data_4GQD # _model_server_result.job_id b92B5_Ri_ZeeGXC_Mmo_Kg _model_server_result.datetime_utc '2025-03-03 00:23:45' _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 4gqd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":101}' # _entry.id 4GQD # _exptl.entry_id 4GQD _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.92 _cell.angle_gamma 90 _cell.entry_id 4GQD _cell.length_a 65.692 _cell.length_b 23.565 _cell.length_c 37.286 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GQD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 52.378509 0 34.828103 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G 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 covale ? covale1 A O3' DA 6 A DA 6 1_555 A P UCL 7 A UCL 7 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.613 ? covale ? covale2 A O3' UCL 7 A UCL 7 1_555 A P DC 8 A DC 8 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.608 ? covale ? covale3 D O3' DA 6 D DA 36 1_555 D P UCL 7 D UCL 37 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.603 ? covale ? covale4 D O3' UCL 7 D UCL 37 1_555 D P DC 8 D DC 38 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.603 ? metalc ? metalc1 B O2 DC 2 B DC 12 1_555 F NA NA . B NA 101 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.143 ? metalc ? metalc2 B OP1 DG 9 B DG 19 1_555 G NA NA . B NA 102 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc3 F NA NA . B NA 101 1_555 I O HOH . B HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc4 F NA NA . B NA 101 1_555 D O2 DC 2 D DC 32 1_555 ? ? ? ? B ? ? ? ? ? ? ? 3.099 ? metalc ? metalc5 F NA NA . B NA 101 1_555 K O HOH . D HOH 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc6 G NA NA . B NA 102 1_555 D OP1 DG 9 D DG 39 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.678 ? metalc ? metalc7 G NA NA . B NA 102 1_555 K O HOH . D HOH 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? hydrog 'DC-DG PAIR' hydrog1 A O2 DC 1 A DC 1 1_555 B N2 DG 10 B DG 20 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog5 A N1 DG 3 A DG 3 1_555 B O2 DC 8 B DC 18 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DG 4 A DG 4 1_555 B N3 DC 7 B DC 17 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 4 A DG 4 1_555 B O2 DC 7 B DC 17 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 4 A DG 4 1_555 B N4 DC 7 B DC 17 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 6 A DA 6 1_555 B N3 DT 5 B DT 15 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 6 A DA 6 1_555 B O4 DT 5 B DT 15 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? # _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 4GQD _atom_sites.fract_transf_matrix[1][1] 0.015223 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005819 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.042436 _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] 0.028713 _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 E 3 NA A 1 101 272 NA NA . F 3 NA B 1 101 265 NA NA . G 3 NA B 1 102 269 NA NA . H 4 HOH A 1 201 80 HOH HOH . H 4 HOH A 2 202 127 HOH HOH . H 4 HOH A 3 203 141 HOH HOH . H 4 HOH A 4 204 150 HOH HOH . H 4 HOH A 5 205 259 HOH HOH . H 4 HOH A 6 206 274 HOH HOH . H 4 HOH A 7 207 297 HOH HOH . H 4 HOH A 8 208 304 HOH HOH . H 4 HOH A 9 209 315 HOH HOH . H 4 HOH A 10 210 319 HOH HOH . H 4 HOH A 11 211 328 HOH HOH . H 4 HOH A 12 212 343 HOH HOH . H 4 HOH A 13 213 349 HOH HOH . H 4 HOH A 14 214 423 HOH HOH . H 4 HOH A 15 215 425 HOH HOH . I 4 HOH B 1 201 49 HOH HOH . I 4 HOH B 2 202 79 HOH HOH . I 4 HOH B 3 203 81 HOH HOH . I 4 HOH B 4 204 88 HOH HOH . I 4 HOH B 5 205 111 HOH HOH . I 4 HOH B 6 206 118 HOH HOH . I 4 HOH B 7 207 125 HOH HOH . I 4 HOH B 8 208 144 HOH HOH . I 4 HOH B 9 209 145 HOH HOH . I 4 HOH B 10 210 252 HOH HOH . I 4 HOH B 11 211 264 HOH HOH . I 4 HOH B 12 212 278 HOH HOH . I 4 HOH B 13 213 290 HOH HOH . I 4 HOH B 14 214 308 HOH HOH . I 4 HOH B 15 215 351 HOH HOH . I 4 HOH B 16 216 401 HOH HOH . I 4 HOH B 17 217 402 HOH HOH . I 4 HOH B 18 218 405 HOH HOH . I 4 HOH B 19 219 406 HOH HOH . I 4 HOH B 20 220 407 HOH HOH . I 4 HOH B 21 221 410 HOH HOH . I 4 HOH B 22 222 411 HOH HOH . I 4 HOH B 23 223 412 HOH HOH . I 4 HOH B 24 224 414 HOH HOH . I 4 HOH B 25 225 426 HOH HOH . I 4 HOH B 26 226 122 HOH HOH . J 4 HOH C 1 101 244 HOH HOH . J 4 HOH C 2 102 251 HOH HOH . J 4 HOH C 3 103 348 HOH HOH . J 4 HOH C 4 104 47 HOH HOH . J 4 HOH C 5 105 67 HOH HOH . J 4 HOH C 6 106 75 HOH HOH . J 4 HOH C 7 107 113 HOH HOH . J 4 HOH C 8 108 246 HOH HOH . J 4 HOH C 9 109 268 HOH HOH . J 4 HOH C 10 110 276 HOH HOH . J 4 HOH C 11 111 285 HOH HOH . J 4 HOH C 12 112 292 HOH HOH . J 4 HOH C 13 113 295 HOH HOH . J 4 HOH C 14 114 305 HOH HOH . J 4 HOH C 15 115 309 HOH HOH . J 4 HOH C 16 116 314 HOH HOH . J 4 HOH C 17 117 324 HOH HOH . J 4 HOH C 18 118 335 HOH HOH . J 4 HOH C 19 119 403 HOH HOH . J 4 HOH C 20 120 404 HOH HOH . J 4 HOH C 21 121 408 HOH HOH . J 4 HOH C 22 122 419 HOH HOH . J 4 HOH C 23 123 422 HOH HOH . K 4 HOH D 1 101 43 HOH HOH . K 4 HOH D 2 102 62 HOH HOH . K 4 HOH D 3 103 86 HOH HOH . K 4 HOH D 4 104 99 HOH HOH . K 4 HOH D 5 105 123 HOH HOH . K 4 HOH D 6 106 130 HOH HOH . K 4 HOH D 7 107 137 HOH HOH . K 4 HOH D 8 108 248 HOH HOH . K 4 HOH D 9 109 250 HOH HOH . K 4 HOH D 10 110 253 HOH HOH . K 4 HOH D 11 111 257 HOH HOH . K 4 HOH D 12 112 258 HOH HOH . K 4 HOH D 13 113 263 HOH HOH . K 4 HOH D 14 114 270 HOH HOH . K 4 HOH D 15 115 271 HOH HOH . K 4 HOH D 16 116 293 HOH HOH . K 4 HOH D 17 117 294 HOH HOH . K 4 HOH D 18 118 298 HOH HOH . K 4 HOH D 19 119 301 HOH HOH . K 4 HOH D 20 120 310 HOH HOH . K 4 HOH D 21 121 334 HOH HOH . K 4 HOH D 22 122 347 HOH HOH . K 4 HOH D 23 123 413 HOH HOH . K 4 HOH D 24 124 409 HOH HOH . K 4 HOH D 25 125 415 HOH HOH . K 4 HOH D 26 126 416 HOH HOH . K 4 HOH D 27 127 417 HOH HOH . K 4 HOH D 28 128 418 HOH HOH . K 4 HOH D 29 129 429 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 F _atom_site.label_entity_id 3 _atom_site.Cartn_x 17.273 _atom_site.Cartn_y 16.004 _atom_site.Cartn_z 6.443 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.09 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 101 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #