data_9E5F # _model_server_result.job_id ArOhlHmyGAzQkLU7zhTlNQ _model_server_result.datetime_utc '2025-01-22 19:08:51' _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 9e5f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 9E5F # _exptl.entry_id 9E5F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 9E5F _cell.length_a 40.175 _cell.length_b 53.63 _cell.length_c 90.206 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9E5F _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc3 D MG MG . A MG 203 1_555 E O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc4 D MG MG . A MG 203 1_555 E O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 D MG MG . A MG 203 1_555 E O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc6 D MG MG . A MG 203 1_555 E O HOH . A HOH 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 157 n n PB O2B GDP sing 158 n n PB O3B GDP sing 159 n n PB O3A GDP sing 160 n n O2B HOB2 GDP sing 161 n n O3B HOB3 GDP sing 162 n n O3A PA GDP sing 163 n n PA O1A GDP doub 164 n n PA O2A GDP sing 165 n n PA O5' GDP sing 166 n n O2A HOA2 GDP sing 167 n n O5' C5' GDP sing 168 n n C5' C4' GDP sing 169 n n C5' H5' GDP sing 170 n n C5' "H5''" GDP sing 171 n n C4' O4' GDP sing 172 n n C4' C3' GDP sing 173 n n C4' H4' GDP sing 174 n n O4' C1' GDP sing 175 n n C3' O3' GDP sing 176 n n C3' C2' GDP sing 177 n n C3' H3' GDP sing 178 n n O3' HO3' GDP sing 179 n n C2' O2' GDP sing 180 n n C2' C1' GDP sing 181 n n C2' H2' GDP sing 182 n n O2' HO2' GDP sing 183 n n C1' N9 GDP sing 184 n n C1' H1' GDP sing 185 n n N9 C8 GDP sing 186 n y N9 C4 GDP sing 187 n y C8 N7 GDP doub 188 n y C8 H8 GDP sing 189 n n N7 C5 GDP sing 190 n y C5 C6 GDP sing 191 n n C5 C4 GDP doub 192 n y C6 O6 GDP doub 193 n n C6 N1 GDP sing 194 n n N1 C2 GDP sing 195 n n N1 HN1 GDP sing 196 n n C2 N2 GDP sing 197 n n C2 N3 GDP doub 198 n n N2 HN21 GDP sing 199 n n N2 HN22 GDP sing 200 n n N3 C4 GDP sing 201 n n # _atom_sites.entry_id 9E5F _atom_sites.fract_transf_matrix[1][1] 0.024891 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018646 _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] 0.011086 _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 GDP A 1 201 200 GDP GDP . C 3 A1BEJ A 1 202 2 A1BEJ INC . D 4 MG A 1 203 1 MG MG . E 5 HOH A 1 301 96 HOH HOH . E 5 HOH A 2 302 139 HOH HOH . E 5 HOH A 3 303 101 HOH HOH . E 5 HOH A 4 304 105 HOH HOH . E 5 HOH A 5 305 119 HOH HOH . E 5 HOH A 6 306 154 HOH HOH . E 5 HOH A 7 307 79 HOH HOH . E 5 HOH A 8 308 12 HOH HOH . E 5 HOH A 9 309 6 HOH HOH . E 5 HOH A 10 310 66 HOH HOH . E 5 HOH A 11 311 47 HOH HOH . E 5 HOH A 12 312 86 HOH HOH . E 5 HOH A 13 313 84 HOH HOH . E 5 HOH A 14 314 42 HOH HOH . E 5 HOH A 15 315 50 HOH HOH . E 5 HOH A 16 316 107 HOH HOH . E 5 HOH A 17 317 92 HOH HOH . E 5 HOH A 18 318 134 HOH HOH . E 5 HOH A 19 319 16 HOH HOH . E 5 HOH A 20 320 140 HOH HOH . E 5 HOH A 21 321 23 HOH HOH . E 5 HOH A 22 322 68 HOH HOH . E 5 HOH A 23 323 59 HOH HOH . E 5 HOH A 24 324 76 HOH HOH . E 5 HOH A 25 325 82 HOH HOH . E 5 HOH A 26 326 145 HOH HOH . E 5 HOH A 27 327 155 HOH HOH . E 5 HOH A 28 328 141 HOH HOH . E 5 HOH A 29 329 152 HOH HOH . E 5 HOH A 30 330 75 HOH HOH . E 5 HOH A 31 331 90 HOH HOH . E 5 HOH A 32 332 113 HOH HOH . E 5 HOH A 33 333 21 HOH HOH . E 5 HOH A 34 334 53 HOH HOH . E 5 HOH A 35 335 72 HOH HOH . E 5 HOH A 36 336 22 HOH HOH . E 5 HOH A 37 337 31 HOH HOH . E 5 HOH A 38 338 156 HOH HOH . E 5 HOH A 39 339 41 HOH HOH . E 5 HOH A 40 340 138 HOH HOH . E 5 HOH A 41 341 28 HOH HOH . E 5 HOH A 42 342 91 HOH HOH . E 5 HOH A 43 343 11 HOH HOH . E 5 HOH A 44 344 3 HOH HOH . E 5 HOH A 45 345 57 HOH HOH . E 5 HOH A 46 346 15 HOH HOH . E 5 HOH A 47 347 65 HOH HOH . E 5 HOH A 48 348 26 HOH HOH . E 5 HOH A 49 349 61 HOH HOH . E 5 HOH A 50 350 106 HOH HOH . E 5 HOH A 51 351 9 HOH HOH . E 5 HOH A 52 352 14 HOH HOH . E 5 HOH A 53 353 40 HOH HOH . E 5 HOH A 54 354 136 HOH HOH . E 5 HOH A 55 355 32 HOH HOH . E 5 HOH A 56 356 110 HOH HOH . E 5 HOH A 57 357 62 HOH HOH . E 5 HOH A 58 358 54 HOH HOH . E 5 HOH A 59 359 45 HOH HOH . E 5 HOH A 60 360 2 HOH HOH . E 5 HOH A 61 361 10 HOH HOH . E 5 HOH A 62 362 78 HOH HOH . E 5 HOH A 63 363 94 HOH HOH . E 5 HOH A 64 364 51 HOH HOH . E 5 HOH A 65 365 69 HOH HOH . E 5 HOH A 66 366 1 HOH HOH . E 5 HOH A 67 367 13 HOH HOH . E 5 HOH A 68 368 27 HOH HOH . E 5 HOH A 69 369 43 HOH HOH . E 5 HOH A 70 370 58 HOH HOH . E 5 HOH A 71 371 8 HOH HOH . E 5 HOH A 72 372 71 HOH HOH . E 5 HOH A 73 373 87 HOH HOH . E 5 HOH A 74 374 48 HOH HOH . E 5 HOH A 75 375 24 HOH HOH . E 5 HOH A 76 376 111 HOH HOH . E 5 HOH A 77 377 55 HOH HOH . E 5 HOH A 78 378 17 HOH HOH . E 5 HOH A 79 379 146 HOH HOH . E 5 HOH A 80 380 103 HOH HOH . E 5 HOH A 81 381 36 HOH HOH . E 5 HOH A 82 382 74 HOH HOH . E 5 HOH A 83 383 37 HOH HOH . E 5 HOH A 84 384 132 HOH HOH . E 5 HOH A 85 385 52 HOH HOH . E 5 HOH A 86 386 85 HOH HOH . E 5 HOH A 87 387 33 HOH HOH . E 5 HOH A 88 388 73 HOH HOH . E 5 HOH A 89 389 60 HOH HOH . E 5 HOH A 90 390 99 HOH HOH . E 5 HOH A 91 391 122 HOH HOH . E 5 HOH A 92 392 109 HOH HOH . E 5 HOH A 93 393 20 HOH HOH . E 5 HOH A 94 394 29 HOH HOH . E 5 HOH A 95 395 35 HOH HOH . E 5 HOH A 96 396 18 HOH HOH . E 5 HOH A 97 397 34 HOH HOH . E 5 HOH A 98 398 56 HOH HOH . E 5 HOH A 99 399 25 HOH HOH . E 5 HOH A 100 400 39 HOH HOH . E 5 HOH A 101 401 4 HOH HOH . E 5 HOH A 102 402 81 HOH HOH . E 5 HOH A 103 403 46 HOH HOH . E 5 HOH A 104 404 38 HOH HOH . E 5 HOH A 105 405 7 HOH HOH . E 5 HOH A 106 406 147 HOH HOH . E 5 HOH A 107 407 77 HOH HOH . E 5 HOH A 108 408 89 HOH HOH . E 5 HOH A 109 409 5 HOH HOH . E 5 HOH A 110 410 112 HOH HOH . E 5 HOH A 111 411 121 HOH HOH . E 5 HOH A 112 412 67 HOH HOH . E 5 HOH A 113 413 80 HOH HOH . E 5 HOH A 114 414 88 HOH HOH . E 5 HOH A 115 415 44 HOH HOH . E 5 HOH A 116 416 97 HOH HOH . E 5 HOH A 117 417 108 HOH HOH . E 5 HOH A 118 418 19 HOH HOH . E 5 HOH A 119 419 114 HOH HOH . E 5 HOH A 120 420 49 HOH HOH . E 5 HOH A 121 421 64 HOH HOH . E 5 HOH A 122 422 100 HOH HOH . E 5 HOH A 123 423 137 HOH HOH . E 5 HOH A 124 424 144 HOH HOH . E 5 HOH A 125 425 83 HOH HOH . E 5 HOH A 126 426 102 HOH HOH . E 5 HOH A 127 427 150 HOH HOH . E 5 HOH A 128 428 126 HOH HOH . E 5 HOH A 129 429 125 HOH HOH . E 5 HOH A 130 430 120 HOH HOH . E 5 HOH A 131 431 153 HOH HOH . E 5 HOH A 132 432 118 HOH HOH . E 5 HOH A 133 433 95 HOH HOH . E 5 HOH A 134 434 123 HOH HOH . E 5 HOH A 135 435 104 HOH HOH . E 5 HOH A 136 436 151 HOH HOH . E 5 HOH A 137 437 142 HOH HOH . E 5 HOH A 138 438 128 HOH HOH . E 5 HOH A 139 439 143 HOH HOH . E 5 HOH A 140 440 63 HOH HOH . E 5 HOH A 141 441 129 HOH HOH . E 5 HOH A 142 442 148 HOH HOH . E 5 HOH A 143 443 30 HOH HOH . E 5 HOH A 144 444 130 HOH HOH . E 5 HOH A 145 445 116 HOH HOH . E 5 HOH A 146 446 135 HOH HOH . E 5 HOH A 147 447 124 HOH HOH . E 5 HOH A 148 448 70 HOH HOH . E 5 HOH A 149 449 117 HOH HOH . E 5 HOH A 150 450 115 HOH HOH . E 5 HOH A 151 451 98 HOH HOH . E 5 HOH A 152 452 93 HOH HOH . E 5 HOH A 153 453 131 HOH HOH . E 5 HOH A 154 454 149 HOH HOH . E 5 HOH A 155 455 133 HOH HOH . E 5 HOH A 156 456 127 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 PB GDP . . . B 2 28.053 -4.168 -16.107 1 11.56 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 27.093 -3.181 -15.559 1 10.93 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 28.988 -3.601 -17.159 1 13.19 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 27.426 -5.475 -16.555 1 11.85 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 29.005 -4.515 -14.814 1 12.85 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 29.703 -5.877 -14.398 1 13.19 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 28.76 -6.786 -13.736 1 13.84 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 30.477 -6.374 -15.576 1 15.97 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 30.706 -5.374 -13.271 1 14.13 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 31.782 -4.462 -13.577 1 14.45 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 32.937 -4.683 -12.624 1 16.64 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 32.554 -4.338 -11.257 1 15.64 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 33.449 -6.111 -12.504 1 18.78 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 34.861 -6.097 -12.259 1 22.43 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 32.711 -6.702 -11.296 1 18.5 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 33.385 -7.754 -10.649 1 21.53 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 32.637 -5.475 -10.412 1 17.16 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 31.484 -5.468 -9.54 1 15.12 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 30.166 -5.596 -9.897 1 14.35 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 29.347 -5.507 -8.89 1 13.15 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 30.177 -5.31 -7.797 1 13.66 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 29.854 -5.084 -6.43 1 13.28 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 28.731 -5.011 -5.913 1 13.19 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 30.997 -4.848 -5.658 1 14.21 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 32.276 -4.878 -6.141 1 15.8 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 33.235 -4.685 -5.249 1 18.37 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 32.579 -5.104 -7.414 1 16.39 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 31.489 -5.26 -8.192 1 15.23 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #