data_3UMR # _model_server_result.job_id JD_y4ePaFB2MBZ5s-p2-KQ _model_server_result.datetime_utc '2024-10-11 00:30:30' _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 3umr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 3UMR # _exptl.entry_id 3UMR _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 3UMR _cell.length_a 121.952 _cell.length_b 121.952 _cell.length_c 67.382 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UMR _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3UMR _atom_sites.fract_transf_matrix[1][1] 0.0082 _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] 0.0082 _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] 0.014841 _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 1 400 400 GDP GDP . C 3 SO4 A 1 355 1 SO4 SO4 . D 4 CL A 1 356 1 CL CL . E 4 CL A 1 357 2 CL CL . F 4 CL A 1 358 3 CL CL . G 5 GOL A 1 359 1 GOL GOL . H 6 HOH A 1 360 1 HOH HOH . H 6 HOH A 2 361 2 HOH HOH . H 6 HOH A 3 362 3 HOH HOH . H 6 HOH A 4 363 4 HOH HOH . H 6 HOH A 5 364 5 HOH HOH . H 6 HOH A 6 365 6 HOH HOH . H 6 HOH A 7 366 7 HOH HOH . H 6 HOH A 8 367 8 HOH HOH . H 6 HOH A 9 368 9 HOH HOH . H 6 HOH A 10 369 10 HOH HOH . H 6 HOH A 11 370 11 HOH HOH . H 6 HOH A 12 371 12 HOH HOH . H 6 HOH A 13 372 13 HOH HOH . H 6 HOH A 14 373 14 HOH HOH . H 6 HOH A 15 374 15 HOH HOH . H 6 HOH A 16 375 16 HOH HOH . H 6 HOH A 17 376 17 HOH HOH . H 6 HOH A 18 377 18 HOH HOH . H 6 HOH A 19 378 20 HOH HOH . H 6 HOH A 20 379 21 HOH HOH . H 6 HOH A 21 380 22 HOH HOH . H 6 HOH A 22 381 23 HOH HOH . H 6 HOH A 23 382 24 HOH HOH . H 6 HOH A 24 383 25 HOH HOH . H 6 HOH A 25 384 26 HOH HOH . H 6 HOH A 26 385 27 HOH HOH . H 6 HOH A 27 386 28 HOH HOH . H 6 HOH A 28 387 29 HOH HOH . H 6 HOH A 29 388 30 HOH HOH . H 6 HOH A 30 389 31 HOH HOH . H 6 HOH A 31 390 32 HOH HOH . H 6 HOH A 32 391 33 HOH HOH . H 6 HOH A 33 392 34 HOH HOH . H 6 HOH A 34 393 35 HOH HOH . H 6 HOH A 35 394 36 HOH HOH . H 6 HOH A 36 395 37 HOH HOH . H 6 HOH A 37 396 38 HOH HOH . H 6 HOH A 38 397 39 HOH HOH . H 6 HOH A 39 398 40 HOH HOH . H 6 HOH A 40 399 41 HOH HOH . H 6 HOH A 41 401 42 HOH HOH . H 6 HOH A 42 402 43 HOH HOH . H 6 HOH A 43 403 44 HOH HOH . H 6 HOH A 44 404 45 HOH HOH . H 6 HOH A 45 405 46 HOH HOH . H 6 HOH A 46 406 47 HOH HOH . H 6 HOH A 47 407 48 HOH HOH . H 6 HOH A 48 408 49 HOH HOH . H 6 HOH A 49 409 50 HOH HOH . H 6 HOH A 50 410 51 HOH HOH . H 6 HOH A 51 411 52 HOH HOH . H 6 HOH A 52 412 53 HOH HOH . H 6 HOH A 53 413 54 HOH HOH . H 6 HOH A 54 414 55 HOH HOH . H 6 HOH A 55 415 56 HOH HOH . H 6 HOH A 56 416 57 HOH HOH . H 6 HOH A 57 417 58 HOH HOH . H 6 HOH A 58 418 59 HOH HOH . H 6 HOH A 59 419 60 HOH HOH . H 6 HOH A 60 420 61 HOH HOH . H 6 HOH A 61 421 62 HOH HOH . H 6 HOH A 62 422 63 HOH HOH . H 6 HOH A 63 423 64 HOH HOH . H 6 HOH A 64 424 65 HOH HOH . H 6 HOH A 65 425 66 HOH HOH . H 6 HOH A 66 426 67 HOH HOH . H 6 HOH A 67 427 68 HOH HOH . H 6 HOH A 68 428 69 HOH HOH . H 6 HOH A 69 429 70 HOH HOH . H 6 HOH A 70 430 71 HOH HOH . H 6 HOH A 71 431 72 HOH HOH . H 6 HOH A 72 432 73 HOH HOH . H 6 HOH A 73 433 74 HOH HOH . H 6 HOH A 74 434 75 HOH HOH . H 6 HOH A 75 435 76 HOH HOH . H 6 HOH A 76 436 77 HOH HOH . H 6 HOH A 77 437 78 HOH HOH . H 6 HOH A 78 438 79 HOH HOH . H 6 HOH A 79 439 80 HOH HOH . H 6 HOH A 80 440 81 HOH HOH . H 6 HOH A 81 441 83 HOH HOH . H 6 HOH A 82 442 84 HOH HOH . H 6 HOH A 83 443 85 HOH HOH . H 6 HOH A 84 444 86 HOH HOH . H 6 HOH A 85 445 87 HOH HOH . H 6 HOH A 86 446 88 HOH HOH . H 6 HOH A 87 447 89 HOH HOH . H 6 HOH A 88 448 90 HOH HOH . H 6 HOH A 89 449 91 HOH HOH . H 6 HOH A 90 450 92 HOH HOH . H 6 HOH A 91 451 93 HOH HOH . H 6 HOH A 92 452 94 HOH HOH . H 6 HOH A 93 453 95 HOH HOH . H 6 HOH A 94 454 96 HOH HOH . H 6 HOH A 95 455 97 HOH HOH . H 6 HOH A 96 456 98 HOH HOH . H 6 HOH A 97 457 99 HOH HOH . H 6 HOH A 98 458 100 HOH HOH . H 6 HOH A 99 459 101 HOH HOH . H 6 HOH A 100 460 102 HOH HOH . H 6 HOH A 101 461 103 HOH HOH . H 6 HOH A 102 462 104 HOH HOH . H 6 HOH A 103 463 105 HOH HOH . H 6 HOH A 104 464 106 HOH HOH . H 6 HOH A 105 465 107 HOH HOH . H 6 HOH A 106 466 108 HOH HOH . H 6 HOH A 107 467 109 HOH HOH . H 6 HOH A 108 468 110 HOH HOH . H 6 HOH A 109 469 111 HOH HOH . H 6 HOH A 110 470 112 HOH HOH . H 6 HOH A 111 471 113 HOH HOH . H 6 HOH A 112 472 114 HOH HOH . H 6 HOH A 113 473 115 HOH HOH . H 6 HOH A 114 474 117 HOH HOH . H 6 HOH A 115 475 118 HOH HOH . H 6 HOH A 116 476 119 HOH HOH . H 6 HOH A 117 477 120 HOH HOH . H 6 HOH A 118 478 121 HOH HOH . H 6 HOH A 119 479 122 HOH HOH . H 6 HOH A 120 480 123 HOH HOH . H 6 HOH A 121 481 124 HOH HOH . H 6 HOH A 122 482 125 HOH HOH . H 6 HOH A 123 483 126 HOH HOH . H 6 HOH A 124 484 127 HOH HOH . H 6 HOH A 125 485 128 HOH HOH . H 6 HOH A 126 486 129 HOH HOH . H 6 HOH A 127 487 131 HOH HOH . H 6 HOH A 128 488 132 HOH HOH . H 6 HOH A 129 489 133 HOH HOH . H 6 HOH A 130 490 134 HOH HOH . H 6 HOH A 131 491 135 HOH HOH . H 6 HOH A 132 492 136 HOH HOH . H 6 HOH A 133 493 137 HOH HOH . H 6 HOH A 134 494 138 HOH HOH . H 6 HOH A 135 495 139 HOH HOH . H 6 HOH A 136 496 141 HOH HOH . H 6 HOH A 137 497 142 HOH HOH . H 6 HOH A 138 498 143 HOH HOH . H 6 HOH A 139 499 144 HOH HOH . H 6 HOH A 140 500 145 HOH HOH . H 6 HOH A 141 501 146 HOH HOH . H 6 HOH A 142 502 147 HOH HOH . H 6 HOH A 143 503 148 HOH HOH . H 6 HOH A 144 504 149 HOH HOH . H 6 HOH A 145 505 150 HOH HOH . H 6 HOH A 146 506 151 HOH HOH . H 6 HOH A 147 507 152 HOH HOH . H 6 HOH A 148 508 154 HOH HOH . H 6 HOH A 149 509 155 HOH HOH . H 6 HOH A 150 510 156 HOH HOH . H 6 HOH A 151 511 157 HOH HOH . H 6 HOH A 152 512 158 HOH HOH . H 6 HOH A 153 513 159 HOH HOH . H 6 HOH A 154 514 160 HOH HOH . H 6 HOH A 155 515 164 HOH HOH . H 6 HOH A 156 516 165 HOH HOH . H 6 HOH A 157 517 166 HOH HOH . H 6 HOH A 158 518 168 HOH HOH . H 6 HOH A 159 519 169 HOH HOH . H 6 HOH A 160 520 170 HOH HOH . H 6 HOH A 161 521 171 HOH HOH . H 6 HOH A 162 522 172 HOH HOH . H 6 HOH A 163 523 176 HOH HOH . H 6 HOH A 164 524 177 HOH HOH . H 6 HOH A 165 525 178 HOH HOH . H 6 HOH A 166 526 179 HOH HOH . H 6 HOH A 167 527 180 HOH HOH . H 6 HOH A 168 528 181 HOH HOH . H 6 HOH A 169 529 184 HOH HOH . H 6 HOH A 170 530 188 HOH HOH . H 6 HOH A 171 531 189 HOH HOH . H 6 HOH A 172 532 192 HOH HOH . H 6 HOH A 173 533 196 HOH HOH . H 6 HOH A 174 534 198 HOH HOH . H 6 HOH A 175 535 199 HOH HOH . H 6 HOH A 176 536 200 HOH HOH . H 6 HOH A 177 537 201 HOH HOH . H 6 HOH A 178 538 202 HOH HOH . H 6 HOH A 179 539 203 HOH HOH . H 6 HOH A 180 540 205 HOH HOH . H 6 HOH A 181 541 206 HOH HOH . H 6 HOH A 182 542 208 HOH HOH . H 6 HOH A 183 543 209 HOH HOH . H 6 HOH A 184 544 210 HOH HOH . H 6 HOH A 185 545 211 HOH HOH . H 6 HOH A 186 546 212 HOH HOH . H 6 HOH A 187 547 213 HOH HOH . H 6 HOH A 188 548 214 HOH HOH . H 6 HOH A 189 549 216 HOH HOH . H 6 HOH A 190 550 217 HOH HOH . H 6 HOH A 191 551 219 HOH HOH . H 6 HOH A 192 552 221 HOH HOH . H 6 HOH A 193 553 224 HOH HOH . H 6 HOH A 194 554 225 HOH HOH . H 6 HOH A 195 555 226 HOH HOH . H 6 HOH A 196 556 227 HOH HOH . H 6 HOH A 197 557 228 HOH HOH . H 6 HOH A 198 558 229 HOH HOH . H 6 HOH A 199 559 230 HOH HOH . H 6 HOH A 200 560 231 HOH HOH . H 6 HOH A 201 561 232 HOH HOH . H 6 HOH A 202 562 233 HOH HOH . H 6 HOH A 203 563 234 HOH HOH . H 6 HOH A 204 564 235 HOH HOH . H 6 HOH A 205 565 236 HOH HOH . H 6 HOH A 206 566 237 HOH HOH . H 6 HOH A 207 567 238 HOH HOH . H 6 HOH A 208 568 239 HOH HOH . H 6 HOH A 209 569 240 HOH HOH . H 6 HOH A 210 570 241 HOH HOH . H 6 HOH A 211 571 243 HOH HOH . H 6 HOH A 212 572 245 HOH HOH . H 6 HOH A 213 573 247 HOH HOH . H 6 HOH A 214 574 255 HOH HOH . H 6 HOH A 215 575 264 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 22.235 -38.461 1.319 1 29.2 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . B 2 23.661 -37.972 1.288 1 25.99 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . B 2 21.787 -38.79 2.727 1 29.23 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . B 2 21.314 -37.44 0.71 1 28.65 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . B 2 21.982 -39.798 0.467 1 25.4 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . B 2 23.092 -40.805 -0.12 1 25.24 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . B 2 24.003 -41.203 0.996 1 25.56 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . B 2 23.881 -40.188 -1.241 1 26.81 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . B 2 22.24 -42.012 -0.761 1 25.82 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . B 2 21.644 -42.954 0.112 1 29.51 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . B 2 21.791 -44.355 -0.484 1 27.6 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . B 2 21.08 -44.414 -1.708 1 25.33 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . B 2 23.248 -44.673 -0.811 1 25.88 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . B 2 23.474 -46.041 -0.494 1 25.83 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . B 2 23.354 -44.486 -2.313 1 27.65 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . B 2 24.247 -45.364 -2.974 1 25.81 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . B 2 21.954 -44.83 -2.768 1 22.02 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . B 2 21.495 -44.067 -3.933 1 26.61 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . B 2 21.489 -42.735 -4.107 1 27.08 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . B 2 20.873 -42.417 -5.28 1 28.45 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . B 2 20.492 -43.59 -5.859 1 27.7 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . B 2 19.787 -43.988 -7.094 1 25.45 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . B 2 19.415 -43.115 -7.921 1 27.8 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . B 2 19.574 -45.3 -7.299 1 27.58 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . B 2 19.947 -46.255 -6.429 1 29.06 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . B 2 19.676 -47.54 -6.745 1 27.32 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . B 2 20.589 -45.973 -5.255 1 26.26 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . B 2 20.887 -44.671 -4.959 1 28.91 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #