 5 A_DG5:DC6_A A 5 ? A 6 ? 19 1 1 A DC 6 1_555 A DG 5 2_555 0.322 0.021 0.859 -22.433 -12.642 4.884 6 A_DC6:DG5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 2_555 0.332 -0.192 0.311 -13.520 -9.512 0.492 7 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DT 8 1_555 A DA 3 2_555 -0.018 -0.125 0.131 -0.230 -4.008 1.174 8 A_DT8:DA3_A A 8 ? A 3 ? 20 1 1 A DG 9 1_555 A DC 2 2_555 -0.158 -0.195 0.084 2.642 -9.297 -2.603 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 2_555 -0.044 -0.206 0.065 5.517 -16.318 2.094 10 A_DG10:DC1_A A 10 ? A 1 ? 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 A DG 10 2_555 A DC 2 1_555 A DG 9 2_555 -0.575 0.691 3.297 1.819 9.797 27.242 -0.871 1.567 3.297 19.971 -3.709 28.975 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 2_555 A DA 3 1_555 A DT 8 2_555 0.214 2.798 3.264 -0.814 -8.727 50.862 3.769 -0.297 2.778 -10.075 0.939 51.562 2 AA_DC2DA3:DT8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DA 3 1_555 A DT 8 2_555 A DG 4 1_555 A DC 7 2_555 0.663 0.777 3.077 -3.571 9.845 21.526 -1.259 -2.736 2.992 24.574 8.913 23.911 3 AA_DA3DG4:DC7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 2_555 A DG 5 1_555 A DC 6 2_555 -0.343 0.237 2.990 -5.492 -2.959 33.565 0.835 -0.217 2.976 -5.069 9.410 34.123 4 AA_DG4DG5:DC6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DG 5 1_555 A DC 6 2_555 A DC 6 1_555 A DG 5 2_555 0.000 -0.369 4.476 0.000 -4.108 52.383 -0.049 0.000 4.491 -4.645 0.000 52.532 5 AA_DG5DC6:DG5DC6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DC 6 1_555 A DG 5 2_555 A DC 7 1_555 A DG 4 2_555 0.343 0.237 2.990 5.492 -2.958 33.565 0.835 0.217 2.976 -5.069 -9.410 34.123 6 AA_DC6DC7:DG4DG5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 2_555 A DT 8 1_555 A DA 3 2_555 -0.663 0.777 3.077 3.571 9.845 21.526 -1.259 2.736 2.992 24.574 -8.913 23.911 7 AA_DC7DT8:DA3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DT 8 1_555 A DA 3 2_555 A DG 9 1_555 A DC 2 2_555 -0.214 2.798 3.264 0.814 -8.727 50.862 3.769 0.297 2.778 -10.075 -0.939 51.562 8 AA_DT8DG9:DC2DA3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 2_555 A DG 10 1_555 A DC 1 2_555 0.575 0.691 3.297 -1.819 9.797 27.242 -0.871 -1.567 3.297 19.971 3.709 28.975 9 AA_DG9DG10:DC1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # _atom_sites.entry_id 3I5E _atom_sites.fract_transf_matrix[1][1] 0.031420 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.015819 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.039007 _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] 0.032763 _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 CA N O P # loop_