data_9U5T # _model_server_result.job_id AGenAuvthYn6RBeXgBMY_Q _model_server_result.datetime_utc '2025-08-02 19:39:56' _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 9u5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 9U5T # _exptl.entry_id 9U5T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 9U5T _cell.length_a 95.037 _cell.length_b 95.037 _cell.length_c 121.012 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9U5T _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 author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 4 _struct_asym.id D _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 23 A SER 17 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc2 B MG MG . A MG 301 1_555 D O1B GDP . A GDP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc3 B MG MG . A MG 301 1_555 F O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc4 B MG MG . A MG 301 1_555 F O HOH . A HOH 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc5 B MG MG . A MG 301 1_555 F O HOH . A HOH 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc6 B MG MG . A MG 301 1_555 F O HOH . A HOH 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? # _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 166 n n PB O2B GDP sing 167 n n PB O3B GDP sing 168 n n PB O3A GDP sing 169 n n O2B HOB2 GDP sing 170 n n O3B HOB3 GDP sing 171 n n O3A PA GDP sing 172 n n PA O1A GDP doub 173 n n PA O2A GDP sing 174 n n PA O5' GDP sing 175 n n O2A HOA2 GDP sing 176 n n O5' C5' GDP sing 177 n n C5' C4' GDP sing 178 n n C5' H5' GDP sing 179 n n C5' "H5''" GDP sing 180 n n C4' O4' GDP sing 181 n n C4' C3' GDP sing 182 n n C4' H4' GDP sing 183 n n O4' C1' GDP sing 184 n n C3' O3' GDP sing 185 n n C3' C2' GDP sing 186 n n C3' H3' GDP sing 187 n n O3' HO3' GDP sing 188 n n C2' O2' GDP sing 189 n n C2' C1' GDP sing 190 n n C2' H2' GDP sing 191 n n O2' HO2' GDP sing 192 n n C1' N9 GDP sing 193 n n C1' H1' GDP sing 194 n n N9 C8 GDP sing 195 n y N9 C4 GDP sing 196 n y C8 N7 GDP doub 197 n y C8 H8 GDP sing 198 n n N7 C5 GDP sing 199 n y C5 C6 GDP sing 200 n n C5 C4 GDP doub 201 n y C6 O6 GDP doub 202 n n C6 N1 GDP sing 203 n n N1 C2 GDP sing 204 n n N1 HN1 GDP sing 205 n n C2 N2 GDP sing 206 n n C2 N3 GDP doub 207 n n N2 HN21 GDP sing 208 n n N2 HN22 GDP sing 209 n n N3 C4 GDP sing 210 n n # _atom_sites.entry_id 9U5T _atom_sites.fract_transf_matrix[1][1] 0.010522 _atom_sites.fract_transf_matrix[1][2] 0.006075 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01215 _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] 0.008264 _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 1 301 301 MG MG . C 3 A1EN3 A 1 302 302 A1EN3 DRG . D 4 GDP A 1 303 303 GDP GDP . E 5 PEG A 1 304 1 PEG PEG . F 6 HOH A 1 401 106 HOH HOH . F 6 HOH A 2 402 42 HOH HOH . F 6 HOH A 3 403 136 HOH HOH . F 6 HOH A 4 404 167 HOH HOH . F 6 HOH A 5 405 13 HOH HOH . F 6 HOH A 6 406 50 HOH HOH . F 6 HOH A 7 407 164 HOH HOH . F 6 HOH A 8 408 44 HOH HOH . F 6 HOH A 9 409 40 HOH HOH . F 6 HOH A 10 410 20 HOH HOH . F 6 HOH A 11 411 77 HOH HOH . F 6 HOH A 12 412 84 HOH HOH . F 6 HOH A 13 413 51 HOH HOH . F 6 HOH A 14 414 80 HOH HOH . F 6 HOH A 15 415 67 HOH HOH . F 6 HOH A 16 416 101 HOH HOH . F 6 HOH A 17 417 26 HOH HOH . F 6 HOH A 18 418 135 HOH HOH . F 6 HOH A 19 419 97 HOH HOH . F 6 HOH A 20 420 138 HOH HOH . F 6 HOH A 21 421 12 HOH HOH . F 6 HOH A 22 422 117 HOH HOH . F 6 HOH A 23 423 60 HOH HOH . F 6 HOH A 24 424 175 HOH HOH . F 6 HOH A 25 425 89 HOH HOH . F 6 HOH A 26 426 114 HOH HOH . F 6 HOH A 27 427 96 HOH HOH . F 6 HOH A 28 428 65 HOH HOH . F 6 HOH A 29 429 14 HOH HOH . F 6 HOH A 30 430 146 HOH HOH . F 6 HOH A 31 431 157 HOH HOH . F 6 HOH A 32 432 33 HOH HOH . F 6 HOH A 33 433 39 HOH HOH . F 6 HOH A 34 434 170 HOH HOH . F 6 HOH A 35 435 142 HOH HOH . F 6 HOH A 36 436 45 HOH HOH . F 6 HOH A 37 437 28 HOH HOH . F 6 HOH A 38 438 130 HOH HOH . F 6 HOH A 39 439 78 HOH HOH . F 6 HOH A 40 440 25 HOH HOH . F 6 HOH A 41 441 2 HOH HOH . F 6 HOH A 42 442 36 HOH HOH . F 6 HOH A 43 443 1 HOH HOH . F 6 HOH A 44 444 151 HOH HOH . F 6 HOH A 45 445 23 HOH HOH . F 6 HOH A 46 446 110 HOH HOH . F 6 HOH A 47 447 93 HOH HOH . F 6 HOH A 48 448 3 HOH HOH . F 6 HOH A 49 449 49 HOH HOH . F 6 HOH A 50 450 7 HOH HOH . F 6 HOH A 51 451 148 HOH HOH . F 6 HOH A 52 452 24 HOH HOH . F 6 HOH A 53 453 29 HOH HOH . F 6 HOH A 54 454 55 HOH HOH . F 6 HOH A 55 455 8 HOH HOH . F 6 HOH A 56 456 4 HOH HOH . F 6 HOH A 57 457 102 HOH HOH . F 6 HOH A 58 458 181 HOH HOH . F 6 HOH A 59 459 17 HOH HOH . F 6 HOH A 60 460 85 HOH HOH . F 6 HOH A 61 461 125 HOH HOH . F 6 HOH A 62 462 66 HOH HOH . F 6 HOH A 63 463 113 HOH HOH . F 6 HOH A 64 464 18 HOH HOH . F 6 HOH A 65 465 71 HOH HOH . F 6 HOH A 66 466 73 HOH HOH . F 6 HOH A 67 467 34 HOH HOH . F 6 HOH A 68 468 15 HOH HOH . F 6 HOH A 69 469 16 HOH HOH . F 6 HOH A 70 470 32 HOH HOH . F 6 HOH A 71 471 10 HOH HOH . F 6 HOH A 72 472 11 HOH HOH . F 6 HOH A 73 473 111 HOH HOH . F 6 HOH A 74 474 62 HOH HOH . F 6 HOH A 75 475 6 HOH HOH . F 6 HOH A 76 476 90 HOH HOH . F 6 HOH A 77 477 124 HOH HOH . F 6 HOH A 78 478 5 HOH HOH . F 6 HOH A 79 479 81 HOH HOH . F 6 HOH A 80 480 150 HOH HOH . F 6 HOH A 81 481 43 HOH HOH . F 6 HOH A 82 482 87 HOH HOH . F 6 HOH A 83 483 31 HOH HOH . F 6 HOH A 84 484 21 HOH HOH . F 6 HOH A 85 485 48 HOH HOH . F 6 HOH A 86 486 57 HOH HOH . F 6 HOH A 87 487 137 HOH HOH . F 6 HOH A 88 488 54 HOH HOH . F 6 HOH A 89 489 133 HOH HOH . F 6 HOH A 90 490 53 HOH HOH . F 6 HOH A 91 491 61 HOH HOH . F 6 HOH A 92 492 149 HOH HOH . F 6 HOH A 93 493 79 HOH HOH . F 6 HOH A 94 494 134 HOH HOH . F 6 HOH A 95 495 9 HOH HOH . F 6 HOH A 96 496 74 HOH HOH . F 6 HOH A 97 497 141 HOH HOH . F 6 HOH A 98 498 131 HOH HOH . F 6 HOH A 99 499 118 HOH HOH . F 6 HOH A 100 500 52 HOH HOH . F 6 HOH A 101 501 115 HOH HOH . F 6 HOH A 102 502 35 HOH HOH . F 6 HOH A 103 503 46 HOH HOH . F 6 HOH A 104 504 140 HOH HOH . F 6 HOH A 105 505 75 HOH HOH . F 6 HOH A 106 506 153 HOH HOH . F 6 HOH A 107 507 112 HOH HOH . F 6 HOH A 108 508 27 HOH HOH . F 6 HOH A 109 509 172 HOH HOH . F 6 HOH A 110 510 59 HOH HOH . F 6 HOH A 111 511 38 HOH HOH . F 6 HOH A 112 512 82 HOH HOH . F 6 HOH A 113 513 107 HOH HOH . F 6 HOH A 114 514 37 HOH HOH . F 6 HOH A 115 515 19 HOH HOH . F 6 HOH A 116 516 109 HOH HOH . F 6 HOH A 117 517 83 HOH HOH . F 6 HOH A 118 518 69 HOH HOH . F 6 HOH A 119 519 120 HOH HOH . F 6 HOH A 120 520 22 HOH HOH . F 6 HOH A 121 521 158 HOH HOH . F 6 HOH A 122 522 76 HOH HOH . F 6 HOH A 123 523 92 HOH HOH . F 6 HOH A 124 524 103 HOH HOH . F 6 HOH A 125 525 105 HOH HOH . F 6 HOH A 126 526 116 HOH HOH . F 6 HOH A 127 527 123 HOH HOH . F 6 HOH A 128 528 159 HOH HOH . F 6 HOH A 129 529 64 HOH HOH . F 6 HOH A 130 530 72 HOH HOH . F 6 HOH A 131 531 63 HOH HOH . F 6 HOH A 132 532 41 HOH HOH . F 6 HOH A 133 533 132 HOH HOH . F 6 HOH A 134 534 143 HOH HOH . F 6 HOH A 135 535 147 HOH HOH . F 6 HOH A 136 536 145 HOH HOH . F 6 HOH A 137 537 180 HOH HOH . F 6 HOH A 138 538 86 HOH HOH . F 6 HOH A 139 539 68 HOH HOH . F 6 HOH A 140 540 58 HOH HOH . F 6 HOH A 141 541 139 HOH HOH . F 6 HOH A 142 542 108 HOH HOH . F 6 HOH A 143 543 182 HOH HOH . F 6 HOH A 144 544 98 HOH HOH . F 6 HOH A 145 545 94 HOH HOH . F 6 HOH A 146 546 47 HOH HOH . F 6 HOH A 147 547 127 HOH HOH . F 6 HOH A 148 548 119 HOH HOH . F 6 HOH A 149 549 166 HOH HOH . F 6 HOH A 150 550 122 HOH HOH . F 6 HOH A 151 551 30 HOH HOH . F 6 HOH A 152 552 99 HOH HOH . F 6 HOH A 153 553 162 HOH HOH . F 6 HOH A 154 554 165 HOH HOH . F 6 HOH A 155 555 129 HOH HOH . F 6 HOH A 156 556 70 HOH HOH . F 6 HOH A 157 557 126 HOH HOH . F 6 HOH A 158 558 100 HOH HOH . F 6 HOH A 159 559 178 HOH HOH . F 6 HOH A 160 560 173 HOH HOH . F 6 HOH A 161 561 56 HOH HOH . F 6 HOH A 162 562 144 HOH HOH . F 6 HOH A 163 563 152 HOH HOH . F 6 HOH A 164 564 155 HOH HOH . F 6 HOH A 165 565 95 HOH HOH . F 6 HOH A 166 566 176 HOH HOH . F 6 HOH A 167 567 154 HOH HOH . F 6 HOH A 168 568 156 HOH HOH . F 6 HOH A 169 569 174 HOH HOH . F 6 HOH A 170 570 104 HOH HOH . F 6 HOH A 171 571 168 HOH HOH . F 6 HOH A 172 572 88 HOH HOH . F 6 HOH A 173 573 169 HOH HOH . F 6 HOH A 174 574 91 HOH HOH . F 6 HOH A 175 575 161 HOH HOH . F 6 HOH A 176 576 177 HOH HOH . F 6 HOH A 177 577 163 HOH HOH . F 6 HOH A 178 578 121 HOH HOH . F 6 HOH A 179 579 128 HOH HOH . F 6 HOH A 180 580 160 HOH HOH . F 6 HOH A 181 581 179 HOH HOH . F 6 HOH A 182 582 171 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 . . . D 4 -8.315 14.145 21.644 1 9.32 ? PB GDP 303 A 1 HETATM 2 O O1B GDP . . . D 4 -8.787 15.461 21.071 1 9.2 ? O1B GDP 303 A 1 HETATM 3 O O2B GDP . . . D 4 -7.195 14.318 22.683 1 9.26 ? O2B GDP 303 A 1 HETATM 4 O O3B GDP . . . D 4 -7.954 13.078 20.608 1 9.92 ? O3B GDP 303 A 1 HETATM 5 O O3A GDP . . . D 4 -9.541 13.538 22.452 1 10.27 ? O3A GDP 303 A 1 HETATM 6 P PA GDP . . . D 4 -11.124 13.858 22.326 1 10.02 ? PA GDP 303 A 1 HETATM 7 O O1A GDP . . . D 4 -11.663 13.555 20.949 1 12.13 ? O1A GDP 303 A 1 HETATM 8 O O2A GDP . . . D 4 -11.453 15.09 23.056 1 11.56 ? O2A GDP 303 A 1 HETATM 9 O O5' GDP . . . D 4 -11.737 12.741 23.321 1 10.19 ? O5' GDP 303 A 1 HETATM 10 C C5' GDP . . . D 4 -11.585 11.424 22.938 1 11.39 ? C5' GDP 303 A 1 HETATM 11 C C4' GDP . . . D 4 -12.756 10.615 23.408 1 12.45 ? C4' GDP 303 A 1 HETATM 12 O O4' GDP . . . D 4 -12.741 10.536 24.841 1 10.79 ? O4' GDP 303 A 1 HETATM 13 C C3' GDP . . . D 4 -14.077 11.224 23.001 1 13.26 ? C3' GDP 303 A 1 HETATM 14 O O3' GDP . . . D 4 -14.946 10.117 22.82 1 16 ? O3' GDP 303 A 1 HETATM 15 C C2' GDP . . . D 4 -14.488 12.006 24.218 1 13.18 ? C2' GDP 303 A 1 HETATM 16 O O2' GDP . . . D 4 -15.889 12.157 24.406 1 16.11 ? O2' GDP 303 A 1 HETATM 17 C C1' GDP . . . D 4 -13.912 11.195 25.351 1 11.57 ? C1' GDP 303 A 1 HETATM 18 N N9 GDP . . . D 4 -13.589 12.074 26.521 1 10.25 ? N9 GDP 303 A 1 HETATM 19 C C8 GDP . . . D 4 -12.818 13.188 26.508 1 9.85 ? C8 GDP 303 A 1 HETATM 20 N N7 GDP . . . D 4 -12.653 13.703 27.733 1 9.35 ? N7 GDP 303 A 1 HETATM 21 C C5 GDP . . . D 4 -13.366 12.858 28.571 1 9.64 ? C5 GDP 303 A 1 HETATM 22 C C6 GDP . . . D 4 -13.671 12.839 29.978 1 9.78 ? C6 GDP 303 A 1 HETATM 23 O O6 GDP . . . D 4 -13.142 13.673 30.8 1 9.44 ? O6 GDP 303 A 1 HETATM 24 N N1 GDP . . . D 4 -14.427 11.777 30.446 1 10.23 ? N1 GDP 303 A 1 HETATM 25 C C2 GDP . . . D 4 -14.951 10.825 29.594 1 10.78 ? C2 GDP 303 A 1 HETATM 26 N N2 GDP . . . D 4 -15.693 9.857 30.116 1 11.34 ? N2 GDP 303 A 1 HETATM 27 N N3 GDP . . . D 4 -14.694 10.788 28.284 1 9.65 ? N3 GDP 303 A 1 HETATM 28 C C4 GDP . . . D 4 -13.963 11.799 27.742 1 9.95 ? C4 GDP 303 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #