data_7EDT # _model_server_result.job_id 1ZjEfw3sm44lJxJj9X9UnQ _model_server_result.datetime_utc '2024-12-04 09:26:11' _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 7edt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 7EDT # _exptl.entry_id 7EDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 93.85 _cell.angle_beta 106.02 _cell.angle_gamma 103.21 _cell.entry_id 7EDT _cell.length_a 24.296 _cell.length_b 24.852 _cell.length_c 28.249 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A O3' G 9 A G 9 1_555 A P 5BU 10 A 5BU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale2 A O3' 5BU 10 A 5BU 10 1_555 A P C 11 A C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale3 B O3' G 9 B G 21 1_555 B P 5BU 10 B 5BU 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale4 B O3' 5BU 10 B 5BU 22 1_555 B P C 11 B C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? metalc ? metalc1 A O2' C 6 A C 6 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc2 A OP2 C 7 A C 7 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 A O6 G 8 A G 8 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc4 D NA NA . A NA 402 1_555 E O HOH . A HOH 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc5 D NA NA . A NA 402 1_555 F O HOH . B HOH 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 1 1_555 B N3 C 12 B C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 1 1_555 B O2 C 12 B C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 1 1_555 B N4 C 12 B C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 2 1_555 B N3 C 11 B C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 2 1_555 B O2 C 11 B C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 2 1_555 B N4 C 11 B C 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 A 3 A A 3 1_555 B N3 5BU 10 B 5BU 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 A 3 A A 3 1_555 B O4 5BU 10 B 5BU 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 C 4 A C 4 1_555 B N1 G 9 B G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 C 4 A C 4 1_555 B O6 G 9 B G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 C 4 A C 4 1_555 B N2 G 9 B G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog12 A N3 U 5 A U 5 1_555 B O6 G 8 B G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog13 A O2 U 5 A U 5 1_555 B N1 G 8 B G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog14 A O2 C 6 A C 6 1_555 B N4 C 7 B C 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog15 A N4 C 7 A C 7 1_555 B O2 C 6 B C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog16 A N1 G 8 A G 8 1_555 B O2 U 5 B U 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog17 A O6 G 8 A G 8 1_555 B N3 U 5 B U 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 G 9 A G 9 1_555 B N3 C 4 B C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 G 9 A G 9 1_555 B O2 C 4 B C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 G 9 A G 9 1_555 B N4 C 4 B C 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 5BU 10 A 5BU 10 1_555 B N1 A 3 B A 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O4 5BU 10 A 5BU 10 1_555 B N6 A 3 B A 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 C 11 A C 11 1_555 B N1 G 2 B G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N4 C 11 A C 11 1_555 B O6 G 2 B G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O2 C 11 A C 11 1_555 B N2 G 2 B G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N3 C 12 A C 12 1_555 B N1 G 1 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N4 C 12 A C 12 1_555 B O6 G 1 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O2 C 12 A C 12 1_555 B N2 G 1 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7EDT _atom_sites.fract_transf_matrix[1][1] 0.041159 _atom_sites.fract_transf_matrix[1][2] 0.009663 _atom_sites.fract_transf_matrix[1][3] 0.013291 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.041333 _atom_sites.fract_transf_matrix[2][3] 0.005811 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.037192 _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 C 2 SPM A 1 401 401 SPM SPM . D 3 NA A 1 402 1 NA NA . E 4 HOH A 1 501 336 HOH HOH . E 4 HOH A 2 502 202 HOH HOH . E 4 HOH A 3 503 227 HOH HOH . E 4 HOH A 4 504 269 HOH HOH . E 4 HOH A 5 505 127 HOH HOH . E 4 HOH A 6 506 273 HOH HOH . E 4 HOH A 7 507 157 HOH HOH . E 4 HOH A 8 508 165 HOH HOH . E 4 HOH A 9 509 197 HOH HOH . E 4 HOH A 10 510 200 HOH HOH . E 4 HOH A 11 511 188 HOH HOH . E 4 HOH A 12 512 159 HOH HOH . E 4 HOH A 13 513 106 HOH HOH . E 4 HOH A 14 514 109 HOH HOH . E 4 HOH A 15 515 120 HOH HOH . E 4 HOH A 16 516 115 HOH HOH . E 4 HOH A 17 517 233 HOH HOH . E 4 HOH A 18 518 125 HOH HOH . E 4 HOH A 19 519 163 HOH HOH . E 4 HOH A 20 520 128 HOH HOH . E 4 HOH A 21 521 103 HOH HOH . E 4 HOH A 22 522 146 HOH HOH . E 4 HOH A 23 523 258 HOH HOH . E 4 HOH A 24 524 231 HOH HOH . E 4 HOH A 25 525 250 HOH HOH . E 4 HOH A 26 526 153 HOH HOH . E 4 HOH A 27 527 122 HOH HOH . E 4 HOH A 28 528 123 HOH HOH . E 4 HOH A 29 529 190 HOH HOH . E 4 HOH A 30 530 105 HOH HOH . E 4 HOH A 31 531 256 HOH HOH . E 4 HOH A 32 532 175 HOH HOH . E 4 HOH A 33 533 230 HOH HOH . E 4 HOH A 34 534 140 HOH HOH . E 4 HOH A 35 535 143 HOH HOH . E 4 HOH A 36 536 116 HOH HOH . E 4 HOH A 37 537 102 HOH HOH . E 4 HOH A 38 538 131 HOH HOH . E 4 HOH A 39 539 174 HOH HOH . E 4 HOH A 40 540 214 HOH HOH . E 4 HOH A 41 541 181 HOH HOH . E 4 HOH A 42 542 107 HOH HOH . E 4 HOH A 43 543 178 HOH HOH . E 4 HOH A 44 544 170 HOH HOH . E 4 HOH A 45 545 132 HOH HOH . E 4 HOH A 46 546 111 HOH HOH . E 4 HOH A 47 547 240 HOH HOH . E 4 HOH A 48 548 201 HOH HOH . E 4 HOH A 49 549 150 HOH HOH . E 4 HOH A 50 550 162 HOH HOH . E 4 HOH A 51 551 168 HOH HOH . E 4 HOH A 52 552 110 HOH HOH . E 4 HOH A 53 553 161 HOH HOH . E 4 HOH A 54 554 169 HOH HOH . E 4 HOH A 55 555 272 HOH HOH . E 4 HOH A 56 556 180 HOH HOH . E 4 HOH A 57 557 172 HOH HOH . E 4 HOH A 58 558 193 HOH HOH . E 4 HOH A 59 559 267 HOH HOH . E 4 HOH A 60 560 192 HOH HOH . E 4 HOH A 61 561 289 HOH HOH . E 4 HOH A 62 562 237 HOH HOH . E 4 HOH A 63 563 290 HOH HOH . E 4 HOH A 64 564 114 HOH HOH . E 4 HOH A 65 565 158 HOH HOH . E 4 HOH A 66 566 204 HOH HOH . E 4 HOH A 67 567 210 HOH HOH . E 4 HOH A 68 568 212 HOH HOH . E 4 HOH A 69 569 321 HOH HOH . E 4 HOH A 70 570 314 HOH HOH . E 4 HOH A 71 571 217 HOH HOH . E 4 HOH A 72 572 263 HOH HOH . E 4 HOH A 73 573 270 HOH HOH . E 4 HOH A 74 574 322 HOH HOH . E 4 HOH A 75 575 326 HOH HOH . E 4 HOH A 76 576 313 HOH HOH . E 4 HOH A 77 577 293 HOH HOH . F 4 HOH B 1 101 185 HOH HOH . F 4 HOH B 2 102 337 HOH HOH . F 4 HOH B 3 103 275 HOH HOH . F 4 HOH B 4 104 189 HOH HOH . F 4 HOH B 5 105 309 HOH HOH . F 4 HOH B 6 106 129 HOH HOH . F 4 HOH B 7 107 221 HOH HOH . F 4 HOH B 8 108 134 HOH HOH . F 4 HOH B 9 109 171 HOH HOH . F 4 HOH B 10 110 176 HOH HOH . F 4 HOH B 11 111 155 HOH HOH . F 4 HOH B 12 112 137 HOH HOH . F 4 HOH B 13 113 130 HOH HOH . F 4 HOH B 14 114 135 HOH HOH . F 4 HOH B 15 115 308 HOH HOH . F 4 HOH B 16 116 154 HOH HOH . F 4 HOH B 17 117 118 HOH HOH . F 4 HOH B 18 118 104 HOH HOH . F 4 HOH B 19 119 166 HOH HOH . F 4 HOH B 20 120 160 HOH HOH . F 4 HOH B 21 121 126 HOH HOH . F 4 HOH B 22 122 121 HOH HOH . F 4 HOH B 23 123 198 HOH HOH . F 4 HOH B 24 124 177 HOH HOH . F 4 HOH B 25 125 199 HOH HOH . F 4 HOH B 26 126 297 HOH HOH . F 4 HOH B 27 127 264 HOH HOH . F 4 HOH B 28 128 141 HOH HOH . F 4 HOH B 29 129 164 HOH HOH . F 4 HOH B 30 130 281 HOH HOH . F 4 HOH B 31 131 216 HOH HOH . F 4 HOH B 32 132 151 HOH HOH . F 4 HOH B 33 133 223 HOH HOH . F 4 HOH B 34 134 101 HOH HOH . F 4 HOH B 35 135 124 HOH HOH . F 4 HOH B 36 136 108 HOH HOH . F 4 HOH B 37 137 144 HOH HOH . F 4 HOH B 38 138 156 HOH HOH . F 4 HOH B 39 139 117 HOH HOH . F 4 HOH B 40 140 173 HOH HOH . F 4 HOH B 41 141 196 HOH HOH . F 4 HOH B 42 142 276 HOH HOH . F 4 HOH B 43 143 208 HOH HOH . F 4 HOH B 44 144 139 HOH HOH . F 4 HOH B 45 145 112 HOH HOH . F 4 HOH B 46 146 182 HOH HOH . F 4 HOH B 47 147 136 HOH HOH . F 4 HOH B 48 148 310 HOH HOH . F 4 HOH B 49 149 300 HOH HOH . F 4 HOH B 50 150 213 HOH HOH . F 4 HOH B 51 151 191 HOH HOH . F 4 HOH B 52 152 149 HOH HOH . F 4 HOH B 53 153 119 HOH HOH . F 4 HOH B 54 154 243 HOH HOH . F 4 HOH B 55 155 142 HOH HOH . F 4 HOH B 56 156 259 HOH HOH . F 4 HOH B 57 157 335 HOH HOH . F 4 HOH B 58 158 138 HOH HOH . F 4 HOH B 59 159 277 HOH HOH . F 4 HOH B 60 160 113 HOH HOH . F 4 HOH B 61 161 167 HOH HOH . F 4 HOH B 62 162 133 HOH HOH . F 4 HOH B 63 163 247 HOH HOH . F 4 HOH B 64 164 261 HOH HOH . F 4 HOH B 65 165 184 HOH HOH . F 4 HOH B 66 166 187 HOH HOH . F 4 HOH B 67 167 249 HOH HOH . F 4 HOH B 68 168 179 HOH HOH . F 4 HOH B 69 169 148 HOH HOH . F 4 HOH B 70 170 205 HOH HOH . F 4 HOH B 71 171 268 HOH HOH . F 4 HOH B 72 172 152 HOH HOH . F 4 HOH B 73 173 209 HOH HOH . F 4 HOH B 74 174 266 HOH HOH . F 4 HOH B 75 175 257 HOH HOH . F 4 HOH B 76 176 278 HOH HOH . F 4 HOH B 77 177 262 HOH HOH . F 4 HOH B 78 178 242 HOH HOH . F 4 HOH B 79 179 234 HOH HOH . F 4 HOH B 80 180 145 HOH HOH . F 4 HOH B 81 181 255 HOH HOH . F 4 HOH B 82 182 282 HOH HOH . F 4 HOH B 83 183 238 HOH HOH . F 4 HOH B 84 184 226 HOH HOH . F 4 HOH B 85 185 316 HOH HOH . F 4 HOH B 86 186 294 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x -3.606 _atom_site.Cartn_y 1.383 _atom_site.Cartn_z 9.182 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 10.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 402 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #