data_8YO0 # _model_server_result.job_id fWB15uW9_Fmk8QfvzHY1Bw _model_server_result.datetime_utc '2024-12-24 17:13:49' _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 8yo0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8YO0 # _exptl.entry_id 8YO0 _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 8YO0 _cell.length_a 40.787 _cell.length_b 51.606 _cell.length_c 74.597 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YO0 _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 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 _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 23 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc3 C MG MG . A MG 202 1_555 D O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 8YO0 _atom_sites.fract_transf_matrix[1][1] 0.024518 _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] 0.019378 _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] 0.013405 _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 1 201 201 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 HOH A 1 301 88 HOH HOH . D 4 HOH A 2 302 80 HOH HOH . D 4 HOH A 3 303 103 HOH HOH . D 4 HOH A 4 304 65 HOH HOH . D 4 HOH A 5 305 92 HOH HOH . D 4 HOH A 6 306 97 HOH HOH . D 4 HOH A 7 307 68 HOH HOH . D 4 HOH A 8 308 143 HOH HOH . D 4 HOH A 9 309 2 HOH HOH . D 4 HOH A 10 310 198 HOH HOH . D 4 HOH A 11 311 35 HOH HOH . D 4 HOH A 12 312 173 HOH HOH . D 4 HOH A 13 313 26 HOH HOH . D 4 HOH A 14 314 91 HOH HOH . D 4 HOH A 15 315 185 HOH HOH . D 4 HOH A 16 316 156 HOH HOH . D 4 HOH A 17 317 25 HOH HOH . D 4 HOH A 18 318 16 HOH HOH . D 4 HOH A 19 319 1 HOH HOH . D 4 HOH A 20 320 4 HOH HOH . D 4 HOH A 21 321 151 HOH HOH . D 4 HOH A 22 322 116 HOH HOH . D 4 HOH A 23 323 14 HOH HOH . D 4 HOH A 24 324 174 HOH HOH . D 4 HOH A 25 325 20 HOH HOH . D 4 HOH A 26 326 58 HOH HOH . D 4 HOH A 27 327 66 HOH HOH . D 4 HOH A 28 328 49 HOH HOH . D 4 HOH A 29 329 12 HOH HOH . D 4 HOH A 30 330 152 HOH HOH . D 4 HOH A 31 331 7 HOH HOH . D 4 HOH A 32 332 42 HOH HOH . D 4 HOH A 33 333 81 HOH HOH . D 4 HOH A 34 334 37 HOH HOH . D 4 HOH A 35 335 62 HOH HOH . D 4 HOH A 36 336 95 HOH HOH . D 4 HOH A 37 337 6 HOH HOH . D 4 HOH A 38 338 17 HOH HOH . D 4 HOH A 39 339 71 HOH HOH . D 4 HOH A 40 340 86 HOH HOH . D 4 HOH A 41 341 164 HOH HOH . D 4 HOH A 42 342 27 HOH HOH . D 4 HOH A 43 343 38 HOH HOH . D 4 HOH A 44 344 124 HOH HOH . D 4 HOH A 45 345 28 HOH HOH . D 4 HOH A 46 346 11 HOH HOH . D 4 HOH A 47 347 18 HOH HOH . D 4 HOH A 48 348 19 HOH HOH . D 4 HOH A 49 349 34 HOH HOH . D 4 HOH A 50 350 69 HOH HOH . D 4 HOH A 51 351 73 HOH HOH . D 4 HOH A 52 352 184 HOH HOH . D 4 HOH A 53 353 64 HOH HOH . D 4 HOH A 54 354 44 HOH HOH . D 4 HOH A 55 355 47 HOH HOH . D 4 HOH A 56 356 146 HOH HOH . D 4 HOH A 57 357 126 HOH HOH . D 4 HOH A 58 358 10 HOH HOH . D 4 HOH A 59 359 46 HOH HOH . D 4 HOH A 60 360 15 HOH HOH . D 4 HOH A 61 361 98 HOH HOH . D 4 HOH A 62 362 108 HOH HOH . D 4 HOH A 63 363 22 HOH HOH . D 4 HOH A 64 364 75 HOH HOH . D 4 HOH A 65 365 55 HOH HOH . D 4 HOH A 66 366 29 HOH HOH . D 4 HOH A 67 367 72 HOH HOH . D 4 HOH A 68 368 106 HOH HOH . D 4 HOH A 69 369 5 HOH HOH . D 4 HOH A 70 370 8 HOH HOH . D 4 HOH A 71 371 84 HOH HOH . D 4 HOH A 72 372 67 HOH HOH . D 4 HOH A 73 373 74 HOH HOH . D 4 HOH A 74 374 13 HOH HOH . D 4 HOH A 75 375 63 HOH HOH . D 4 HOH A 76 376 52 HOH HOH . D 4 HOH A 77 377 30 HOH HOH . D 4 HOH A 78 378 113 HOH HOH . D 4 HOH A 79 379 9 HOH HOH . D 4 HOH A 80 380 60 HOH HOH . D 4 HOH A 81 381 147 HOH HOH . D 4 HOH A 82 382 39 HOH HOH . D 4 HOH A 83 383 78 HOH HOH . D 4 HOH A 84 384 70 HOH HOH . D 4 HOH A 85 385 148 HOH HOH . D 4 HOH A 86 386 57 HOH HOH . D 4 HOH A 87 387 45 HOH HOH . D 4 HOH A 88 388 50 HOH HOH . D 4 HOH A 89 389 33 HOH HOH . D 4 HOH A 90 390 180 HOH HOH . D 4 HOH A 91 391 76 HOH HOH . D 4 HOH A 92 392 94 HOH HOH . D 4 HOH A 93 393 83 HOH HOH . D 4 HOH A 94 394 51 HOH HOH . D 4 HOH A 95 395 132 HOH HOH . D 4 HOH A 96 396 21 HOH HOH . D 4 HOH A 97 397 195 HOH HOH . D 4 HOH A 98 398 159 HOH HOH . D 4 HOH A 99 399 117 HOH HOH . D 4 HOH A 100 400 48 HOH HOH . D 4 HOH A 101 401 131 HOH HOH . D 4 HOH A 102 402 107 HOH HOH . D 4 HOH A 103 403 53 HOH HOH . D 4 HOH A 104 404 41 HOH HOH . D 4 HOH A 105 405 3 HOH HOH . D 4 HOH A 106 406 144 HOH HOH . D 4 HOH A 107 407 127 HOH HOH . D 4 HOH A 108 408 204 HOH HOH . D 4 HOH A 109 409 165 HOH HOH . D 4 HOH A 110 410 54 HOH HOH . D 4 HOH A 111 411 158 HOH HOH . D 4 HOH A 112 412 40 HOH HOH . D 4 HOH A 113 413 142 HOH HOH . D 4 HOH A 114 414 128 HOH HOH . D 4 HOH A 115 415 150 HOH HOH . D 4 HOH A 116 416 24 HOH HOH . D 4 HOH A 117 417 77 HOH HOH . D 4 HOH A 118 418 32 HOH HOH . D 4 HOH A 119 419 109 HOH HOH . D 4 HOH A 120 420 31 HOH HOH . D 4 HOH A 121 421 197 HOH HOH . D 4 HOH A 122 422 194 HOH HOH . D 4 HOH A 123 423 137 HOH HOH . D 4 HOH A 124 424 183 HOH HOH . D 4 HOH A 125 425 23 HOH HOH . D 4 HOH A 126 426 130 HOH HOH . D 4 HOH A 127 427 105 HOH HOH . D 4 HOH A 128 428 176 HOH HOH . D 4 HOH A 129 429 157 HOH HOH . D 4 HOH A 130 430 85 HOH HOH . D 4 HOH A 131 431 102 HOH HOH . D 4 HOH A 132 432 82 HOH HOH . D 4 HOH A 133 433 133 HOH HOH . D 4 HOH A 134 434 59 HOH HOH . D 4 HOH A 135 435 89 HOH HOH . D 4 HOH A 136 436 154 HOH HOH . D 4 HOH A 137 437 96 HOH HOH . D 4 HOH A 138 438 200 HOH HOH . D 4 HOH A 139 439 138 HOH HOH . D 4 HOH A 140 440 125 HOH HOH . D 4 HOH A 141 441 166 HOH HOH . D 4 HOH A 142 442 121 HOH HOH . D 4 HOH A 143 443 56 HOH HOH . D 4 HOH A 144 444 87 HOH HOH . D 4 HOH A 145 445 61 HOH HOH . D 4 HOH A 146 446 134 HOH HOH . D 4 HOH A 147 447 110 HOH HOH . D 4 HOH A 148 448 169 HOH HOH . D 4 HOH A 149 449 115 HOH HOH . D 4 HOH A 150 450 189 HOH HOH . D 4 HOH A 151 451 122 HOH HOH . D 4 HOH A 152 452 118 HOH HOH . D 4 HOH A 153 453 188 HOH HOH . D 4 HOH A 154 454 136 HOH HOH . D 4 HOH A 155 455 90 HOH HOH . D 4 HOH A 156 456 139 HOH HOH . D 4 HOH A 157 457 163 HOH HOH . D 4 HOH A 158 458 161 HOH HOH . D 4 HOH A 159 459 145 HOH HOH . D 4 HOH A 160 460 140 HOH HOH . D 4 HOH A 161 461 79 HOH HOH . D 4 HOH A 162 462 104 HOH HOH . D 4 HOH A 163 463 162 HOH HOH . D 4 HOH A 164 464 141 HOH HOH . D 4 HOH A 165 465 203 HOH HOH . D 4 HOH A 166 466 129 HOH HOH . D 4 HOH A 167 467 114 HOH HOH . D 4 HOH A 168 468 43 HOH HOH . D 4 HOH A 169 469 153 HOH HOH . D 4 HOH A 170 470 93 HOH HOH . D 4 HOH A 171 471 175 HOH HOH . D 4 HOH A 172 472 119 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 -8.075 -3.927 -13.872 1 6.29 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -7.574 -5.266 -14.379 1 8.54 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -9.497 -3.987 -13.376 1 7.04 -1 O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -7.114 -3.282 -12.9 1 8.16 -1 O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -8.134 -2.996 -15.136 1 8.17 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -7.121 -1.938 -15.758 1 7.2 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -5.81 -2.605 -15.969 1 9.67 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -7.161 -0.669 -14.978 1 8.65 -1 O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -7.777 -1.575 -17.13 1 9.19 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -7.93 -2.601 -18.154 1 11.38 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -8.007 -1.916 -19.497 1 10.61 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -9.23 -1.131 -19.572 1 8.87 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -6.864 -0.938 -19.76 1 9.9 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -6.497 -0.913 -21.142 1 13.44 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -7.506 0.409 -19.408 1 11.4 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -6.915 1.536 -20.046 1 12.98 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -8.923 0.202 -19.925 1 9.9 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -9.91 1.097 -19.305 1 7.23 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -10.052 1.362 -17.964 1 7.29 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -11.049 2.17 -17.716 1 7.08 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -11.589 2.453 -18.961 1 8.47 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -12.68 3.26 -19.328 1 8.89 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -13.399 3.948 -18.598 1 8.28 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -12.884 3.263 -20.694 1 7.18 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -12.148 2.577 -21.614 1 8.67 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -12.501 2.736 -22.903 1 11.19 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -11.109 1.819 -21.293 1 7.89 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -10.892 1.795 -19.95 1 8.06 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 611 _model_server_stats.encode_time_ms 34 _model_server_stats.element_count 28 #