data_5F2E # _model_server_result.job_id fqV5thnRV2xbp02icoDg3A _model_server_result.datetime_utc '2024-11-24 15:55:03' _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 5f2e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":206}' # _entry.id 5F2E # _exptl.entry_id 5F2E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 5F2E _cell.length_a 39.11 _cell.length_b 43.08 _cell.length_c 93.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F2E _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,E,F,G,H _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 6 _struct_asym.id G _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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 E C15 5UT . A 5UT 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 B MG MG . A MG 201 1_555 G O3B GDP . A GDP 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc3 B MG MG . A MG 201 1_555 H O HOH . A HOH 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc4 B MG MG . A MG 201 1_555 H O HOH . A HOH 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc5 B MG MG . A MG 201 1_555 H O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 B MG MG . A MG 201 1_555 H O HOH . A HOH 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? # _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 145 n n PB O2B GDP sing 146 n n PB O3B GDP sing 147 n n PB O3A GDP sing 148 n n O2B HOB2 GDP sing 149 n n O3B HOB3 GDP sing 150 n n O3A PA GDP sing 151 n n PA O1A GDP doub 152 n n PA O2A GDP sing 153 n n PA O5' GDP sing 154 n n O2A HOA2 GDP sing 155 n n O5' C5' GDP sing 156 n n C5' C4' GDP sing 157 n n C5' H5' GDP sing 158 n n C5' "H5''" GDP sing 159 n n C4' O4' GDP sing 160 n n C4' C3' GDP sing 161 n n C4' H4' GDP sing 162 n n O4' C1' GDP sing 163 n n C3' O3' GDP sing 164 n n C3' C2' GDP sing 165 n n C3' H3' GDP sing 166 n n O3' HO3' GDP sing 167 n n C2' O2' GDP sing 168 n n C2' C1' GDP sing 169 n n C2' H2' GDP sing 170 n n O2' HO2' GDP sing 171 n n C1' N9 GDP sing 172 n n C1' H1' GDP sing 173 n n N9 C8 GDP sing 174 n y N9 C4 GDP sing 175 n y C8 N7 GDP doub 176 n y C8 H8 GDP sing 177 n n N7 C5 GDP sing 178 n y C5 C6 GDP sing 179 n n C5 C4 GDP doub 180 n y C6 O6 GDP doub 181 n n C6 N1 GDP sing 182 n n N1 C2 GDP sing 183 n n N1 HN1 GDP sing 184 n n C2 N2 GDP sing 185 n n C2 N3 GDP doub 186 n n N2 HN21 GDP sing 187 n n N2 HN22 GDP sing 188 n n N3 C4 GDP sing 189 n n # _atom_sites.entry_id 5F2E _atom_sites.fract_transf_matrix[1][1] 0.025569 _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] 0.023213 _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] 0.010643 _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 MG A 1 201 200 MG MG . C 3 GOL A 1 202 205 GOL GOL . D 3 GOL A 1 203 207 GOL GOL . E 4 5UT A 1 204 210 5UT 853 . F 5 GLY A 1 205 215 GLY GLY . G 6 GDP A 1 206 220 GDP GDP . H 7 HOH A 1 301 86 HOH HOH . H 7 HOH A 2 302 82 HOH HOH . H 7 HOH A 3 303 175 HOH HOH . H 7 HOH A 4 304 172 HOH HOH . H 7 HOH A 5 305 100 HOH HOH . H 7 HOH A 6 306 168 HOH HOH . H 7 HOH A 7 307 92 HOH HOH . H 7 HOH A 8 308 85 HOH HOH . H 7 HOH A 9 309 90 HOH HOH . H 7 HOH A 10 310 71 HOH HOH . H 7 HOH A 11 311 70 HOH HOH . H 7 HOH A 12 312 126 HOH HOH . H 7 HOH A 13 313 31 HOH HOH . H 7 HOH A 14 314 118 HOH HOH . H 7 HOH A 15 315 79 HOH HOH . H 7 HOH A 16 316 128 HOH HOH . H 7 HOH A 17 317 154 HOH HOH . H 7 HOH A 18 318 133 HOH HOH . H 7 HOH A 19 319 23 HOH HOH . H 7 HOH A 20 320 83 HOH HOH . H 7 HOH A 21 321 77 HOH HOH . H 7 HOH A 22 322 140 HOH HOH . H 7 HOH A 23 323 58 HOH HOH . H 7 HOH A 24 324 48 HOH HOH . H 7 HOH A 25 325 127 HOH HOH . H 7 HOH A 26 326 115 HOH HOH . H 7 HOH A 27 327 109 HOH HOH . H 7 HOH A 28 328 4 HOH HOH . H 7 HOH A 29 329 105 HOH HOH . H 7 HOH A 30 330 106 HOH HOH . H 7 HOH A 31 331 141 HOH HOH . H 7 HOH A 32 332 95 HOH HOH . H 7 HOH A 33 333 108 HOH HOH . H 7 HOH A 34 334 16 HOH HOH . H 7 HOH A 35 335 66 HOH HOH . H 7 HOH A 36 336 55 HOH HOH . H 7 HOH A 37 337 2 HOH HOH . H 7 HOH A 38 338 87 HOH HOH . H 7 HOH A 39 339 131 HOH HOH . H 7 HOH A 40 340 104 HOH HOH . H 7 HOH A 41 341 157 HOH HOH . H 7 HOH A 42 342 6 HOH HOH . H 7 HOH A 43 343 137 HOH HOH . H 7 HOH A 44 344 78 HOH HOH . H 7 HOH A 45 345 21 HOH HOH . H 7 HOH A 46 346 53 HOH HOH . H 7 HOH A 47 347 3 HOH HOH . H 7 HOH A 48 348 101 HOH HOH . H 7 HOH A 49 349 5 HOH HOH . H 7 HOH A 50 350 179 HOH HOH . H 7 HOH A 51 351 80 HOH HOH . H 7 HOH A 52 352 12 HOH HOH . H 7 HOH A 53 353 94 HOH HOH . H 7 HOH A 54 354 136 HOH HOH . H 7 HOH A 55 355 37 HOH HOH . H 7 HOH A 56 356 146 HOH HOH . H 7 HOH A 57 357 11 HOH HOH . H 7 HOH A 58 358 57 HOH HOH . H 7 HOH A 59 359 13 HOH HOH . H 7 HOH A 60 360 153 HOH HOH . H 7 HOH A 61 361 177 HOH HOH . H 7 HOH A 62 362 24 HOH HOH . H 7 HOH A 63 363 173 HOH HOH . H 7 HOH A 64 364 97 HOH HOH . H 7 HOH A 65 365 125 HOH HOH . H 7 HOH A 66 366 160 HOH HOH . H 7 HOH A 67 367 44 HOH HOH . H 7 HOH A 68 368 114 HOH HOH . H 7 HOH A 69 369 119 HOH HOH . H 7 HOH A 70 370 134 HOH HOH . H 7 HOH A 71 371 59 HOH HOH . H 7 HOH A 72 372 39 HOH HOH . H 7 HOH A 73 373 75 HOH HOH . H 7 HOH A 74 374 7 HOH HOH . H 7 HOH A 75 375 139 HOH HOH . H 7 HOH A 76 376 163 HOH HOH . H 7 HOH A 77 377 42 HOH HOH . H 7 HOH A 78 378 56 HOH HOH . H 7 HOH A 79 379 74 HOH HOH . H 7 HOH A 80 380 10 HOH HOH . H 7 HOH A 81 381 62 HOH HOH . H 7 HOH A 82 382 8 HOH HOH . H 7 HOH A 83 383 61 HOH HOH . H 7 HOH A 84 384 135 HOH HOH . H 7 HOH A 85 385 64 HOH HOH . H 7 HOH A 86 386 45 HOH HOH . H 7 HOH A 87 387 20 HOH HOH . H 7 HOH A 88 388 67 HOH HOH . H 7 HOH A 89 389 9 HOH HOH . H 7 HOH A 90 390 38 HOH HOH . H 7 HOH A 91 391 145 HOH HOH . H 7 HOH A 92 392 65 HOH HOH . H 7 HOH A 93 393 60 HOH HOH . H 7 HOH A 94 394 19 HOH HOH . H 7 HOH A 95 395 43 HOH HOH . H 7 HOH A 96 396 28 HOH HOH . H 7 HOH A 97 397 22 HOH HOH . H 7 HOH A 98 398 26 HOH HOH . H 7 HOH A 99 399 98 HOH HOH . H 7 HOH A 100 400 174 HOH HOH . H 7 HOH A 101 401 102 HOH HOH . H 7 HOH A 102 402 32 HOH HOH . H 7 HOH A 103 403 14 HOH HOH . H 7 HOH A 104 404 72 HOH HOH . H 7 HOH A 105 405 166 HOH HOH . H 7 HOH A 106 406 36 HOH HOH . H 7 HOH A 107 407 1 HOH HOH . H 7 HOH A 108 408 120 HOH HOH . H 7 HOH A 109 409 46 HOH HOH . H 7 HOH A 110 410 35 HOH HOH . H 7 HOH A 111 411 161 HOH HOH . H 7 HOH A 112 412 18 HOH HOH . H 7 HOH A 113 413 15 HOH HOH . H 7 HOH A 114 414 51 HOH HOH . H 7 HOH A 115 415 122 HOH HOH . H 7 HOH A 116 416 113 HOH HOH . H 7 HOH A 117 417 148 HOH HOH . H 7 HOH A 118 418 159 HOH HOH . H 7 HOH A 119 419 167 HOH HOH . H 7 HOH A 120 420 63 HOH HOH . H 7 HOH A 121 421 33 HOH HOH . H 7 HOH A 122 422 17 HOH HOH . H 7 HOH A 123 423 41 HOH HOH . H 7 HOH A 124 424 178 HOH HOH . H 7 HOH A 125 425 29 HOH HOH . H 7 HOH A 126 426 27 HOH HOH . H 7 HOH A 127 427 69 HOH HOH . H 7 HOH A 128 428 111 HOH HOH . H 7 HOH A 129 429 151 HOH HOH . H 7 HOH A 130 430 162 HOH HOH . H 7 HOH A 131 431 158 HOH HOH . H 7 HOH A 132 432 143 HOH HOH . H 7 HOH A 133 433 123 HOH HOH . H 7 HOH A 134 434 124 HOH HOH . H 7 HOH A 135 435 150 HOH HOH . H 7 HOH A 136 436 117 HOH HOH . H 7 HOH A 137 437 34 HOH HOH . H 7 HOH A 138 438 103 HOH HOH . H 7 HOH A 139 439 30 HOH HOH . H 7 HOH A 140 440 171 HOH HOH . H 7 HOH A 141 441 49 HOH HOH . H 7 HOH A 142 442 47 HOH HOH . H 7 HOH A 143 443 73 HOH HOH . H 7 HOH A 144 444 76 HOH HOH . H 7 HOH A 145 445 93 HOH HOH . H 7 HOH A 146 446 25 HOH HOH . H 7 HOH A 147 447 142 HOH HOH . H 7 HOH A 148 448 96 HOH HOH . H 7 HOH A 149 449 149 HOH HOH . H 7 HOH A 150 450 170 HOH HOH . H 7 HOH A 151 451 84 HOH HOH . H 7 HOH A 152 452 116 HOH HOH . H 7 HOH A 153 453 88 HOH HOH . H 7 HOH A 154 454 110 HOH HOH . H 7 HOH A 155 455 91 HOH HOH . H 7 HOH A 156 456 99 HOH HOH . H 7 HOH A 157 457 54 HOH HOH . H 7 HOH A 158 458 89 HOH HOH . H 7 HOH A 159 459 112 HOH HOH . H 7 HOH A 160 460 107 HOH HOH . H 7 HOH A 161 461 129 HOH HOH . H 7 HOH A 162 462 138 HOH HOH . H 7 HOH A 163 463 147 HOH HOH . H 7 HOH A 164 464 130 HOH HOH . H 7 HOH A 165 465 169 HOH HOH . H 7 HOH A 166 466 81 HOH HOH . H 7 HOH A 167 467 132 HOH HOH . H 7 HOH A 168 468 52 HOH HOH . H 7 HOH A 169 469 144 HOH HOH . H 7 HOH A 170 470 68 HOH HOH . H 7 HOH A 171 471 152 HOH HOH . H 7 HOH A 172 472 40 HOH HOH . H 7 HOH A 173 473 155 HOH HOH . H 7 HOH A 174 474 164 HOH HOH . H 7 HOH A 175 475 176 HOH HOH . H 7 HOH A 176 476 165 HOH HOH . H 7 HOH A 177 477 121 HOH HOH . H 7 HOH A 178 478 50 HOH HOH . H 7 HOH A 179 479 156 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 . . . G 6 9.054 -1.535 -6.217 1 4.91 ? PB GDP 206 A 1 HETATM 2 O O1B GDP . . . G 6 9.584 -1.134 -7.551 1 5.04 ? O1B GDP 206 A 1 HETATM 3 O O2B GDP . . . G 6 8.076 -0.528 -5.682 1 4.62 ? O2B GDP 206 A 1 HETATM 4 O O3B GDP . . . G 6 10.116 -1.975 -5.255 1 4.74 ? O3B GDP 206 A 1 HETATM 5 O O3A GDP . . . G 6 8.191 -2.851 -6.537 1 4.77 ? O3A GDP 206 A 1 HETATM 6 P PA GDP . . . G 6 7.885 -4.119 -5.567 1 5.15 ? PA GDP 206 A 1 HETATM 7 O O1A GDP . . . G 6 8.972 -5.078 -5.651 1 5.35 ? O1A GDP 206 A 1 HETATM 8 O O2A GDP . . . G 6 7.447 -3.575 -4.26 1 5.5 ? O2A GDP 206 A 1 HETATM 9 O O5' GDP . . . G 6 6.691 -4.821 -6.338 1 5.06 ? O5' GDP 206 A 1 HETATM 10 C C5' GDP . . . G 6 5.451 -4.141 -6.479 1 5.82 ? C5' GDP 206 A 1 HETATM 11 C C4' GDP . . . G 6 4.291 -5.135 -6.567 1 7.23 ? C4' GDP 206 A 1 HETATM 12 O O4' GDP . . . G 6 4.486 -5.854 -7.885 1 6.57 ? O4' GDP 206 A 1 HETATM 13 C C3' GDP . . . G 6 4.311 -6.202 -5.538 1 9.56 ? C3' GDP 206 A 1 HETATM 14 O O3' GDP . . . G 6 2.951 -6.682 -5.139 1 13.61 ? O3' GDP 206 A 1 HETATM 15 C C2' GDP . . . G 6 5.049 -7.345 -6.149 1 9.31 ? C2' GDP 206 A 1 HETATM 16 O O2' GDP . . . G 6 4.802 -8.681 -5.607 1 12.82 ? O2' GDP 206 A 1 HETATM 17 C C1' GDP . . . G 6 4.575 -7.195 -7.6 1 7.14 ? C1' GDP 206 A 1 HETATM 18 N N9 GDP . . . G 6 5.586 -7.723 -8.51 1 5.8 ? N9 GDP 206 A 1 HETATM 19 C C8 GDP . . . G 6 6.916 -7.352 -8.633 1 5.27 ? C8 GDP 206 A 1 HETATM 20 N N7 GDP . . . G 6 7.53 -7.979 -9.617 1 5.4 ? N7 GDP 206 A 1 HETATM 21 C C5 GDP . . . G 6 6.547 -8.773 -10.178 1 5.56 ? C5 GDP 206 A 1 HETATM 22 C C6 GDP . . . G 6 6.632 -9.601 -11.345 1 5.83 ? C6 GDP 206 A 1 HETATM 23 O O6 GDP . . . G 6 7.624 -9.839 -12.055 1 6.74 ? O6 GDP 206 A 1 HETATM 24 N N1 GDP . . . G 6 5.426 -10.219 -11.631 1 6.42 ? N1 GDP 206 A 1 HETATM 25 C C2 GDP . . . G 6 4.285 -9.995 -10.945 1 7.71 ? C2 GDP 206 A 1 HETATM 26 N N2 GDP . . . G 6 3.194 -10.64 -11.359 1 9.34 ? N2 GDP 206 A 1 HETATM 27 N N3 GDP . . . G 6 4.152 -9.188 -9.863 1 6.44 ? N3 GDP 206 A 1 HETATM 28 C C4 GDP . . . G 6 5.321 -8.608 -9.498 1 6.05 ? C4 GDP 206 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #