data_8TXG # _model_server_result.job_id gFRShKVWlxkNM6sDhDbgyQ _model_server_result.datetime_utc '2024-10-20 19:08:37' _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 8txg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8TXG # _exptl.entry_id 8TXG _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 120 _cell.entry_id 8TXG _cell.length_a 74.327 _cell.length_b 74.327 _cell.length_c 202.985 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TXG _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_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 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _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 8TXG _atom_sites.fract_transf_matrix[1][1] 0.013454 _atom_sites.fract_transf_matrix[1][2] 0.007768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015535 _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] 0.004926 _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 MG A 1 202 201 MG MG . D 4 VQT A 1 203 900 VQT UNL . E 5 HOH A 1 301 138 HOH HOH . E 5 HOH A 2 302 11 HOH HOH . E 5 HOH A 3 303 83 HOH HOH . E 5 HOH A 4 304 64 HOH HOH . E 5 HOH A 5 305 27 HOH HOH . E 5 HOH A 6 306 87 HOH HOH . E 5 HOH A 7 307 25 HOH HOH . E 5 HOH A 8 308 121 HOH HOH . E 5 HOH A 9 309 110 HOH HOH . E 5 HOH A 10 310 71 HOH HOH . E 5 HOH A 11 311 143 HOH HOH . E 5 HOH A 12 312 48 HOH HOH . E 5 HOH A 13 313 72 HOH HOH . E 5 HOH A 14 314 31 HOH HOH . E 5 HOH A 15 315 99 HOH HOH . E 5 HOH A 16 316 67 HOH HOH . E 5 HOH A 17 317 97 HOH HOH . E 5 HOH A 18 318 103 HOH HOH . E 5 HOH A 19 319 7 HOH HOH . E 5 HOH A 20 320 54 HOH HOH . E 5 HOH A 21 321 44 HOH HOH . E 5 HOH A 22 322 126 HOH HOH . E 5 HOH A 23 323 101 HOH HOH . E 5 HOH A 24 324 127 HOH HOH . E 5 HOH A 25 325 13 HOH HOH . E 5 HOH A 26 326 89 HOH HOH . E 5 HOH A 27 327 53 HOH HOH . E 5 HOH A 28 328 73 HOH HOH . E 5 HOH A 29 329 68 HOH HOH . E 5 HOH A 30 330 94 HOH HOH . E 5 HOH A 31 331 108 HOH HOH . E 5 HOH A 32 332 4 HOH HOH . E 5 HOH A 33 333 47 HOH HOH . E 5 HOH A 34 334 141 HOH HOH . E 5 HOH A 35 335 12 HOH HOH . E 5 HOH A 36 336 56 HOH HOH . E 5 HOH A 37 337 128 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 1 HOH HOH . E 5 HOH A 40 340 26 HOH HOH . E 5 HOH A 41 341 9 HOH HOH . E 5 HOH A 42 342 45 HOH HOH . E 5 HOH A 43 343 22 HOH HOH . E 5 HOH A 44 344 40 HOH HOH . E 5 HOH A 45 345 66 HOH HOH . E 5 HOH A 46 346 74 HOH HOH . E 5 HOH A 47 347 80 HOH HOH . E 5 HOH A 48 348 112 HOH HOH . E 5 HOH A 49 349 129 HOH HOH . E 5 HOH A 50 350 3 HOH HOH . E 5 HOH A 51 351 123 HOH HOH . E 5 HOH A 52 352 117 HOH HOH . E 5 HOH A 53 353 105 HOH HOH . E 5 HOH A 54 354 57 HOH HOH . E 5 HOH A 55 355 119 HOH HOH . E 5 HOH A 56 356 82 HOH HOH . E 5 HOH A 57 357 93 HOH HOH . E 5 HOH A 58 358 10 HOH HOH . E 5 HOH A 59 359 60 HOH HOH . E 5 HOH A 60 360 35 HOH HOH . E 5 HOH A 61 361 90 HOH HOH . E 5 HOH A 62 362 8 HOH HOH . E 5 HOH A 63 363 84 HOH HOH . E 5 HOH A 64 364 19 HOH HOH . E 5 HOH A 65 365 85 HOH HOH . E 5 HOH A 66 366 61 HOH HOH . E 5 HOH A 67 367 33 HOH HOH . E 5 HOH A 68 368 106 HOH HOH . E 5 HOH A 69 369 59 HOH HOH . E 5 HOH A 70 370 28 HOH HOH . E 5 HOH A 71 371 24 HOH HOH . E 5 HOH A 72 372 20 HOH HOH . E 5 HOH A 73 373 37 HOH HOH . E 5 HOH A 74 374 81 HOH HOH . E 5 HOH A 75 375 75 HOH HOH . E 5 HOH A 76 376 102 HOH HOH . E 5 HOH A 77 377 2 HOH HOH . E 5 HOH A 78 378 104 HOH HOH . E 5 HOH A 79 379 125 HOH HOH . E 5 HOH A 80 380 17 HOH HOH . E 5 HOH A 81 381 120 HOH HOH . E 5 HOH A 82 382 76 HOH HOH . E 5 HOH A 83 383 55 HOH HOH . E 5 HOH A 84 384 115 HOH HOH . E 5 HOH A 85 385 16 HOH HOH . E 5 HOH A 86 386 46 HOH HOH . E 5 HOH A 87 387 36 HOH HOH . E 5 HOH A 88 388 142 HOH HOH . E 5 HOH A 89 389 78 HOH HOH . E 5 HOH A 90 390 136 HOH HOH . E 5 HOH A 91 391 15 HOH HOH . E 5 HOH A 92 392 91 HOH HOH . E 5 HOH A 93 393 145 HOH HOH . E 5 HOH A 94 394 139 HOH HOH . E 5 HOH A 95 395 116 HOH HOH . E 5 HOH A 96 396 49 HOH HOH . E 5 HOH A 97 397 77 HOH HOH . E 5 HOH A 98 398 29 HOH HOH . E 5 HOH A 99 399 39 HOH HOH . E 5 HOH A 100 400 14 HOH HOH . E 5 HOH A 101 401 63 HOH HOH . E 5 HOH A 102 402 30 HOH HOH . E 5 HOH A 103 403 69 HOH HOH . E 5 HOH A 104 404 5 HOH HOH . E 5 HOH A 105 405 114 HOH HOH . E 5 HOH A 106 406 96 HOH HOH . E 5 HOH A 107 407 92 HOH HOH . E 5 HOH A 108 408 23 HOH HOH . E 5 HOH A 109 409 21 HOH HOH . E 5 HOH A 110 410 70 HOH HOH . E 5 HOH A 111 411 51 HOH HOH . E 5 HOH A 112 412 50 HOH HOH . E 5 HOH A 113 413 109 HOH HOH . E 5 HOH A 114 414 148 HOH HOH . E 5 HOH A 115 415 41 HOH HOH . E 5 HOH A 116 416 58 HOH HOH . E 5 HOH A 117 417 32 HOH HOH . E 5 HOH A 118 418 131 HOH HOH . E 5 HOH A 119 419 140 HOH HOH . E 5 HOH A 120 420 6 HOH HOH . E 5 HOH A 121 421 95 HOH HOH . E 5 HOH A 122 422 118 HOH HOH . E 5 HOH A 123 423 62 HOH HOH . E 5 HOH A 124 424 100 HOH HOH . E 5 HOH A 125 425 52 HOH HOH . E 5 HOH A 126 426 65 HOH HOH . E 5 HOH A 127 427 132 HOH HOH . E 5 HOH A 128 428 124 HOH HOH . E 5 HOH A 129 429 122 HOH HOH . E 5 HOH A 130 430 43 HOH HOH . E 5 HOH A 131 431 18 HOH HOH . E 5 HOH A 132 432 34 HOH HOH . E 5 HOH A 133 433 137 HOH HOH . E 5 HOH A 134 434 88 HOH HOH . E 5 HOH A 135 435 133 HOH HOH . E 5 HOH A 136 436 144 HOH HOH . E 5 HOH A 137 437 111 HOH HOH . E 5 HOH A 138 438 42 HOH HOH . E 5 HOH A 139 439 135 HOH HOH . E 5 HOH A 140 440 86 HOH HOH . E 5 HOH A 141 441 146 HOH HOH . E 5 HOH A 142 442 113 HOH HOH . E 5 HOH A 143 443 134 HOH HOH . E 5 HOH A 144 444 130 HOH HOH . E 5 HOH A 145 445 107 HOH HOH . E 5 HOH A 146 446 147 HOH HOH . E 5 HOH A 147 447 79 HOH HOH . E 5 HOH A 148 448 98 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 -28.144 -31.132 17.404 1 15.98 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -27.33 -30.11 16.672 1 15.56 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -29.454 -30.599 17.949 1 16.39 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -27.351 -31.876 18.464 1 15.05 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -28.435 -32.226 16.28 1 15.71 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -28.71 -33.79 16.37 1 16.54 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -27.45 -34.551 16.389 1 16.84 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -29.59 -34.047 17.541 1 16.85 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -29.459 -34.05 14.996 1 16.97 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -30.758 -33.498 14.682 1 17 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -31.508 -34.478 13.811 1 17.17 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -30.833 -34.607 12.537 1 18.19 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -31.623 -35.902 14.358 1 17.96 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -32.819 -36.53 13.887 1 18.83 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -30.396 -36.577 13.754 1 18.48 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -30.464 -37.997 13.73 1 18.32 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -30.392 -35.948 12.366 1 18.13 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -29.061 -35.905 11.751 1 18.18 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -27.884 -35.467 12.311 1 17.88 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -26.878 -35.462 11.47 1 17.27 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -27.428 -35.923 10.284 1 17.81 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -26.847 -36.121 9.005 1 18.1 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -25.682 -35.905 8.674 1 17.87 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -27.766 -36.577 8.079 1 18.91 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -29.091 -36.812 8.335 1 19.75 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -29.847 -37.223 7.309 1 21.09 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -29.647 -36.64 9.532 1 18.91 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -28.771 -36.203 10.449 1 18.11 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #