data_403D # _entry.id 403D # _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 403D pdb_0000403d 10.2210/pdb403d/pdb RCSB BDD001 ? ? WWPDB D_1000179204 ? ? # 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 1998-07-06 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' software 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_conn_type 8 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.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_software.name' 11 4 'Structure model' '_struct_conn.conn_type_id' 12 4 'Structure model' '_struct_conn.id' 13 4 'Structure model' '_struct_conn.pdbx_dist_value' 14 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 15 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 17 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 23 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 29 4 'Structure model' '_struct_conn_type.id' 30 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 403D _pdbx_database_status.recvd_initial_deposition_date 1998-06-10 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Robinson, H.' 1 'Gao, Y.-G.' 2 'Bauer, C.' 3 'Roberts, C.' 4 'Switzer, C.' 5 'Wang, A.H.-J.' 6 # _citation.id primary _citation.title ;2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 37 _citation.page_first 10897 _citation.page_last 10905 _citation.year 1998 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9692982 _citation.pdbx_database_id_DOI 10.1021/bi980818l # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Robinson, H.' 1 ? primary 'Gao, Y.G.' 2 ? primary 'Bauer, C.' 3 ? primary 'Roberts, C.' 4 ? primary 'Switzer, C.' 5 ? primary 'Wang, A.H.' 6 ? # 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(*CP*GP*CP*(IGU)P*AP*AP*TP*TP*TP*GP*CP*G)-3') ; 3678.403 2 ? ? ? ? 2 non-polymer syn "2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 452.551 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 128 ? ? ? ? # _entity_keywords.entity_id 2 _entity_keywords.text 'HOECHST 33342' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(IGU)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTTGCG _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 "2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" HT1 3 'MAGNESIUM ION' MG 4 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 DG n 1 3 DC n 1 4 IGU n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DT n 1 10 DG n 1 11 DC n 1 12 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 HT1 non-polymer . "2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 'HOECHST 33342' 'C27 H28 N6 O' 452.551 IGU 'DNA linking' n "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 IGU 4 4 4 IGU +A A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 IGU 4 16 16 IGU +A B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DT 9 21 21 DT T B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HT1 1 25 25 HT1 HT1 A . D 3 MG 1 26 26 MG MO6 A . E 4 HOH 1 1001 1001 HOH HOH A . E 4 HOH 2 1003 1003 HOH HOH A . E 4 HOH 3 1005 1005 HOH HOH A . E 4 HOH 4 1006 1006 HOH HOH A . E 4 HOH 5 1007 1007 HOH HOH A . E 4 HOH 6 1010 1010 HOH HOH A . E 4 HOH 7 1011 1011 HOH HOH A . E 4 HOH 8 1014 1014 HOH HOH A . E 4 HOH 9 1015 1015 HOH HOH A . E 4 HOH 10 1016 1016 HOH HOH A . E 4 HOH 11 1017 1017 HOH HOH A . E 4 HOH 12 1018 1018 HOH HOH A . E 4 HOH 13 1021 1021 HOH HOH A . E 4 HOH 14 1022 1022 HOH HOH A . E 4 HOH 15 1026 1026 HOH HOH A . E 4 HOH 16 1028 1028 HOH HOH A . E 4 HOH 17 1030 1030 HOH HOH A . E 4 HOH 18 1031 1031 HOH HOH A . E 4 HOH 19 1033 1033 HOH HOH A . E 4 HOH 20 1035 1035 HOH HOH A . E 4 HOH 21 1038 1038 HOH HOH A . E 4 HOH 22 1040 1040 HOH HOH A . E 4 HOH 23 1042 1042 HOH HOH A . E 4 HOH 24 1043 1043 HOH HOH A . E 4 HOH 25 1044 1044 HOH HOH A . E 4 HOH 26 1046 1046 HOH HOH A . E 4 HOH 27 1048 1048 HOH HOH A . E 4 HOH 28 1050 1050 HOH HOH A . E 4 HOH 29 1051 1051 HOH HOH A . E 4 HOH 30 1052 1052 HOH HOH A . E 4 HOH 31 1053 1053 HOH HOH A . E 4 HOH 32 1054 1054 HOH HOH A . E 4 HOH 33 1056 1056 HOH HOH A . E 4 HOH 34 1057 1057 HOH HOH A . E 4 HOH 35 1059 1059 HOH HOH A . E 4 HOH 36 1063 1063 HOH HOH A . E 4 HOH 37 1064 1064 HOH HOH A . E 4 HOH 38 1065 1065 HOH HOH A . E 4 HOH 39 1068 1068 HOH HOH A . E 4 HOH 40 1069 1069 HOH HOH A . E 4 HOH 41 1072 1072 HOH HOH A . E 4 HOH 42 1076 1076 HOH HOH A . E 4 HOH 43 1077 1077 HOH HOH A . E 4 HOH 44 1078 1078 HOH HOH A . E 4 HOH 45 1079 1079 HOH HOH A . E 4 HOH 46 1084 1084 HOH HOH A . E 4 HOH 47 1091 1091 HOH HOH A . E 4 HOH 48 1093 1093 HOH HOH A . E 4 HOH 49 1102 1102 HOH HOH A . E 4 HOH 50 1107 1107 HOH HOH A . E 4 HOH 51 1110 1110 HOH HOH A . E 4 HOH 52 1112 1112 HOH HOH A . E 4 HOH 53 1113 1113 HOH HOH A . E 4 HOH 54 1114 1114 HOH HOH A . E 4 HOH 55 1115 1115 HOH HOH A . E 4 HOH 56 1116 1116 HOH HOH A . E 4 HOH 57 1118 1118 HOH HOH A . E 4 HOH 58 1119 1119 HOH HOH A . E 4 HOH 59 1122 1122 HOH HOH A . E 4 HOH 60 1125 1125 HOH HOH A . E 4 HOH 61 1131 1131 HOH HOH A . E 4 HOH 62 1139 26 HOH MO6 A . E 4 HOH 63 1140 26 HOH MO6 A . E 4 HOH 64 1141 26 HOH MO6 A . F 4 HOH 1 1002 1002 HOH HOH B . F 4 HOH 2 1004 1004 HOH HOH B . F 4 HOH 3 1008 1008 HOH HOH B . F 4 HOH 4 1009 1009 HOH HOH B . F 4 HOH 5 1012 1012 HOH HOH B . F 4 HOH 6 1013 1013 HOH HOH B . F 4 HOH 7 1019 1019 HOH HOH B . F 4 HOH 8 1020 1020 HOH HOH B . F 4 HOH 9 1023 1023 HOH HOH B . F 4 HOH 10 1024 1024 HOH HOH B . F 4 HOH 11 1025 1025 HOH HOH B . F 4 HOH 12 1027 1027 HOH HOH B . F 4 HOH 13 1029 1029 HOH HOH B . F 4 HOH 14 1032 1032 HOH HOH B . F 4 HOH 15 1034 1034 HOH HOH B . F 4 HOH 16 1036 1036 HOH HOH B . F 4 HOH 17 1037 1037 HOH HOH B . F 4 HOH 18 1039 1039 HOH HOH B . F 4 HOH 19 1041 1041 HOH HOH B . F 4 HOH 20 1045 1045 HOH HOH B . F 4 HOH 21 1047 1047 HOH HOH B . F 4 HOH 22 1049 1049 HOH HOH B . F 4 HOH 23 1055 1055 HOH HOH B . F 4 HOH 24 1058 1058 HOH HOH B . F 4 HOH 25 1060 1060 HOH HOH B . F 4 HOH 26 1061 1061 HOH HOH B . F 4 HOH 27 1062 1062 HOH HOH B . F 4 HOH 28 1067 1067 HOH HOH B . F 4 HOH 29 1070 1070 HOH HOH B . F 4 HOH 30 1073 1073 HOH HOH B . F 4 HOH 31 1074 1074 HOH HOH B . F 4 HOH 32 1075 1075 HOH HOH B . F 4 HOH 33 1080 1080 HOH HOH B . F 4 HOH 34 1082 1082 HOH HOH B . F 4 HOH 35 1086 1086 HOH HOH B . F 4 HOH 36 1087 1087 HOH HOH B . F 4 HOH 37 1089 1089 HOH HOH B . F 4 HOH 38 1090 1090 HOH HOH B . F 4 HOH 39 1092 1092 HOH HOH B . F 4 HOH 40 1094 1094 HOH HOH B . F 4 HOH 41 1096 1096 HOH HOH B . F 4 HOH 42 1097 1097 HOH HOH B . F 4 HOH 43 1098 1098 HOH HOH B . F 4 HOH 44 1099 1099 HOH HOH B . F 4 HOH 45 1100 1100 HOH HOH B . F 4 HOH 46 1101 1101 HOH HOH B . F 4 HOH 47 1103 1103 HOH HOH B . F 4 HOH 48 1105 1105 HOH HOH B . F 4 HOH 49 1106 1106 HOH HOH B . F 4 HOH 50 1108 1108 HOH HOH B . F 4 HOH 51 1109 1109 HOH HOH B . F 4 HOH 52 1111 1111 HOH HOH B . F 4 HOH 53 1117 1117 HOH HOH B . F 4 HOH 54 1120 1120 HOH HOH B . F 4 HOH 55 1124 1124 HOH HOH B . F 4 HOH 56 1126 1126 HOH HOH B . F 4 HOH 57 1130 1130 HOH HOH B . F 4 HOH 58 1132 1132 HOH HOH B . F 4 HOH 59 1134 1134 HOH HOH B . F 4 HOH 60 1136 1136 HOH HOH B . F 4 HOH 61 1137 1137 HOH HOH B . F 4 HOH 62 1138 26 HOH MO6 B . F 4 HOH 63 1142 26 HOH MO6 B . F 4 HOH 64 1143 26 HOH MO6 B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 bioteX 'data reduction' . ? 2 bioteX 'data scaling' . ? 3 # _cell.entry_id 403D _cell.length_a 25.759 _cell.length_b 41.084 _cell.length_c 64.307 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 403D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 403D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.14 _exptl_crystal.density_percent_sol 52.0000 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 'SODIUM CACODYLATE' ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 123.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1997-08-27 _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 . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 403D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 1.400 _reflns.number_obs 11253 _reflns.number_all 11253 _reflns.percent_possible_obs 80.300 _reflns.pdbx_Rmerge_I_obs 0.053 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.000 _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.entry_id 403D _refine.ls_number_reflns_obs 11253 _refine.ls_number_reflns_all 11253 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 1.400 _refine.ls_percent_reflns_obs 80.300 _refine.ls_R_factor_obs 0.242 _refine.ls_R_factor_all 0.245 _refine.ls_R_factor_R_work 0.245 _refine.ls_R_factor_R_free 0.316 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 564 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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_ls_cross_valid_method R-FREE _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ISOTROPIC _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_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 488 _refine_hist.pdbx_number_atoms_ligand 35 _refine_hist.number_atoms_solvent 128 _refine_hist.number_atoms_total 651 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 403D _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.219 _pdbx_refine.R_factor_obs_4sig_cutoff 0.216 _pdbx_refine.free_R_factor_4sig_cutoff 0.296 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.00 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 446.00 _pdbx_refine.number_reflns_obs_4sig_cutoff 8608 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 403D _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 403D _struct.title ;5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 403D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA-DRUG COMPLEX, B-DNA 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 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 403D _struct_ref.pdbx_db_accession 403D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 403D A 1 ? 12 ? 403D 1 ? 12 ? 1 12 2 1 403D B 1 ? 12 ? 403D 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DC 3 "O3'" ? ? ? 1_555 A IGU 4 P ? ? A DC 3 A IGU 4 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale2 covale both ? A IGU 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A IGU 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale3 covale both ? B DC 3 "O3'" ? ? ? 1_555 B IGU 4 P ? ? B DC 15 B IGU 16 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale4 covale both ? B IGU 4 "O3'" ? ? ? 1_555 B DA 5 P ? ? B IGU 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.611 ? ? metalc1 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 1139 1_555 ? ? ? ? ? ? ? 2.052 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 1140 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 26 A HOH 1141 1_555 ? ? ? ? ? ? ? 2.063 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 26 B HOH 1138 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 26 B HOH 1142 1_555 ? ? ? ? ? ? ? 2.086 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 26 B HOH 1143 1_555 ? ? ? ? ? ? ? 2.045 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B IGU 4 N1 ? ? A DT 9 B IGU 16 1_555 ? ? ? ? ? ? 'DT-IGU MISPAIR' ? ? ? hydrog19 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 ? E HOH . ? A HOH 1139 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 1140 ? 1_555 91.9 ? 2 O ? E HOH . ? A HOH 1139 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 1141 ? 1_555 90.8 ? 3 O ? E HOH . ? A HOH 1140 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? E HOH . ? A HOH 1141 ? 1_555 88.8 ? 4 O ? E HOH . ? A HOH 1139 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1138 ? 1_555 176.3 ? 5 O ? E HOH . ? A HOH 1140 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1138 ? 1_555 91.7 ? 6 O ? E HOH . ? A HOH 1141 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1138 ? 1_555 90.1 ? 7 O ? E HOH . ? A HOH 1139 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1142 ? 1_555 87.2 ? 8 O ? E HOH . ? A HOH 1140 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1142 ? 1_555 179.1 ? 9 O ? E HOH . ? A HOH 1141 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1142 ? 1_555 90.9 ? 10 O ? F HOH . ? B HOH 1138 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1142 ? 1_555 89.2 ? 11 O ? E HOH . ? A HOH 1139 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1143 ? 1_555 89.6 ? 12 O ? E HOH . ? A HOH 1140 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1143 ? 1_555 90.5 ? 13 O ? E HOH . ? A HOH 1141 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1143 ? 1_555 179.2 ? 14 O ? F HOH . ? B HOH 1138 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1143 ? 1_555 89.6 ? 15 O ? F HOH . ? B HOH 1142 ? 1_555 MG ? D MG . ? A MG 26 ? 1_555 O ? F HOH . ? B HOH 1143 ? 1_555 89.8 ? # 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 HT1 25 ? 15 'BINDING SITE FOR RESIDUE HT1 A 25' AC2 Software A MG 26 ? 6 'BINDING SITE FOR RESIDUE MG A 26' 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 15 IGU A 4 ? IGU A 4 . ? 1_555 ? 2 AC1 15 DA A 5 ? DA A 5 . ? 1_555 ? 3 AC1 15 DA A 6 ? DA A 6 . ? 1_555 ? 4 AC1 15 DT A 7 ? DT A 7 . ? 1_555 ? 5 AC1 15 DT A 8 ? DT A 8 . ? 1_555 ? 6 AC1 15 DT A 9 ? DT A 9 . ? 1_555 ? 7 AC1 15 DG A 12 ? DG A 12 . ? 2_565 ? 8 AC1 15 HOH E . ? HOH A 1035 . ? 1_555 ? 9 AC1 15 HOH E . ? HOH A 1072 . ? 1_555 ? 10 AC1 15 HOH E . ? HOH A 1093 . ? 1_555 ? 11 AC1 15 DA B 6 ? DA B 18 . ? 1_555 ? 12 AC1 15 DT B 7 ? DT B 19 . ? 1_555 ? 13 AC1 15 DT B 8 ? DT B 20 . ? 1_555 ? 14 AC1 15 DT B 9 ? DT B 21 . ? 1_555 ? 15 AC1 15 HOH F . ? HOH B 1101 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 1139 . ? 1_555 ? 17 AC2 6 HOH E . ? HOH A 1140 . ? 1_555 ? 18 AC2 6 HOH E . ? HOH A 1141 . ? 1_555 ? 19 AC2 6 HOH F . ? HOH B 1138 . ? 1_555 ? 20 AC2 6 HOH F . ? HOH B 1142 . ? 1_555 ? 21 AC2 6 HOH F . ? HOH B 1143 . ? 1_555 ? # 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 C6 A DG 2 ? ? O6 A DG 2 ? ? 1.333 1.237 0.096 0.009 N 2 1 C6 A DG 10 ? ? O6 A DG 10 ? ? 1.331 1.237 0.094 0.009 N 3 1 C6 A DG 12 ? ? O6 A DG 12 ? ? 1.326 1.237 0.089 0.009 N 4 1 C6 B DG 14 ? ? O6 B DG 14 ? ? 1.319 1.237 0.082 0.009 N 5 1 C6 B DG 22 ? ? O6 B DG 22 ? ? 1.331 1.237 0.094 0.009 N 6 1 C6 B DG 24 ? ? O6 B DG 24 ? ? 1.316 1.237 0.079 0.009 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 DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 100.99 108.00 -7.01 0.70 N 2 1 "C3'" A DC 3 ? ? "O3'" A DC 3 ? ? P A IGU 4 ? ? 127.08 119.70 7.38 1.20 Y 3 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 102.15 108.00 -5.85 0.70 N 4 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? 104.37 109.40 -5.03 0.80 N 5 1 "C1'" A DT 7 ? ? "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? 103.10 110.10 -7.00 1.00 N 6 1 "O4'" A DC 11 ? ? "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? 99.44 104.50 -5.06 0.40 N 7 1 N3 A DG 12 ? ? C2 A DG 12 ? ? N2 A DG 12 ? ? 124.36 119.90 4.46 0.70 N 8 1 N1 B DC 13 ? ? C2 B DC 13 ? ? O2 B DC 13 ? ? 123.24 118.90 4.34 0.60 N 9 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P B DG 14 ? ? 111.80 119.70 -7.90 1.20 Y 10 1 C6 B DC 15 ? ? N1 B DC 15 ? ? C2 B DC 15 ? ? 117.73 120.30 -2.57 0.40 N 11 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? "C2'" B DG 24 ? ? 110.68 106.80 3.88 0.50 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 DC A 3 ? ? 0.061 'SIDE CHAIN' 2 1 DA A 5 ? ? 0.052 'SIDE CHAIN' 3 1 DT A 7 ? ? 0.073 'SIDE CHAIN' 4 1 DC A 11 ? ? 0.123 'SIDE CHAIN' 5 1 DG B 14 ? ? 0.058 'SIDE CHAIN' 6 1 DA B 17 ? ? 0.060 'SIDE CHAIN' 7 1 DT B 21 ? ? 0.078 'SIDE CHAIN' 8 1 DC B 23 ? ? 0.097 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A IGU 4 A IGU 4 ? DG "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" 2 B IGU 4 B IGU 16 ? DG "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 HT1 C1 C Y N 147 HT1 O1 O N N 148 HT1 C2 C Y N 149 HT1 C3 C Y N 150 HT1 C4 C Y N 151 HT1 C5 C Y N 152 HT1 C6 C Y N 153 HT1 C7 C Y N 154 HT1 N1 N Y N 155 HT1 C8 C Y N 156 HT1 C9 C Y N 157 HT1 N2 N Y N 158 HT1 C10 C Y N 159 HT1 C11 C Y N 160 HT1 C12 C Y N 161 HT1 C13 C Y N 162 HT1 C14 C Y N 163 HT1 N3 N Y N 164 HT1 C15 C Y N 165 HT1 C16 C Y N 166 HT1 N4 N Y N 167 HT1 C17 C Y N 168 HT1 C18 C Y N 169 HT1 C19 C Y N 170 HT1 C20 C Y N 171 HT1 N5 N N N 172 HT1 C21 C N N 173 HT1 C22 C N N 174 HT1 N6 N N N 175 HT1 C23 C N N 176 HT1 C24 C N N 177 HT1 C25 C N N 178 HT1 C26 C N N 179 HT1 C27 C N N 180 HT1 H2 H N N 181 HT1 H3 H N N 182 HT1 H5 H N N 183 HT1 H6 H N N 184 HT1 HN1 H N N 185 HT1 H10 H N N 186 HT1 H11 H N N 187 HT1 H13 H N N 188 HT1 HN3 H N N 189 HT1 H17 H N N 190 HT1 H18 H N N 191 HT1 H20 H N N 192 HT1 H211 H N N 193 HT1 H212 H N N 194 HT1 H221 H N N 195 HT1 H222 H N N 196 HT1 H231 H N N 197 HT1 H232 H N N 198 HT1 H241 H N N 199 HT1 H242 H N N 200 HT1 H251 H N N 201 HT1 H252 H N N 202 HT1 H253 H N N 203 HT1 H261 H N N 204 HT1 H262 H N N 205 HT1 H271 H N N 206 HT1 H272 H N N 207 HT1 H273 H N N 208 IGU P P N N 209 IGU OP1 O N N 210 IGU OP2 O N N 211 IGU OP3 O N N 212 IGU "O5'" O N N 213 IGU "C5'" C N N 214 IGU "C4'" C N R 215 IGU "O4'" O N N 216 IGU "C3'" C N S 217 IGU "O3'" O N N 218 IGU "C2'" C N N 219 IGU "C1'" C N R 220 IGU N9 N N N 221 IGU C8 C N N 222 IGU N7 N N N 223 IGU C6 C N N 224 IGU N6 N N N 225 IGU C5 C N N 226 IGU N1 N N N 227 IGU C2 C N N 228 IGU O2 O N N 229 IGU N3 N N N 230 IGU C4 C N N 231 IGU HOP2 H N N 232 IGU HOP3 H N N 233 IGU "H5'" H N N 234 IGU "H5''" H N N 235 IGU "H4'" H N N 236 IGU "H3'" H N N 237 IGU "HO3'" H N N 238 IGU "H2'" H N N 239 IGU "H2''" H N N 240 IGU "H1'" H N N 241 IGU H8 H N N 242 IGU HN61 H N N 243 IGU HN62 H N N 244 IGU HN1 H N N 245 MG MG MG N N 246 # 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 HT1 C1 O1 sing N N 152 HT1 C1 C2 doub Y N 153 HT1 C1 C6 sing Y N 154 HT1 O1 C26 sing N N 155 HT1 C2 C3 sing Y N 156 HT1 C2 H2 sing N N 157 HT1 C3 C4 doub Y N 158 HT1 C3 H3 sing N N 159 HT1 C4 C5 sing Y N 160 HT1 C4 C7 sing Y N 161 HT1 C5 C6 doub Y N 162 HT1 C5 H5 sing N N 163 HT1 C6 H6 sing N N 164 HT1 C7 N1 sing Y N 165 HT1 C7 N2 doub Y N 166 HT1 N1 C8 sing Y N 167 HT1 N1 HN1 sing N N 168 HT1 C8 C9 doub Y N 169 HT1 C8 C13 sing Y N 170 HT1 C9 N2 sing Y N 171 HT1 C9 C10 sing Y N 172 HT1 C10 C11 doub Y N 173 HT1 C10 H10 sing N N 174 HT1 C11 C12 sing Y N 175 HT1 C11 H11 sing N N 176 HT1 C12 C13 doub Y N 177 HT1 C12 C14 sing Y N 178 HT1 C13 H13 sing N N 179 HT1 C14 N3 sing Y N 180 HT1 C14 N4 doub Y N 181 HT1 N3 C15 sing Y N 182 HT1 N3 HN3 sing N N 183 HT1 C15 C16 doub Y N 184 HT1 C15 C20 sing Y N 185 HT1 C16 N4 sing Y N 186 HT1 C16 C17 sing Y N 187 HT1 C17 C18 doub Y N 188 HT1 C17 H17 sing N N 189 HT1 C18 C19 sing Y N 190 HT1 C18 H18 sing N N 191 HT1 C19 C20 doub Y N 192 HT1 C19 N5 sing N N 193 HT1 C20 H20 sing N N 194 HT1 N5 C21 sing N N 195 HT1 N5 C24 sing N N 196 HT1 C21 C22 sing N N 197 HT1 C21 H211 sing N N 198 HT1 C21 H212 sing N N 199 HT1 C22 N6 sing N N 200 HT1 C22 H221 sing N N 201 HT1 C22 H222 sing N N 202 HT1 N6 C23 sing N N 203 HT1 N6 C25 sing N N 204 HT1 C23 C24 sing N N 205 HT1 C23 H231 sing N N 206 HT1 C23 H232 sing N N 207 HT1 C24 H241 sing N N 208 HT1 C24 H242 sing N N 209 HT1 C25 H251 sing N N 210 HT1 C25 H252 sing N N 211 HT1 C25 H253 sing N N 212 HT1 C26 C27 sing N N 213 HT1 C26 H261 sing N N 214 HT1 C26 H262 sing N N 215 HT1 C27 H271 sing N N 216 HT1 C27 H272 sing N N 217 HT1 C27 H273 sing N N 218 IGU P OP1 doub N N 219 IGU P OP2 sing N N 220 IGU P OP3 sing N N 221 IGU P "O5'" sing N N 222 IGU OP2 HOP2 sing N N 223 IGU OP3 HOP3 sing N N 224 IGU "O5'" "C5'" sing N N 225 IGU "C5'" "C4'" sing N N 226 IGU "C5'" "H5'" sing N N 227 IGU "C5'" "H5''" sing N N 228 IGU "C4'" "O4'" sing N N 229 IGU "C4'" "C3'" sing N N 230 IGU "C4'" "H4'" sing N N 231 IGU "O4'" "C1'" sing N N 232 IGU "C3'" "O3'" sing N N 233 IGU "C3'" "C2'" sing N N 234 IGU "C3'" "H3'" sing N N 235 IGU "O3'" "HO3'" sing N N 236 IGU "C2'" "C1'" sing N N 237 IGU "C2'" "H2'" sing N N 238 IGU "C2'" "H2''" sing N N 239 IGU "C1'" N9 sing N N 240 IGU "C1'" "H1'" sing N N 241 IGU N9 C8 sing N N 242 IGU N9 C4 sing N N 243 IGU C8 N7 doub N N 244 IGU C8 H8 sing N N 245 IGU N7 C5 sing N N 246 IGU C6 N6 sing N N 247 IGU C6 C5 doub N N 248 IGU C6 N1 sing N N 249 IGU N6 HN61 sing N N 250 IGU N6 HN62 sing N N 251 IGU C5 C4 sing N N 252 IGU N1 C2 sing N N 253 IGU C2 O2 doub N N 254 IGU C2 N3 sing N N 255 IGU N3 C4 doub N N 256 IGU N1 HN1 sing N N 257 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 403D 'double helix' 403D 'b-form double helix' 403D 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.172 -0.244 0.086 -0.407 -11.453 -3.207 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.255 -0.108 -0.121 -12.093 -15.990 -1.256 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.046 -0.183 0.005 -6.852 -4.206 1.628 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.255 -0.127 -0.126 4.946 -18.626 7.704 4 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.116 -0.151 0.092 -0.469 -20.982 8.543 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.058 -0.132 -0.074 -2.912 -21.667 5.210 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.064 -0.154 -0.023 -9.201 -13.928 2.077 7 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DT 9 1_555 B IGU 4 1_555 -2.024 -0.171 -0.148 -7.997 -15.385 -3.740 8 A_DT9:IGU16_B A 9 ? B 16 ? ? ? 1 A DG 10 1_555 B DC 3 1_555 -0.287 -0.250 -0.038 -5.475 -4.965 1.580 9 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.377 -0.305 0.402 -2.381 -13.930 0.228 10 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.132 0.078 0.106 -4.093 -8.163 4.177 11 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 0.464 0.268 3.560 2.820 7.155 34.227 -0.740 -0.303 3.568 11.970 -4.718 35.056 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 1.154 0.330 3.121 0.583 -1.733 39.307 0.686 -1.648 3.120 -2.575 -0.866 39.348 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DA 5 1_555 B DT 8 1_555 -0.272 1.063 6.414 2.633 5.108 67.172 0.569 0.445 6.458 4.608 -2.375 67.388 3 AA_DC3DA5:DT20DG22_BB A 3 ? B 22 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.241 -0.124 3.305 -3.229 2.500 35.013 -0.578 -0.880 3.254 4.138 5.345 35.243 4 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.028 -0.547 3.228 1.113 0.872 33.545 -1.088 0.229 3.211 1.510 -1.928 33.574 5 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.159 -0.297 3.385 1.766 2.382 34.503 -0.876 0.547 3.346 4.006 -2.970 34.626 6 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DT 9 1_555 B IGU 4 1_555 0.106 0.511 3.217 2.803 -5.040 35.494 1.529 0.218 3.117 -8.200 -4.560 35.944 7 AA_DT8DT9:IGU16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DT 9 1_555 B IGU 4 1_555 A DG 10 1_555 B DC 3 1_555 0.249 0.772 3.458 -3.343 6.054 32.970 0.273 -1.016 3.500 10.523 5.811 33.668 8 AA_DT9DG10:DC15IGU16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.653 0.854 3.279 -3.450 -8.718 44.142 1.887 0.546 3.105 -11.447 4.529 45.077 9 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.099 0.585 3.351 3.105 1.472 34.651 0.747 0.322 3.368 2.464 -5.196 34.816 10 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 403D _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.038821 _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] 0.024340 _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] 0.015550 _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 O P # loop_