data_7RT2 # _model_server_result.job_id 6RvFyd-bfpvIF_7UiNa9fQ _model_server_result.datetime_utc '2024-11-22 11:57:38' _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 7rt2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7RT2 # _exptl.entry_id 7RT2 _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 7RT2 _cell.length_a 40.96 _cell.length_b 52.972 _cell.length_c 90.708 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RT2 _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 C MG MG . A MG 202 1_555 G O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc4 C MG MG . A MG 202 1_555 G O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc5 C MG MG . A MG 202 1_555 G O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc6 C MG MG . A MG 202 1_555 G O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? # _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 172 n n PB O2B GDP sing 173 n n PB O3B GDP sing 174 n n PB O3A GDP sing 175 n n O2B HOB2 GDP sing 176 n n O3B HOB3 GDP sing 177 n n O3A PA GDP sing 178 n n PA O1A GDP doub 179 n n PA O2A GDP sing 180 n n PA O5' GDP sing 181 n n O2A HOA2 GDP sing 182 n n O5' C5' GDP sing 183 n n C5' C4' GDP sing 184 n n C5' H5' GDP sing 185 n n C5' "H5''" GDP sing 186 n n C4' O4' GDP sing 187 n n C4' C3' GDP sing 188 n n C4' H4' GDP sing 189 n n O4' C1' GDP sing 190 n n C3' O3' GDP sing 191 n n C3' C2' GDP sing 192 n n C3' H3' GDP sing 193 n n O3' HO3' GDP sing 194 n n C2' O2' GDP sing 195 n n C2' C1' GDP sing 196 n n C2' H2' GDP sing 197 n n O2' HO2' GDP sing 198 n n C1' N9 GDP sing 199 n n C1' H1' GDP sing 200 n n N9 C8 GDP sing 201 n y N9 C4 GDP sing 202 n y C8 N7 GDP doub 203 n y C8 H8 GDP sing 204 n n N7 C5 GDP sing 205 n y C5 C6 GDP sing 206 n n C5 C4 GDP doub 207 n y C6 O6 GDP doub 208 n n C6 N1 GDP sing 209 n n N1 C2 GDP sing 210 n n N1 HN1 GDP sing 211 n n C2 N2 GDP sing 212 n n C2 N3 GDP doub 213 n n N2 HN21 GDP sing 214 n n N2 HN22 GDP sing 215 n n N3 C4 GDP sing 216 n n # _atom_sites.entry_id 7RT2 _atom_sites.fract_transf_matrix[1][1] 0.024414 _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] 0.018878 _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] 0.011024 _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 1 202 202 MG MG . D 4 7NL A 1 203 301 7NL L98 . E 5 GOL A 1 204 401 GOL GOL . F 6 EDO A 1 205 501 EDO EDO . G 7 HOH A 1 301 91 HOH HOH . G 7 HOH A 2 302 138 HOH HOH . G 7 HOH A 3 303 110 HOH HOH . G 7 HOH A 4 304 103 HOH HOH . G 7 HOH A 5 305 54 HOH HOH . G 7 HOH A 6 306 67 HOH HOH . G 7 HOH A 7 307 134 HOH HOH . G 7 HOH A 8 308 117 HOH HOH . G 7 HOH A 9 309 61 HOH HOH . G 7 HOH A 10 310 175 HOH HOH . G 7 HOH A 11 311 28 HOH HOH . G 7 HOH A 12 312 111 HOH HOH . G 7 HOH A 13 313 56 HOH HOH . G 7 HOH A 14 314 60 HOH HOH . G 7 HOH A 15 315 17 HOH HOH . G 7 HOH A 16 316 73 HOH HOH . G 7 HOH A 17 317 18 HOH HOH . G 7 HOH A 18 318 160 HOH HOH . G 7 HOH A 19 319 156 HOH HOH . G 7 HOH A 20 320 89 HOH HOH . G 7 HOH A 21 321 53 HOH HOH . G 7 HOH A 22 322 26 HOH HOH . G 7 HOH A 23 323 4 HOH HOH . G 7 HOH A 24 324 19 HOH HOH . G 7 HOH A 25 325 49 HOH HOH . G 7 HOH A 26 326 1 HOH HOH . G 7 HOH A 27 327 149 HOH HOH . G 7 HOH A 28 328 2 HOH HOH . G 7 HOH A 29 329 173 HOH HOH . G 7 HOH A 30 330 55 HOH HOH . G 7 HOH A 31 331 9 HOH HOH . G 7 HOH A 32 332 147 HOH HOH . G 7 HOH A 33 333 33 HOH HOH . G 7 HOH A 34 334 109 HOH HOH . G 7 HOH A 35 335 96 HOH HOH . G 7 HOH A 36 336 52 HOH HOH . G 7 HOH A 37 337 15 HOH HOH . G 7 HOH A 38 338 6 HOH HOH . G 7 HOH A 39 339 128 HOH HOH . G 7 HOH A 40 340 62 HOH HOH . G 7 HOH A 41 341 166 HOH HOH . G 7 HOH A 42 342 94 HOH HOH . G 7 HOH A 43 343 20 HOH HOH . G 7 HOH A 44 344 12 HOH HOH . G 7 HOH A 45 345 119 HOH HOH . G 7 HOH A 46 346 3 HOH HOH . G 7 HOH A 47 347 36 HOH HOH . G 7 HOH A 48 348 179 HOH HOH . G 7 HOH A 49 349 101 HOH HOH . G 7 HOH A 50 350 8 HOH HOH . G 7 HOH A 51 351 81 HOH HOH . G 7 HOH A 52 352 87 HOH HOH . G 7 HOH A 53 353 47 HOH HOH . G 7 HOH A 54 354 11 HOH HOH . G 7 HOH A 55 355 108 HOH HOH . G 7 HOH A 56 356 124 HOH HOH . G 7 HOH A 57 357 88 HOH HOH . G 7 HOH A 58 358 13 HOH HOH . G 7 HOH A 59 359 120 HOH HOH . G 7 HOH A 60 360 22 HOH HOH . G 7 HOH A 61 361 40 HOH HOH . G 7 HOH A 62 362 65 HOH HOH . G 7 HOH A 63 363 35 HOH HOH . G 7 HOH A 64 364 21 HOH HOH . G 7 HOH A 65 365 93 HOH HOH . G 7 HOH A 66 366 23 HOH HOH . G 7 HOH A 67 367 7 HOH HOH . G 7 HOH A 68 368 43 HOH HOH . G 7 HOH A 69 369 31 HOH HOH . G 7 HOH A 70 370 25 HOH HOH . G 7 HOH A 71 371 121 HOH HOH . G 7 HOH A 72 372 144 HOH HOH . G 7 HOH A 73 373 57 HOH HOH . G 7 HOH A 74 374 86 HOH HOH . G 7 HOH A 75 375 50 HOH HOH . G 7 HOH A 76 376 102 HOH HOH . G 7 HOH A 77 377 153 HOH HOH . G 7 HOH A 78 378 14 HOH HOH . G 7 HOH A 79 379 30 HOH HOH . G 7 HOH A 80 380 135 HOH HOH . G 7 HOH A 81 381 76 HOH HOH . G 7 HOH A 82 382 98 HOH HOH . G 7 HOH A 83 383 59 HOH HOH . G 7 HOH A 84 384 5 HOH HOH . G 7 HOH A 85 385 100 HOH HOH . G 7 HOH A 86 386 126 HOH HOH . G 7 HOH A 87 387 133 HOH HOH . G 7 HOH A 88 388 82 HOH HOH . G 7 HOH A 89 389 64 HOH HOH . G 7 HOH A 90 390 79 HOH HOH . G 7 HOH A 91 391 58 HOH HOH . G 7 HOH A 92 392 51 HOH HOH . G 7 HOH A 93 393 177 HOH HOH . G 7 HOH A 94 394 152 HOH HOH . G 7 HOH A 95 395 72 HOH HOH . G 7 HOH A 96 396 85 HOH HOH . G 7 HOH A 97 397 78 HOH HOH . G 7 HOH A 98 398 99 HOH HOH . G 7 HOH A 99 399 106 HOH HOH . G 7 HOH A 100 400 41 HOH HOH . G 7 HOH A 101 401 125 HOH HOH . G 7 HOH A 102 402 83 HOH HOH . G 7 HOH A 103 403 113 HOH HOH . G 7 HOH A 104 404 69 HOH HOH . G 7 HOH A 105 405 63 HOH HOH . G 7 HOH A 106 406 71 HOH HOH . G 7 HOH A 107 407 10 HOH HOH . G 7 HOH A 108 408 45 HOH HOH . G 7 HOH A 109 409 139 HOH HOH . G 7 HOH A 110 410 107 HOH HOH . G 7 HOH A 111 411 105 HOH HOH . G 7 HOH A 112 412 68 HOH HOH . G 7 HOH A 113 413 39 HOH HOH . G 7 HOH A 114 414 129 HOH HOH . G 7 HOH A 115 415 44 HOH HOH . G 7 HOH A 116 416 132 HOH HOH . G 7 HOH A 117 417 42 HOH HOH . G 7 HOH A 118 418 165 HOH HOH . G 7 HOH A 119 419 146 HOH HOH . G 7 HOH A 120 420 115 HOH HOH . G 7 HOH A 121 421 70 HOH HOH . G 7 HOH A 122 422 27 HOH HOH . G 7 HOH A 123 423 46 HOH HOH . G 7 HOH A 124 424 90 HOH HOH . G 7 HOH A 125 425 16 HOH HOH . G 7 HOH A 126 426 167 HOH HOH . G 7 HOH A 127 427 161 HOH HOH . G 7 HOH A 128 428 163 HOH HOH . G 7 HOH A 129 429 75 HOH HOH . G 7 HOH A 130 430 112 HOH HOH . G 7 HOH A 131 431 118 HOH HOH . G 7 HOH A 132 432 80 HOH HOH . G 7 HOH A 133 433 145 HOH HOH . G 7 HOH A 134 434 84 HOH HOH . G 7 HOH A 135 435 142 HOH HOH . G 7 HOH A 136 436 95 HOH HOH . G 7 HOH A 137 437 104 HOH HOH . G 7 HOH A 138 438 127 HOH HOH . G 7 HOH A 139 439 174 HOH HOH . G 7 HOH A 140 440 141 HOH HOH . G 7 HOH A 141 441 122 HOH HOH . G 7 HOH A 142 442 170 HOH HOH . G 7 HOH A 143 443 171 HOH HOH . G 7 HOH A 144 444 38 HOH HOH . G 7 HOH A 145 445 148 HOH HOH . G 7 HOH A 146 446 164 HOH HOH . G 7 HOH A 147 447 97 HOH HOH . G 7 HOH A 148 448 114 HOH HOH . G 7 HOH A 149 449 159 HOH HOH . G 7 HOH A 150 450 172 HOH HOH . G 7 HOH A 151 451 178 HOH HOH . G 7 HOH A 152 452 92 HOH HOH . G 7 HOH A 153 453 130 HOH HOH . G 7 HOH A 154 454 74 HOH HOH . G 7 HOH A 155 455 150 HOH HOH . G 7 HOH A 156 456 143 HOH HOH . G 7 HOH A 157 457 158 HOH HOH . G 7 HOH A 158 458 169 HOH HOH . G 7 HOH A 159 459 176 HOH HOH . G 7 HOH A 160 460 140 HOH HOH . G 7 HOH A 161 461 29 HOH HOH . G 7 HOH A 162 462 137 HOH HOH . G 7 HOH A 163 463 162 HOH HOH . G 7 HOH A 164 464 151 HOH HOH . G 7 HOH A 165 465 131 HOH HOH . G 7 HOH A 166 466 66 HOH HOH . G 7 HOH A 167 467 116 HOH HOH . G 7 HOH A 168 468 157 HOH HOH . G 7 HOH A 169 469 154 HOH HOH . G 7 HOH A 170 470 136 HOH HOH . G 7 HOH A 171 471 155 HOH HOH . G 7 HOH A 172 472 168 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 7.941 -4.18 -16.693 1 13.48 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 8.82 -3.626 -17.831 1 14.3 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 7.038 -3.176 -16.082 1 12.7 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 7.271 -5.497 -17.131 1 13.45 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 8.959 -4.567 -15.477 1 13.44 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 9.544 -5.996 -15.084 1 14.47 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 10.309 -6.559 -16.236 1 15.69 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 8.482 -6.803 -14.426 1 15.14 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 10.546 -5.562 -13.917 1 14.32 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 11.64 -4.698 -14.241 1 13.52 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 12.829 -5.024 -13.345 1 13.91 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 12.455 -4.647 -12.002 1 15.99 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 13.212 -6.505 -13.343 1 14.94 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 14.636 -6.688 -13.127 1 19.05 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 12.473 -6.976 -12.083 1 15.62 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 13.063 -8.135 -11.471 1 19.78 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 12.61 -5.798 -11.14 1 15.28 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 11.462 -5.727 -10.205 1 13.7 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 10.138 -5.789 -10.524 1 13.75 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 9.349 -5.587 -9.439 1 14.18 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 10.194 -5.46 -8.389 1 15.04 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 10.05 -5.265 -6.962 1 14.04 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 8.965 -5.141 -6.397 1 15.15 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 11.193 -5.105 -6.264 1 14.35 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 12.461 -5.208 -6.773 1 16.56 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 13.504 -5.04 -5.946 1 20.13 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 12.696 -5.403 -8.097 1 15.62 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 11.579 -5.534 -8.868 1 13.93 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #