data_4DSO # _model_server_result.job_id 9cjSZvXIrmDH5MfnxE557w _model_server_result.datetime_utc '2024-11-12 07:44:39' _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 4dso # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4DSO # _exptl.entry_id 4DSO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 4DSO _cell.length_a 79.374 _cell.length_b 79.374 _cell.length_c 77.749 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DSO _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 2 _struct_asym.id B _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 metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc2 A OG1 THR 36 A THR 35 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc3 B O3G GSP . A GSP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc4 B O2B GSP . A GSP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc5 C MG MG . A MG 202 1_555 F O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc6 C MG MG . A MG 202 1_555 F O HOH . A HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 PG O3B GSP sing 159 n n PG S1G GSP doub 160 n n PG O2G GSP sing 161 n n PG O3G GSP sing 162 n n O3B PB GSP sing 163 n n O2G HOG2 GSP sing 164 n n O3G HOG3 GSP sing 165 n n PB O1B GSP doub 166 n n PB O2B GSP sing 167 n n PB O3A GSP sing 168 n n O2B HOB2 GSP sing 169 n n PA O1A GSP doub 170 n n PA O2A GSP sing 171 n n PA O3A GSP sing 172 n n PA O5' GSP sing 173 n n O2A HOA2 GSP sing 174 n n O5' C5' GSP sing 175 n n C5' C4' GSP sing 176 n n C5' "H5'1" GSP sing 177 n n C5' "H5'2" GSP sing 178 n n C4' O4' GSP sing 179 n n C4' C3' GSP sing 180 n n C4' H4' GSP sing 181 n n O4' C1' GSP sing 182 n n C3' O3' GSP sing 183 n n C3' C2' GSP sing 184 n n C3' H3' GSP sing 185 n n O3' HO3' GSP sing 186 n n C2' O2' GSP sing 187 n n C2' C1' GSP sing 188 n n C2' H2' GSP sing 189 n n O2' HO2' GSP sing 190 n n C1' N9 GSP sing 191 n n C1' H1' GSP sing 192 n n N9 C8 GSP sing 193 n y N9 C4 GSP sing 194 n y C8 N7 GSP doub 195 n y C8 H8 GSP sing 196 n n N7 C5 GSP sing 197 n y C5 C6 GSP sing 198 n n C5 C4 GSP doub 199 n y C6 O6 GSP doub 200 n n C6 N1 GSP sing 201 n n N1 C2 GSP sing 202 n n N1 HN1 GSP sing 203 n n C2 N2 GSP sing 204 n n C2 N3 GSP doub 205 n n N2 HN21 GSP sing 206 n n N2 HN22 GSP sing 207 n n N3 C4 GSP sing 208 n n # _atom_sites.entry_id 4DSO _atom_sites.fract_transf_matrix[1][1] 0.012599 _atom_sites.fract_transf_matrix[1][2] 0.007274 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014548 _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] 0.012862 _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 GSP A 1 201 1 GSP GSP . C 3 MG A 1 202 2 MG MG . D 4 BEN A 1 203 3 BEN BEN . E 5 GOL A 1 204 4 GOL GOL . F 6 HOH A 1 301 1 HOH HOH . F 6 HOH A 2 302 2 HOH HOH . F 6 HOH A 3 303 3 HOH HOH . F 6 HOH A 4 304 4 HOH HOH . F 6 HOH A 5 305 5 HOH HOH . F 6 HOH A 6 306 6 HOH HOH . F 6 HOH A 7 307 7 HOH HOH . F 6 HOH A 8 308 8 HOH HOH . F 6 HOH A 9 309 9 HOH HOH . F 6 HOH A 10 310 10 HOH HOH . F 6 HOH A 11 311 11 HOH HOH . F 6 HOH A 12 312 12 HOH HOH . F 6 HOH A 13 313 13 HOH HOH . F 6 HOH A 14 314 14 HOH HOH . F 6 HOH A 15 315 15 HOH HOH . F 6 HOH A 16 316 16 HOH HOH . F 6 HOH A 17 317 17 HOH HOH . F 6 HOH A 18 318 18 HOH HOH . F 6 HOH A 19 319 19 HOH HOH . F 6 HOH A 20 320 20 HOH HOH . F 6 HOH A 21 321 21 HOH HOH . F 6 HOH A 22 322 22 HOH HOH . F 6 HOH A 23 323 23 HOH HOH . F 6 HOH A 24 324 24 HOH HOH . F 6 HOH A 25 325 25 HOH HOH . F 6 HOH A 26 326 26 HOH HOH . F 6 HOH A 27 327 27 HOH HOH . F 6 HOH A 28 328 28 HOH HOH . F 6 HOH A 29 329 29 HOH HOH . F 6 HOH A 30 330 30 HOH HOH . F 6 HOH A 31 331 31 HOH HOH . F 6 HOH A 32 332 32 HOH HOH . F 6 HOH A 33 333 33 HOH HOH . F 6 HOH A 34 334 34 HOH HOH . F 6 HOH A 35 335 35 HOH HOH . F 6 HOH A 36 336 36 HOH HOH . F 6 HOH A 37 337 37 HOH HOH . F 6 HOH A 38 338 38 HOH HOH . F 6 HOH A 39 339 39 HOH HOH . F 6 HOH A 40 340 40 HOH HOH . F 6 HOH A 41 341 41 HOH HOH . F 6 HOH A 42 342 42 HOH HOH . F 6 HOH A 43 343 43 HOH HOH . F 6 HOH A 44 344 44 HOH HOH . F 6 HOH A 45 345 45 HOH HOH . F 6 HOH A 46 346 46 HOH HOH . F 6 HOH A 47 347 47 HOH HOH . F 6 HOH A 48 348 48 HOH HOH . F 6 HOH A 49 349 49 HOH HOH . F 6 HOH A 50 350 50 HOH HOH . F 6 HOH A 51 351 51 HOH HOH . F 6 HOH A 52 352 52 HOH HOH . F 6 HOH A 53 353 53 HOH HOH . F 6 HOH A 54 354 54 HOH HOH . F 6 HOH A 55 355 55 HOH HOH . F 6 HOH A 56 356 56 HOH HOH . F 6 HOH A 57 357 57 HOH HOH . F 6 HOH A 58 358 58 HOH HOH . F 6 HOH A 59 359 59 HOH HOH . F 6 HOH A 60 360 60 HOH HOH . F 6 HOH A 61 361 61 HOH HOH . F 6 HOH A 62 362 62 HOH HOH . F 6 HOH A 63 363 63 HOH HOH . F 6 HOH A 64 364 64 HOH HOH . F 6 HOH A 65 365 65 HOH HOH . F 6 HOH A 66 366 66 HOH HOH . F 6 HOH A 67 367 67 HOH HOH . F 6 HOH A 68 368 68 HOH HOH . F 6 HOH A 69 369 69 HOH HOH . F 6 HOH A 70 370 70 HOH HOH . F 6 HOH A 71 371 71 HOH HOH . F 6 HOH A 72 372 72 HOH HOH . F 6 HOH A 73 373 73 HOH HOH . F 6 HOH A 74 374 74 HOH HOH . F 6 HOH A 75 375 75 HOH HOH . F 6 HOH A 76 376 76 HOH HOH . F 6 HOH A 77 377 77 HOH HOH . F 6 HOH A 78 378 78 HOH HOH . F 6 HOH A 79 379 79 HOH HOH . F 6 HOH A 80 380 80 HOH HOH . F 6 HOH A 81 381 81 HOH HOH . F 6 HOH A 82 382 82 HOH HOH . F 6 HOH A 83 383 83 HOH HOH . F 6 HOH A 84 384 84 HOH HOH . F 6 HOH A 85 385 85 HOH HOH . F 6 HOH A 86 386 86 HOH HOH . F 6 HOH A 87 387 87 HOH HOH . F 6 HOH A 88 388 88 HOH HOH . F 6 HOH A 89 389 89 HOH HOH . F 6 HOH A 90 390 90 HOH HOH . F 6 HOH A 91 391 91 HOH HOH . F 6 HOH A 92 392 92 HOH HOH . F 6 HOH A 93 393 93 HOH HOH . F 6 HOH A 94 394 94 HOH HOH . F 6 HOH A 95 395 95 HOH HOH . F 6 HOH A 96 396 96 HOH HOH . F 6 HOH A 97 397 97 HOH HOH . F 6 HOH A 98 398 98 HOH HOH . F 6 HOH A 99 399 99 HOH HOH . F 6 HOH A 100 400 100 HOH HOH . F 6 HOH A 101 401 101 HOH HOH . F 6 HOH A 102 402 102 HOH HOH . F 6 HOH A 103 403 103 HOH HOH . F 6 HOH A 104 404 104 HOH HOH . F 6 HOH A 105 405 105 HOH HOH . F 6 HOH A 106 406 106 HOH HOH . F 6 HOH A 107 407 107 HOH HOH . F 6 HOH A 108 408 108 HOH HOH . F 6 HOH A 109 409 109 HOH HOH . F 6 HOH A 110 410 110 HOH HOH . F 6 HOH A 111 411 111 HOH HOH . F 6 HOH A 112 412 112 HOH HOH . F 6 HOH A 113 413 113 HOH HOH . F 6 HOH A 114 414 114 HOH HOH . F 6 HOH A 115 415 115 HOH HOH . F 6 HOH A 116 416 116 HOH HOH . F 6 HOH A 117 417 117 HOH HOH . F 6 HOH A 118 418 118 HOH HOH . F 6 HOH A 119 419 119 HOH HOH . F 6 HOH A 120 420 120 HOH HOH . F 6 HOH A 121 421 121 HOH HOH . F 6 HOH A 122 422 122 HOH HOH . F 6 HOH A 123 423 123 HOH HOH . F 6 HOH A 124 424 124 HOH HOH . F 6 HOH A 125 425 125 HOH HOH . F 6 HOH A 126 426 126 HOH HOH . F 6 HOH A 127 427 127 HOH HOH . F 6 HOH A 128 428 128 HOH HOH . F 6 HOH A 129 429 129 HOH HOH . F 6 HOH A 130 430 130 HOH HOH . F 6 HOH A 131 431 131 HOH HOH . F 6 HOH A 132 432 132 HOH HOH . F 6 HOH A 133 433 133 HOH HOH . F 6 HOH A 134 434 134 HOH HOH . F 6 HOH A 135 435 135 HOH HOH . F 6 HOH A 136 436 136 HOH HOH . F 6 HOH A 137 437 137 HOH HOH . F 6 HOH A 138 438 138 HOH HOH . F 6 HOH A 139 439 139 HOH HOH . F 6 HOH A 140 440 140 HOH HOH . F 6 HOH A 141 441 141 HOH HOH . F 6 HOH A 142 442 142 HOH HOH . F 6 HOH A 143 443 143 HOH HOH . F 6 HOH A 144 444 144 HOH HOH . F 6 HOH A 145 445 145 HOH HOH . F 6 HOH A 146 446 146 HOH HOH . F 6 HOH A 147 447 147 HOH HOH . F 6 HOH A 148 448 148 HOH HOH . F 6 HOH A 149 449 149 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 P PG GSP . . . B 2 14.712 0.659 8.635 0.7 30.42 ? PG GSP 201 A 1 HETATM 2 O O3B GSP . . . B 2 14.774 -0.178 7.19 1 26.4 ? O3B GSP 201 A 1 HETATM 3 S S1G GSP . . . B 2 13.528 -0.193 9.554 0.7 36.43 ? S1G GSP 201 A 1 HETATM 4 O O2G GSP . . . B 2 14.196 2.094 8.413 0.7 28.84 ? O2G GSP 201 A 1 HETATM 5 O O3G GSP . . . B 2 16.067 0.716 9.316 0.7 26.63 ? O3G GSP 201 A 1 HETATM 6 P PB GSP . . . B 2 15.897 0.049 6.05 1 24.71 ? PB GSP 201 A 1 HETATM 7 O O1B GSP . . . B 2 15.399 0.899 4.952 1 22.35 ? O1B GSP 201 A 1 HETATM 8 O O2B GSP . . . B 2 17.199 0.47 6.576 1 25.68 ? O2B GSP 201 A 1 HETATM 9 P PA GSP . . . B 2 17.28 -2.458 5.429 1 26.69 ? PA GSP 201 A 1 HETATM 10 O O1A GSP . . . B 2 18.529 -1.932 4.834 1 28.59 ? O1A GSP 201 A 1 HETATM 11 O O2A GSP . . . B 2 17.464 -2.938 6.807 1 30.59 ? O2A GSP 201 A 1 HETATM 12 O O3A GSP . . . B 2 16.067 -1.39 5.325 1 23.71 ? O3A GSP 201 A 1 HETATM 13 O O5' GSP . . . B 2 16.781 -3.653 4.449 1 28.05 ? O5' GSP 201 A 1 HETATM 14 C C5' GSP . . . B 2 15.559 -4.352 4.713 1 30.69 ? C5' GSP 201 A 1 HETATM 15 C C4' GSP . . . B 2 15.544 -5.749 4.098 1 28.41 ? C4' GSP 201 A 1 HETATM 16 O O4' GSP . . . B 2 15.653 -5.57 2.695 1 26.96 ? O4' GSP 201 A 1 HETATM 17 C C3' GSP . . . B 2 16.72 -6.604 4.531 1 28.39 ? C3' GSP 201 A 1 HETATM 18 O O3' GSP . . . B 2 16.358 -7.972 4.505 1 29.05 ? O3' GSP 201 A 1 HETATM 19 C C2' GSP . . . B 2 17.76 -6.312 3.466 1 27.84 ? C2' GSP 201 A 1 HETATM 20 O O2' GSP . . . B 2 18.695 -7.341 3.294 1 27.05 ? O2' GSP 201 A 1 HETATM 21 C C1' GSP . . . B 2 16.867 -6.182 2.259 1 26.78 ? C1' GSP 201 A 1 HETATM 22 N N9 GSP . . . B 2 17.444 -5.351 1.187 1 25.57 ? N9 GSP 201 A 1 HETATM 23 C C8 GSP . . . B 2 17.968 -4.098 1.292 1 23.72 ? C8 GSP 201 A 1 HETATM 24 N N7 GSP . . . B 2 18.338 -3.694 0.057 1 21.68 ? N7 GSP 201 A 1 HETATM 25 C C5 GSP . . . B 2 18.079 -4.699 -0.836 1 21.54 ? C5 GSP 201 A 1 HETATM 26 C C6 GSP . . . B 2 18.268 -4.826 -2.206 1 23.32 ? C6 GSP 201 A 1 HETATM 27 O O6 GSP . . . B 2 18.795 -3.909 -2.895 1 23.63 ? O6 GSP 201 A 1 HETATM 28 N N1 GSP . . . B 2 17.855 -5.988 -2.821 1 23.34 ? N1 GSP 201 A 1 HETATM 29 C C2 GSP . . . B 2 17.267 -7.023 -2.088 1 26.4 ? C2 GSP 201 A 1 HETATM 30 N N2 GSP . . . B 2 16.891 -8.142 -2.668 1 26.57 ? N2 GSP 201 A 1 HETATM 31 N N3 GSP . . . B 2 17.093 -6.91 -0.721 1 25.1 ? N3 GSP 201 A 1 HETATM 32 C C4 GSP . . . B 2 17.49 -5.745 -0.119 1 23.95 ? C4 GSP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #