data_3CCO # _model_server_result.job_id IGJmaryqzbBxYYz5ryYmLg _model_server_result.datetime_utc '2024-10-15 04:32:22' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3cco # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 3CCO # _exptl.entry_id 3CCO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 582.691 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3-hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3CCO _cell.length_a 61.35 _cell.length_b 61.35 _cell.length_c 43.63 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CCO _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_564 x,x-y+1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -30.675 53.130659 -14.543333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 B NA NA . A NA 4 1_555 A O4' DG 11 A DG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc2 C K K . A K 30 1_555 A O6 DG 4 A DG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? metalc ? metalc3 C K K . A K 30 1_555 A O6 DG 5 A DG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc4 C K K . A K 30 1_555 A O6 DG 11 A DG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc5 D K K . A K 31 1_555 A O6 DG 3 A DG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? metalc ? metalc6 D K K . A K 31 1_555 A O6 DG 9 A DG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc7 E K K . A K 32 1_555 A O6 DG 3 A DG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc8 E K K . A K 32 1_555 A O6 DG 9 A DG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? hydrog TYPE_11_PAIR hydrog1 A N2 DG 3 A DG 1003 1_555 A N7 DA 8 A DA 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog2 A N3 DG 3 A DG 1003 1_555 A N6 DA 8 A DA 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog3 A N1 DG 3 A DG 1003 1_555 A O6 DG 9 A DG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog4 A N2 DG 3 A DG 1003 1_555 A N7 DG 9 A DG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog5 A N1 DG 4 A DG 1004 1_555 A O6 DG 10 A DG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog6 A N2 DG 4 A DG 1004 1_555 A N7 DG 10 A DG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog7 A N1 DG 5 A DG 1005 1_555 A O6 DG 11 A DG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog8 A N2 DG 5 A DG 1005 1_555 A N7 DG 11 A DG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C30 H42 N6 O6' _chem_comp.formula_weight 582.691 _chem_comp.id NII _chem_comp.mon_nstd_flag . _chem_comp.name 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3-hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O6 C30 NII sing 117 n n C30 C29 NII sing 118 n n C29 C28 NII sing 119 n n C28 N3 NII sing 120 n n N3 C9 NII sing 121 n n C9 C8 NII sing 122 n y C9 C10 NII doub 123 n y C8 C7 NII doub 124 n y C7 C14 NII sing 125 n n C7 C4 NII sing 126 n y C14 O1 NII doub 127 n n C14 N2 NII sing 128 n n N2 C18 NII sing 129 n n N2 C13 NII sing 130 n n C18 C19 NII sing 131 n n C19 C20 NII sing 132 n n C20 N5 NII sing 133 n n N5 C24 NII sing 134 n n N5 C23 NII sing 135 n n C13 O4 NII doub 136 n n C13 C3 NII sing 137 n n C10 C11 NII sing 138 n n C10 C5 NII sing 139 n y C11 O2 NII doub 140 n n C11 N1 NII sing 141 n n N1 C15 NII sing 142 n n N1 C12 NII sing 143 n n C15 C16 NII sing 144 n n C16 C17 NII sing 145 n n C17 N4 NII sing 146 n n N4 C21 NII sing 147 n n N4 C22 NII sing 148 n n C5 C6 NII doub 149 n y C5 C4 NII sing 150 n y C6 C12 NII sing 151 n n C6 C1 NII sing 152 n y C12 O3 NII doub 153 n n C4 C3 NII doub 154 n y C3 C2 NII sing 155 n y C2 C1 NII doub 156 n y C2 N6 NII sing 157 n n N6 C25 NII sing 158 n n C25 C26 NII sing 159 n n C26 C27 NII sing 160 n n C27 O5 NII sing 161 n n O6 HO6 NII sing 162 n n C30 H30 NII sing 163 n n C30 H30A NII sing 164 n n C29 H29 NII sing 165 n n C29 H29A NII sing 166 n n C28 H28 NII sing 167 n n C28 H28A NII sing 168 n n N3 HN3 NII sing 169 n n C8 H8 NII sing 170 n n C18 H18 NII sing 171 n n C18 H18A NII sing 172 n n C19 H19 NII sing 173 n n C19 H19A NII sing 174 n n C20 H20 NII sing 175 n n C20 H20A NII sing 176 n n C24 H24 NII sing 177 n n C24 H24A NII sing 178 n n C24 H24B NII sing 179 n n C23 H23 NII sing 180 n n C23 H23A NII sing 181 n n C23 H23B NII sing 182 n n C15 H15 NII sing 183 n n C15 H15A NII sing 184 n n C16 H16 NII sing 185 n n C16 H16A NII sing 186 n n C17 H17 NII sing 187 n n C17 H17A NII sing 188 n n C21 H21 NII sing 189 n n C21 H21A NII sing 190 n n C21 H21B NII sing 191 n n C22 H22 NII sing 192 n n C22 H22A NII sing 193 n n C22 H22B NII sing 194 n n C1 H1 NII sing 195 n n N6 HN6 NII sing 196 n n C25 H25 NII sing 197 n n C25 H25A NII sing 198 n n C26 H26 NII sing 199 n n C26 H26A NII sing 200 n n C27 H27 NII sing 201 n n C27 H27A NII sing 202 n n O5 HO5 NII sing 203 n n # _atom_sites.entry_id 3CCO _atom_sites.fract_transf_matrix[1][1] 0.0163 _atom_sites.fract_transf_matrix[1][2] 0.009411 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018822 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.02292 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 NA A 1 4 1 NA NA . C 3 K A 1 30 30 K K . D 3 K A 1 31 31 K K . E 3 K A 1 32 32 K K . F 4 NII A 1 1 1 NII P10 . G 4 NII A 1 2 2 NII P10 . H 4 NII A 1 3 3 NII P10 . I 5 HOH A 1 1013 2 HOH HOH . I 5 HOH A 2 1014 3 HOH HOH . I 5 HOH A 3 1015 4 HOH HOH . I 5 HOH A 4 1016 5 HOH HOH . I 5 HOH A 5 1017 6 HOH HOH . I 5 HOH A 6 1018 7 HOH HOH . I 5 HOH A 7 1019 8 HOH HOH . I 5 HOH A 8 1020 9 HOH HOH . I 5 HOH A 9 1021 10 HOH HOH . I 5 HOH A 10 1022 11 HOH HOH . I 5 HOH A 11 1023 12 HOH HOH . I 5 HOH A 12 1024 13 HOH HOH . I 5 HOH A 13 1025 14 HOH HOH . I 5 HOH A 14 1026 15 HOH HOH . I 5 HOH A 15 1027 16 HOH HOH . I 5 HOH A 16 1028 17 HOH HOH . I 5 HOH A 17 1029 18 HOH HOH . I 5 HOH A 18 1030 19 HOH HOH . I 5 HOH A 19 1031 20 HOH HOH . I 5 HOH A 20 1032 21 HOH HOH . I 5 HOH A 21 1033 22 HOH HOH . I 5 HOH A 22 1034 23 HOH HOH . I 5 HOH A 23 1035 24 HOH HOH . I 5 HOH A 24 1036 25 HOH HOH . I 5 HOH A 25 1037 26 HOH HOH . I 5 HOH A 26 1038 27 HOH HOH . I 5 HOH A 27 1039 28 HOH HOH . I 5 HOH A 28 1040 29 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O6 NII . . . F 4 -26.346 17.5 -0.091 0.5 32.32 ? O6 NII 1 A 1 HETATM 2 C C30 NII . . . F 4 -26.792 18.413 -1.101 0.5 32.23 ? C30 NII 1 A 1 HETATM 3 C C29 NII . . . F 4 -25.858 18.381 -2.313 0.5 28.48 ? C29 NII 1 A 1 HETATM 4 C C28 NII . . . F 4 -24.846 19.537 -2.482 0.5 24.32 ? C28 NII 1 A 1 HETATM 5 N N3 NII . . . F 4 -24.524 19.125 -3.827 0.5 23.96 ? N3 NII 1 A 1 HETATM 6 C C9 NII . . . F 4 -24.816 19.667 -5.038 0.5 23.3 ? C9 NII 1 A 1 HETATM 7 C C8 NII . . . F 4 -24.323 18.826 -5.969 0.5 22.02 ? C8 NII 1 A 1 HETATM 8 C C7 NII . . . F 4 -24.454 19.14 -7.288 0.5 22.71 ? C7 NII 1 A 1 HETATM 9 C C14 NII . . . F 4 -23.941 18.223 -8.133 0.5 23.38 ? C14 NII 1 A 1 HETATM 10 O O1 NII . . . F 4 -23.404 17.194 -7.654 0.5 24.25 ? O1 NII 1 A 1 HETATM 11 N N2 NII . . . F 4 -24.027 18.396 -9.432 0.5 23.25 ? N2 NII 1 A 1 HETATM 12 C C18 NII . . . F 4 -23.437 17.313 -10.244 0.5 23.94 ? C18 NII 1 A 1 HETATM 13 C C19 NII . . . F 4 -22.902 16.186 -9.351 0.5 25.4 ? C19 NII 1 A 1 HETATM 14 C C20 NII . . . F 4 -22.541 14.913 -10.128 0.5 28.34 ? C20 NII 1 A 1 HETATM 15 N N5 NII . . . F 4 -21.272 14.32 -9.64 0.5 28.78 ? N5 NII 1 A 1 HETATM 16 C C24 NII . . . F 4 -21.501 13.584 -8.389 0.5 29.25 ? C24 NII 1 A 1 HETATM 17 C C23 NII . . . F 4 -20.754 13.375 -10.649 0.5 29.55 ? C23 NII 1 A 1 HETATM 18 C C13 NII . . . F 4 -24.628 19.491 -9.96 0.5 23.7 ? C13 NII 1 A 1 HETATM 19 O O4 NII . . . F 4 -24.664 19.578 -11.214 0.5 24.43 ? O4 NII 1 A 1 HETATM 20 C C10 NII . . . F 4 -25.449 20.855 -5.453 0.5 23.47 ? C10 NII 1 A 1 HETATM 21 C C11 NII . . . F 4 -25.967 21.755 -4.557 0.5 23.86 ? C11 NII 1 A 1 HETATM 22 O O2 NII . . . F 4 -25.821 21.45 -3.356 0.5 24.03 ? O2 NII 1 A 1 HETATM 23 N N1 NII . . . F 4 -26.585 22.889 -4.959 0.5 23.26 ? N1 NII 1 A 1 HETATM 24 C C15 NII . . . F 4 -27.139 23.806 -3.934 0.5 24.27 ? C15 NII 1 A 1 HETATM 25 C C16 NII . . . F 4 -27.578 25.169 -4.486 0.5 28.81 ? C16 NII 1 A 1 HETATM 26 C C17 NII . . . F 4 -29.079 25.434 -4.37 0.5 32.08 ? C17 NII 1 A 1 HETATM 27 N N4 NII . . . F 4 -29.386 26.645 -5.155 0.5 33.47 ? N4 NII 1 A 1 HETATM 28 C C21 NII . . . F 4 -29.792 26.259 -6.515 0.5 33.26 ? C21 NII 1 A 1 HETATM 29 C C22 NII . . . F 4 -30.457 27.433 -4.517 0.5 35.49 ? C22 NII 1 A 1 HETATM 30 C C5 NII . . . F 4 -25.585 21.156 -6.812 0.5 23.39 ? C5 NII 1 A 1 HETATM 31 C C6 NII . . . F 4 -26.215 22.316 -7.222 0.5 22.53 ? C6 NII 1 A 1 HETATM 32 C C12 NII . . . F 4 -26.715 23.178 -6.257 0.5 23.1 ? C12 NII 1 A 1 HETATM 33 O O3 NII . . . F 4 -27.314 24.231 -6.576 0.5 23.96 ? O3 NII 1 A 1 HETATM 34 C C4 NII . . . F 4 -25.081 20.273 -7.757 0.5 23.38 ? C4 NII 1 A 1 HETATM 35 C C3 NII . . . F 4 -25.191 20.493 -9.133 0.5 23.47 ? C3 NII 1 A 1 HETATM 36 C C2 NII . . . F 4 -25.859 21.681 -9.525 0.5 23.29 ? C2 NII 1 A 1 HETATM 37 C C1 NII . . . F 4 -26.355 22.564 -8.575 0.5 21.94 ? C1 NII 1 A 1 HETATM 38 N N6 NII . . . F 4 -26.121 22.184 -10.752 0.5 24.23 ? N6 NII 1 A 1 HETATM 39 C C25 NII . . . F 4 -25.849 21.686 -12.074 0.5 24.33 ? C25 NII 1 A 1 HETATM 40 C C26 NII . . . F 4 -27.24 21.922 -12.663 0.5 28.25 ? C26 NII 1 A 1 HETATM 41 C C27 NII . . . F 4 -27.701 20.751 -13.529 0.5 31.26 ? C27 NII 1 A 1 HETATM 42 O O5 NII . . . F 4 -27.406 20.984 -14.913 0.5 30.07 ? O5 NII 1 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 537 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 42 #