data_7D8L # _model_server_result.job_id WxaBSf5z4r4jdjLxmIeNtA _model_server_result.datetime_utc '2025-09-08 13:36:31' _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 7d8l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7D8L # _exptl.entry_id 7D8L _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 111.71 _cell.angle_gamma 90 _cell.entry_id 7D8L _cell.length_a 48.968 _cell.length_b 35.907 _cell.length_c 59.46 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D8L _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 OD1 ASN 90 A ASN 90 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc2 A OD2 ASP 106 A ASP 106 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc3 A O ASP 108 A ASP 108 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 A OD2 ASP 110 A ASP 110 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc5 A OD2 ASP 110 A ASP 110 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc6 A OD2 ASP 123 A ASP 123 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 A OE2 GLU 126 A GLU 126 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc8 B O3G GSP . A GSP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? # _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 142 n n PG S1G GSP doub 143 n n PG O2G GSP sing 144 n n PG O3G GSP sing 145 n n O3B PB GSP sing 146 n n O2G HOG2 GSP sing 147 n n O3G HOG3 GSP sing 148 n n PB O1B GSP doub 149 n n PB O2B GSP sing 150 n n PB O3A GSP sing 151 n n O2B HOB2 GSP sing 152 n n PA O1A GSP doub 153 n n PA O2A GSP sing 154 n n PA O3A GSP sing 155 n n PA O5' GSP sing 156 n n O2A HOA2 GSP sing 157 n n O5' C5' GSP sing 158 n n C5' C4' GSP sing 159 n n C5' "H5'1" GSP sing 160 n n C5' "H5'2" GSP sing 161 n n C4' O4' GSP sing 162 n n C4' C3' GSP sing 163 n n C4' H4' GSP sing 164 n n O4' C1' GSP sing 165 n n C3' O3' GSP sing 166 n n C3' C2' GSP sing 167 n n C3' H3' GSP sing 168 n n O3' HO3' GSP sing 169 n n C2' O2' GSP sing 170 n n C2' C1' GSP sing 171 n n C2' H2' GSP sing 172 n n O2' HO2' GSP sing 173 n n C1' N9 GSP sing 174 n n C1' H1' GSP sing 175 n n N9 C8 GSP sing 176 n y N9 C4 GSP sing 177 n y C8 N7 GSP doub 178 n y C8 H8 GSP sing 179 n n N7 C5 GSP sing 180 n y C5 C6 GSP sing 181 n n C5 C4 GSP doub 182 n y C6 O6 GSP doub 183 n n C6 N1 GSP sing 184 n n N1 C2 GSP sing 185 n n N1 HN1 GSP sing 186 n n C2 N2 GSP sing 187 n n C2 N3 GSP doub 188 n n N2 HN21 GSP sing 189 n n N2 HN22 GSP sing 190 n n N3 C4 GSP sing 191 n n # _atom_sites.entry_id 7D8L _atom_sites.fract_transf_matrix[1][1] 0.020421 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00813 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02785 _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] 0.018102 _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 1 201 201 GSP GSP . C 3 MG A 1 202 801 MG MG . D 3 MG A 1 203 901 MG MG . E 4 GOL A 1 204 1401 GOL GOL . F 5 HOH A 1 301 43 HOH HOH . F 5 HOH A 2 302 50 HOH HOH . F 5 HOH A 3 303 68 HOH HOH . F 5 HOH A 4 304 122 HOH HOH . F 5 HOH A 5 305 74 HOH HOH . F 5 HOH A 6 306 123 HOH HOH . F 5 HOH A 7 307 120 HOH HOH . F 5 HOH A 8 308 104 HOH HOH . F 5 HOH A 9 309 16 HOH HOH . F 5 HOH A 10 310 76 HOH HOH . F 5 HOH A 11 311 69 HOH HOH . F 5 HOH A 12 312 28 HOH HOH . F 5 HOH A 13 313 59 HOH HOH . F 5 HOH A 14 314 95 HOH HOH . F 5 HOH A 15 315 25 HOH HOH . F 5 HOH A 16 316 133 HOH HOH . F 5 HOH A 17 317 75 HOH HOH . F 5 HOH A 18 318 1 HOH HOH . F 5 HOH A 19 319 87 HOH HOH . F 5 HOH A 20 320 38 HOH HOH . F 5 HOH A 21 321 7 HOH HOH . F 5 HOH A 22 322 70 HOH HOH . F 5 HOH A 23 323 91 HOH HOH . F 5 HOH A 24 324 12 HOH HOH . F 5 HOH A 25 325 53 HOH HOH . F 5 HOH A 26 326 3 HOH HOH . F 5 HOH A 27 327 27 HOH HOH . F 5 HOH A 28 328 21 HOH HOH . F 5 HOH A 29 329 24 HOH HOH . F 5 HOH A 30 330 13 HOH HOH . F 5 HOH A 31 331 6 HOH HOH . F 5 HOH A 32 332 118 HOH HOH . F 5 HOH A 33 333 78 HOH HOH . F 5 HOH A 34 334 20 HOH HOH . F 5 HOH A 35 335 71 HOH HOH . F 5 HOH A 36 336 79 HOH HOH . F 5 HOH A 37 337 121 HOH HOH . F 5 HOH A 38 338 90 HOH HOH . F 5 HOH A 39 339 45 HOH HOH . F 5 HOH A 40 340 101 HOH HOH . F 5 HOH A 41 341 57 HOH HOH . F 5 HOH A 42 342 10 HOH HOH . F 5 HOH A 43 343 8 HOH HOH . F 5 HOH A 44 344 15 HOH HOH . F 5 HOH A 45 345 77 HOH HOH . F 5 HOH A 46 346 2 HOH HOH . F 5 HOH A 47 347 56 HOH HOH . F 5 HOH A 48 348 17 HOH HOH . F 5 HOH A 49 349 80 HOH HOH . F 5 HOH A 50 350 9 HOH HOH . F 5 HOH A 51 351 85 HOH HOH . F 5 HOH A 52 352 63 HOH HOH . F 5 HOH A 53 353 83 HOH HOH . F 5 HOH A 54 354 31 HOH HOH . F 5 HOH A 55 355 61 HOH HOH . F 5 HOH A 56 356 73 HOH HOH . F 5 HOH A 57 357 96 HOH HOH . F 5 HOH A 58 358 30 HOH HOH . F 5 HOH A 59 359 5 HOH HOH . F 5 HOH A 60 360 40 HOH HOH . F 5 HOH A 61 361 41 HOH HOH . F 5 HOH A 62 362 48 HOH HOH . F 5 HOH A 63 363 54 HOH HOH . F 5 HOH A 64 364 46 HOH HOH . F 5 HOH A 65 365 34 HOH HOH . F 5 HOH A 66 366 127 HOH HOH . F 5 HOH A 67 367 39 HOH HOH . F 5 HOH A 68 368 4 HOH HOH . F 5 HOH A 69 369 36 HOH HOH . F 5 HOH A 70 370 55 HOH HOH . F 5 HOH A 71 371 115 HOH HOH . F 5 HOH A 72 372 22 HOH HOH . F 5 HOH A 73 373 52 HOH HOH . F 5 HOH A 74 374 62 HOH HOH . F 5 HOH A 75 375 58 HOH HOH . F 5 HOH A 76 376 126 HOH HOH . F 5 HOH A 77 377 112 HOH HOH . F 5 HOH A 78 378 11 HOH HOH . F 5 HOH A 79 379 117 HOH HOH . F 5 HOH A 80 380 32 HOH HOH . F 5 HOH A 81 381 132 HOH HOH . F 5 HOH A 82 382 29 HOH HOH . F 5 HOH A 83 383 33 HOH HOH . F 5 HOH A 84 384 66 HOH HOH . F 5 HOH A 85 385 98 HOH HOH . F 5 HOH A 86 386 14 HOH HOH . F 5 HOH A 87 387 103 HOH HOH . F 5 HOH A 88 388 23 HOH HOH . F 5 HOH A 89 389 18 HOH HOH . F 5 HOH A 90 390 44 HOH HOH . F 5 HOH A 91 391 97 HOH HOH . F 5 HOH A 92 392 128 HOH HOH . F 5 HOH A 93 393 37 HOH HOH . F 5 HOH A 94 394 47 HOH HOH . F 5 HOH A 95 395 60 HOH HOH . F 5 HOH A 96 396 86 HOH HOH . F 5 HOH A 97 397 93 HOH HOH . F 5 HOH A 98 398 51 HOH HOH . F 5 HOH A 99 399 109 HOH HOH . F 5 HOH A 100 400 49 HOH HOH . F 5 HOH A 101 401 26 HOH HOH . F 5 HOH A 102 402 84 HOH HOH . F 5 HOH A 103 403 113 HOH HOH . F 5 HOH A 104 404 111 HOH HOH . F 5 HOH A 105 405 94 HOH HOH . F 5 HOH A 106 406 89 HOH HOH . F 5 HOH A 107 407 42 HOH HOH . F 5 HOH A 108 408 110 HOH HOH . F 5 HOH A 109 409 100 HOH HOH . F 5 HOH A 110 410 88 HOH HOH . F 5 HOH A 111 411 106 HOH HOH . F 5 HOH A 112 412 108 HOH HOH . F 5 HOH A 113 413 92 HOH HOH . F 5 HOH A 114 414 119 HOH HOH . F 5 HOH A 115 415 102 HOH HOH . F 5 HOH A 116 416 116 HOH HOH . F 5 HOH A 117 417 114 HOH HOH . F 5 HOH A 118 418 124 HOH HOH . F 5 HOH A 119 419 131 HOH HOH . F 5 HOH A 120 420 105 HOH HOH . F 5 HOH A 121 421 67 HOH HOH . F 5 HOH A 122 422 82 HOH HOH . F 5 HOH A 123 423 129 HOH HOH . F 5 HOH A 124 424 19 HOH HOH . F 5 HOH A 125 425 107 HOH HOH . F 5 HOH A 126 426 81 HOH HOH . F 5 HOH A 127 427 130 HOH HOH . F 5 HOH A 128 428 35 HOH HOH . F 5 HOH A 129 429 64 HOH HOH . F 5 HOH A 130 430 65 HOH HOH . F 5 HOH A 131 431 72 HOH HOH . F 5 HOH A 132 432 125 HOH HOH . F 5 HOH A 133 433 99 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 -30.19 -4.961 27.275 1 14.58 ? PG GSP 201 A 1 HETATM 2 O O3B GSP . . . B 2 -31.129 -4.461 26.081 1 15.43 ? O3B GSP 201 A 1 HETATM 3 S S1G GSP . . . B 2 -30.935 -6.613 28.04 1 16.16 ? S1G GSP 201 A 1 HETATM 4 O O2G GSP . . . B 2 -28.854 -5.174 26.471 1 13.07 ? O2G GSP 201 A 1 HETATM 5 O O3G GSP . . . B 2 -30.133 -3.765 28.19 1 14.35 ? O3G GSP 201 A 1 HETATM 6 P PB GSP . . . B 2 -32.555 -3.779 25.987 1 14.83 ? PB GSP 201 A 1 HETATM 7 O O1B GSP . . . B 2 -32.317 -2.295 26.143 1 16.09 ? O1B GSP 201 A 1 HETATM 8 O O2B GSP . . . B 2 -33.617 -4.349 26.872 1 16.84 ? O2B GSP 201 A 1 HETATM 9 P PA GSP . . . B 2 -34.073 -4.749 23.646 1 15.54 ? PA GSP 201 A 1 HETATM 10 O O1A GSP . . . B 2 -34.278 -6.128 24.171 1 17.56 ? O1A GSP 201 A 1 HETATM 11 O O2A GSP . . . B 2 -35.223 -3.811 23.517 1 18.07 ? O2A GSP 201 A 1 HETATM 12 O O3A GSP . . . B 2 -32.882 -4.002 24.431 1 15.85 ? O3A GSP 201 A 1 HETATM 13 O O5' GSP . . . B 2 -33.483 -4.843 22.165 1 14.96 ? O5' GSP 201 A 1 HETATM 14 C C5' GSP . . . B 2 -32.237 -5.56 22.074 1 13.71 ? C5' GSP 201 A 1 HETATM 15 C C4' GSP . . . B 2 -31.301 -4.81 21.164 1 12.74 ? C4' GSP 201 A 1 HETATM 16 O O4' GSP . . . B 2 -31.792 -4.856 19.802 1 15.14 ? O4' GSP 201 A 1 HETATM 17 C C3' GSP . . . B 2 -31.1 -3.315 21.479 1 14.28 ? C3' GSP 201 A 1 HETATM 18 O O3' GSP . . . B 2 -29.8 -2.874 21.113 1 14.68 ? O3' GSP 201 A 1 HETATM 19 C C2' GSP . . . B 2 -32.108 -2.642 20.563 1 15.23 ? C2' GSP 201 A 1 HETATM 20 O O2' GSP . . . B 2 -31.874 -1.272 20.283 1 15.14 ? O2' GSP 201 A 1 HETATM 21 C C1' GSP . . . B 2 -31.888 -3.529 19.337 1 15.47 ? C1' GSP 201 A 1 HETATM 22 N N9 GSP . . . B 2 -32.972 -3.491 18.378 1 16.26 ? N9 GSP 201 A 1 HETATM 23 C C8 GSP . . . B 2 -34.319 -3.303 18.589 1 15.6 ? C8 GSP 201 A 1 HETATM 24 N N7 GSP . . . B 2 -35.02 -3.32 17.477 1 16.3 ? N7 GSP 201 A 1 HETATM 25 C C5 GSP . . . B 2 -34.059 -3.47 16.479 1 14.96 ? C5 GSP 201 A 1 HETATM 26 C C6 GSP . . . B 2 -34.209 -3.483 15.073 1 16.7 ? C6 GSP 201 A 1 HETATM 27 O O6 GSP . . . B 2 -35.273 -3.397 14.438 1 22.9 ? O6 GSP 201 A 1 HETATM 28 N N1 GSP . . . B 2 -32.96 -3.6 14.427 1 15.98 ? N1 GSP 201 A 1 HETATM 29 C C2 GSP . . . B 2 -31.731 -3.751 15.044 1 14.82 ? C2 GSP 201 A 1 HETATM 30 N N2 GSP . . . B 2 -30.626 -3.849 14.271 1 14.76 ? N2 GSP 201 A 1 HETATM 31 N N3 GSP . . . B 2 -31.587 -3.718 16.369 1 15.37 ? N3 GSP 201 A 1 HETATM 32 C C4 GSP . . . B 2 -32.789 -3.568 17.011 1 14.25 ? C4 GSP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 1054 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #