data_5C4M # _model_server_result.job_id VxEmYG8RCd9hgeuru0iq7A _model_server_result.datetime_utc '2024-11-23 10:59:50' _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 5c4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5C4M # _exptl.entry_id 5C4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 5C4M _cell.length_a 31.796 _cell.length_b 66.271 _cell.length_c 83.679 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C4M _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 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 3 _struct_asym.id C _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 OG1 THR 19 A THR 19 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc2 A O THR 37 A THR 37 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc3 B MG MG . A MG 201 1_555 C O1B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc4 B MG MG . A MG 201 1_555 D O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 B MG MG . A MG 201 1_555 D O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc6 B MG MG . A MG 201 1_555 D O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? # _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 5C4M _atom_sites.fract_transf_matrix[1][1] 0.03145 _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] 0.01509 _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] 0.01195 _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 1 201 300 MG MG . C 3 GDP A 1 202 200 GDP GDP . D 4 HOH A 1 301 257 HOH HOH . D 4 HOH A 2 302 77 HOH HOH . D 4 HOH A 3 303 50 HOH HOH . D 4 HOH A 4 304 87 HOH HOH . D 4 HOH A 5 305 256 HOH HOH . D 4 HOH A 6 306 218 HOH HOH . D 4 HOH A 7 307 142 HOH HOH . D 4 HOH A 8 308 131 HOH HOH . D 4 HOH A 9 309 183 HOH HOH . D 4 HOH A 10 310 39 HOH HOH . D 4 HOH A 11 311 5 HOH HOH . D 4 HOH A 12 312 1 HOH HOH . D 4 HOH A 13 313 15 HOH HOH . D 4 HOH A 14 314 63 HOH HOH . D 4 HOH A 15 315 12 HOH HOH . D 4 HOH A 16 316 59 HOH HOH . D 4 HOH A 17 317 6 HOH HOH . D 4 HOH A 18 318 233 HOH HOH . D 4 HOH A 19 319 255 HOH HOH . D 4 HOH A 20 320 88 HOH HOH . D 4 HOH A 21 321 17 HOH HOH . D 4 HOH A 22 322 27 HOH HOH . D 4 HOH A 23 323 55 HOH HOH . D 4 HOH A 24 324 251 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 124 HOH HOH . D 4 HOH A 27 327 90 HOH HOH . D 4 HOH A 28 328 99 HOH HOH . D 4 HOH A 29 329 58 HOH HOH . D 4 HOH A 30 330 16 HOH HOH . D 4 HOH A 31 331 83 HOH HOH . D 4 HOH A 32 332 92 HOH HOH . D 4 HOH A 33 333 56 HOH HOH . D 4 HOH A 34 334 196 HOH HOH . D 4 HOH A 35 335 46 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 104 HOH HOH . D 4 HOH A 38 338 40 HOH HOH . D 4 HOH A 39 339 20 HOH HOH . D 4 HOH A 40 340 13 HOH HOH . D 4 HOH A 41 341 89 HOH HOH . D 4 HOH A 42 342 202 HOH HOH . D 4 HOH A 43 343 103 HOH HOH . D 4 HOH A 44 344 156 HOH HOH . D 4 HOH A 45 345 10 HOH HOH . D 4 HOH A 46 346 229 HOH HOH . D 4 HOH A 47 347 129 HOH HOH . D 4 HOH A 48 348 110 HOH HOH . D 4 HOH A 49 349 144 HOH HOH . D 4 HOH A 50 350 2 HOH HOH . D 4 HOH A 51 351 14 HOH HOH . D 4 HOH A 52 352 48 HOH HOH . D 4 HOH A 53 353 149 HOH HOH . D 4 HOH A 54 354 115 HOH HOH . D 4 HOH A 55 355 221 HOH HOH . D 4 HOH A 56 356 109 HOH HOH . D 4 HOH A 57 357 18 HOH HOH . D 4 HOH A 58 358 134 HOH HOH . D 4 HOH A 59 359 8 HOH HOH . D 4 HOH A 60 360 37 HOH HOH . D 4 HOH A 61 361 64 HOH HOH . D 4 HOH A 62 362 3 HOH HOH . D 4 HOH A 63 363 94 HOH HOH . D 4 HOH A 64 364 65 HOH HOH . D 4 HOH A 65 365 49 HOH HOH . D 4 HOH A 66 366 79 HOH HOH . D 4 HOH A 67 367 78 HOH HOH . D 4 HOH A 68 368 67 HOH HOH . D 4 HOH A 69 369 114 HOH HOH . D 4 HOH A 70 370 26 HOH HOH . D 4 HOH A 71 371 138 HOH HOH . D 4 HOH A 72 372 19 HOH HOH . D 4 HOH A 73 373 125 HOH HOH . D 4 HOH A 74 374 34 HOH HOH . D 4 HOH A 75 375 66 HOH HOH . D 4 HOH A 76 376 97 HOH HOH . D 4 HOH A 77 377 150 HOH HOH . D 4 HOH A 78 378 128 HOH HOH . D 4 HOH A 79 379 21 HOH HOH . D 4 HOH A 80 380 107 HOH HOH . D 4 HOH A 81 381 121 HOH HOH . D 4 HOH A 82 382 230 HOH HOH . D 4 HOH A 83 383 135 HOH HOH . D 4 HOH A 84 384 81 HOH HOH . D 4 HOH A 85 385 155 HOH HOH . D 4 HOH A 86 386 82 HOH HOH . D 4 HOH A 87 387 113 HOH HOH . D 4 HOH A 88 388 185 HOH HOH . D 4 HOH A 89 389 158 HOH HOH . D 4 HOH A 90 390 28 HOH HOH . D 4 HOH A 91 391 70 HOH HOH . D 4 HOH A 92 392 209 HOH HOH . D 4 HOH A 93 393 154 HOH HOH . D 4 HOH A 94 394 193 HOH HOH . D 4 HOH A 95 395 69 HOH HOH . D 4 HOH A 96 396 53 HOH HOH . D 4 HOH A 97 397 4 HOH HOH . D 4 HOH A 98 398 127 HOH HOH . D 4 HOH A 99 399 108 HOH HOH . D 4 HOH A 100 400 41 HOH HOH . D 4 HOH A 101 401 76 HOH HOH . D 4 HOH A 102 402 32 HOH HOH . D 4 HOH A 103 403 102 HOH HOH . D 4 HOH A 104 404 147 HOH HOH . D 4 HOH A 105 405 93 HOH HOH . D 4 HOH A 106 406 120 HOH HOH . D 4 HOH A 107 407 7 HOH HOH . D 4 HOH A 108 408 174 HOH HOH . D 4 HOH A 109 409 24 HOH HOH . D 4 HOH A 110 410 61 HOH HOH . D 4 HOH A 111 411 38 HOH HOH . D 4 HOH A 112 412 11 HOH HOH . D 4 HOH A 113 413 175 HOH HOH . D 4 HOH A 114 414 210 HOH HOH . D 4 HOH A 115 415 242 HOH HOH . D 4 HOH A 116 416 118 HOH HOH . D 4 HOH A 117 417 146 HOH HOH . D 4 HOH A 118 418 112 HOH HOH . D 4 HOH A 119 419 133 HOH HOH . D 4 HOH A 120 420 35 HOH HOH . D 4 HOH A 121 421 106 HOH HOH . D 4 HOH A 122 422 172 HOH HOH . D 4 HOH A 123 423 181 HOH HOH . D 4 HOH A 124 424 23 HOH HOH . D 4 HOH A 125 425 160 HOH HOH . D 4 HOH A 126 426 153 HOH HOH . D 4 HOH A 127 427 42 HOH HOH . D 4 HOH A 128 428 71 HOH HOH . D 4 HOH A 129 429 51 HOH HOH . D 4 HOH A 130 430 119 HOH HOH . D 4 HOH A 131 431 170 HOH HOH . D 4 HOH A 132 432 165 HOH HOH . D 4 HOH A 133 433 214 HOH HOH . D 4 HOH A 134 434 100 HOH HOH . D 4 HOH A 135 435 145 HOH HOH . D 4 HOH A 136 436 80 HOH HOH . D 4 HOH A 137 437 184 HOH HOH . D 4 HOH A 138 438 122 HOH HOH . D 4 HOH A 139 439 54 HOH HOH . D 4 HOH A 140 440 73 HOH HOH . D 4 HOH A 141 441 205 HOH HOH . D 4 HOH A 142 442 98 HOH HOH . D 4 HOH A 143 443 215 HOH HOH . D 4 HOH A 144 444 33 HOH HOH . D 4 HOH A 145 445 47 HOH HOH . D 4 HOH A 146 446 84 HOH HOH . D 4 HOH A 147 447 101 HOH HOH . D 4 HOH A 148 448 29 HOH HOH . D 4 HOH A 149 449 45 HOH HOH . D 4 HOH A 150 450 219 HOH HOH . D 4 HOH A 151 451 31 HOH HOH . D 4 HOH A 152 452 182 HOH HOH . D 4 HOH A 153 453 176 HOH HOH . D 4 HOH A 154 454 105 HOH HOH . D 4 HOH A 155 455 62 HOH HOH . D 4 HOH A 156 456 75 HOH HOH . D 4 HOH A 157 457 44 HOH HOH . D 4 HOH A 158 458 72 HOH HOH . D 4 HOH A 159 459 123 HOH HOH . D 4 HOH A 160 460 86 HOH HOH . D 4 HOH A 161 461 192 HOH HOH . D 4 HOH A 162 462 9 HOH HOH . D 4 HOH A 163 463 43 HOH HOH . D 4 HOH A 164 464 91 HOH HOH . D 4 HOH A 165 465 111 HOH HOH . D 4 HOH A 166 466 68 HOH HOH . D 4 HOH A 167 467 52 HOH HOH . D 4 HOH A 168 468 166 HOH HOH . D 4 HOH A 169 469 95 HOH HOH . D 4 HOH A 170 470 60 HOH HOH . D 4 HOH A 171 471 132 HOH HOH . D 4 HOH A 172 472 140 HOH HOH . D 4 HOH A 173 473 178 HOH HOH . D 4 HOH A 174 474 117 HOH HOH . D 4 HOH A 175 475 201 HOH HOH . D 4 HOH A 176 476 96 HOH HOH . D 4 HOH A 177 477 200 HOH HOH . D 4 HOH A 178 478 217 HOH HOH . D 4 HOH A 179 479 254 HOH HOH . D 4 HOH A 180 480 85 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 . . . C 3 -13.197 1.412 -1.343 1 11.46 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 -13.522 1.46 -2.795 1 12.14 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 -11.73 1.111 -1.068 1 11.7 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 -14.119 0.587 -0.485 1 12.41 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 -13.337 2.943 -0.804 1 11.86 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 -14.14 4.162 -1.49 1 12.18 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 -13.372 4.712 -2.647 1 12.76 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 -15.556 3.761 -1.686 1 12.87 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 -14.049 5.27 -0.343 1 12.46 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 -14.503 4.97 0.976 1 12.63 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 -14.77 6.237 1.781 1 12.68 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 -13.553 6.982 1.876 1 12.42 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 -15.793 7.175 1.158 1 13.74 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 -16.569 7.769 2.193 1 15.53 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 -14.959 8.232 0.471 1 13.44 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 -15.55 9.529 0.414 1 16.76 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 -13.735 8.289 1.355 1 13.03 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 -12.493 8.663 0.66 1 11.98 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 -12.003 8.083 -0.454 1 11.94 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 -10.835 8.655 -0.799 1 12.52 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 -10.579 9.595 0.113 1 12.49 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 -9.496 10.546 0.339 1 12.75 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 -8.526 10.637 -0.446 1 13.62 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 -9.602 11.326 1.421 1 12.87 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 -10.635 11.291 2.286 1 12.46 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 -10.632 12.132 3.336 1 13.77 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 -11.672 10.444 2.138 1 12.52 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 -11.662 9.592 1.093 1 12.13 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #