data_5XDW # _model_server_result.job_id Gzi8mviuJ94JlS5gnMflaA _model_server_result.datetime_utc '2025-07-14 13:30:40' _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 5xdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5XDW # _exptl.entry_id 5XDW _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 110.71 _cell.angle_gamma 90 _cell.entry_id 5XDW _cell.length_a 71.764 _cell.length_b 51.011 _cell.length_c 88.328 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 O LEU 192 A LEU 200 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc2 A O VAL 195 A VAL 203 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc3 A OD1 ASN 200 A ASN 208 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc4 A O LEU 201 A LEU 209 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc5 C CA CA . A CA 402 1_555 D O HOH . A HOH 553 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc6 C CA CA . A CA 402 1_555 D O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 5XDW _atom_sites.fract_transf_matrix[1][1] 0.013935 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005267 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019604 _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] 0.012103 _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 1 401 1 GDP GDP . C 3 CA A 1 402 1 CA CA . D 4 HOH A 1 501 40 HOH HOH . D 4 HOH A 2 502 129 HOH HOH . D 4 HOH A 3 503 196 HOH HOH . D 4 HOH A 4 504 177 HOH HOH . D 4 HOH A 5 505 22 HOH HOH . D 4 HOH A 6 506 58 HOH HOH . D 4 HOH A 7 507 93 HOH HOH . D 4 HOH A 8 508 54 HOH HOH . D 4 HOH A 9 509 13 HOH HOH . D 4 HOH A 10 510 72 HOH HOH . D 4 HOH A 11 511 7 HOH HOH . D 4 HOH A 12 512 26 HOH HOH . D 4 HOH A 13 513 193 HOH HOH . D 4 HOH A 14 514 126 HOH HOH . D 4 HOH A 15 515 71 HOH HOH . D 4 HOH A 16 516 86 HOH HOH . D 4 HOH A 17 517 43 HOH HOH . D 4 HOH A 18 518 8 HOH HOH . D 4 HOH A 19 519 32 HOH HOH . D 4 HOH A 20 520 133 HOH HOH . D 4 HOH A 21 521 100 HOH HOH . D 4 HOH A 22 522 60 HOH HOH . D 4 HOH A 23 523 96 HOH HOH . D 4 HOH A 24 524 38 HOH HOH . D 4 HOH A 25 525 49 HOH HOH . D 4 HOH A 26 526 157 HOH HOH . D 4 HOH A 27 527 59 HOH HOH . D 4 HOH A 28 528 29 HOH HOH . D 4 HOH A 29 529 5 HOH HOH . D 4 HOH A 30 530 164 HOH HOH . D 4 HOH A 31 531 83 HOH HOH . D 4 HOH A 32 532 109 HOH HOH . D 4 HOH A 33 533 120 HOH HOH . D 4 HOH A 34 534 149 HOH HOH . D 4 HOH A 35 535 76 HOH HOH . D 4 HOH A 36 536 69 HOH HOH . D 4 HOH A 37 537 9 HOH HOH . D 4 HOH A 38 538 92 HOH HOH . D 4 HOH A 39 539 61 HOH HOH . D 4 HOH A 40 540 94 HOH HOH . D 4 HOH A 41 541 150 HOH HOH . D 4 HOH A 42 542 73 HOH HOH . D 4 HOH A 43 543 146 HOH HOH . D 4 HOH A 44 544 63 HOH HOH . D 4 HOH A 45 545 31 HOH HOH . D 4 HOH A 46 546 19 HOH HOH . D 4 HOH A 47 547 105 HOH HOH . D 4 HOH A 48 548 154 HOH HOH . D 4 HOH A 49 549 139 HOH HOH . D 4 HOH A 50 550 194 HOH HOH . D 4 HOH A 51 551 128 HOH HOH . D 4 HOH A 52 552 99 HOH HOH . D 4 HOH A 53 553 3 HOH HOH . D 4 HOH A 54 554 135 HOH HOH . D 4 HOH A 55 555 81 HOH HOH . D 4 HOH A 56 556 4 HOH HOH . D 4 HOH A 57 557 66 HOH HOH . D 4 HOH A 58 558 95 HOH HOH . D 4 HOH A 59 559 50 HOH HOH . D 4 HOH A 60 560 112 HOH HOH . D 4 HOH A 61 561 191 HOH HOH . D 4 HOH A 62 562 108 HOH HOH . D 4 HOH A 63 563 74 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 6 HOH HOH . D 4 HOH A 66 566 80 HOH HOH . D 4 HOH A 67 567 44 HOH HOH . D 4 HOH A 68 568 36 HOH HOH . D 4 HOH A 69 569 140 HOH HOH . D 4 HOH A 70 570 117 HOH HOH . D 4 HOH A 71 571 84 HOH HOH . D 4 HOH A 72 572 12 HOH HOH . D 4 HOH A 73 573 77 HOH HOH . D 4 HOH A 74 574 147 HOH HOH . D 4 HOH A 75 575 153 HOH HOH . D 4 HOH A 76 576 65 HOH HOH . D 4 HOH A 77 577 20 HOH HOH . D 4 HOH A 78 578 145 HOH HOH . D 4 HOH A 79 579 47 HOH HOH . D 4 HOH A 80 580 106 HOH HOH . D 4 HOH A 81 581 136 HOH HOH . D 4 HOH A 82 582 119 HOH HOH . D 4 HOH A 83 583 41 HOH HOH . D 4 HOH A 84 584 2 HOH HOH . D 4 HOH A 85 585 124 HOH HOH . D 4 HOH A 86 586 172 HOH HOH . D 4 HOH A 87 587 142 HOH HOH . D 4 HOH A 88 588 23 HOH HOH . D 4 HOH A 89 589 17 HOH HOH . D 4 HOH A 90 590 163 HOH HOH . D 4 HOH A 91 591 21 HOH HOH . D 4 HOH A 92 592 111 HOH HOH . D 4 HOH A 93 593 37 HOH HOH . D 4 HOH A 94 594 123 HOH HOH . D 4 HOH A 95 595 102 HOH HOH . D 4 HOH A 96 596 18 HOH HOH . D 4 HOH A 97 597 82 HOH HOH . D 4 HOH A 98 598 182 HOH HOH . D 4 HOH A 99 599 67 HOH HOH . D 4 HOH A 100 600 35 HOH HOH . D 4 HOH A 101 601 175 HOH HOH . D 4 HOH A 102 602 115 HOH HOH . D 4 HOH A 103 603 25 HOH HOH . D 4 HOH A 104 604 78 HOH HOH . D 4 HOH A 105 605 155 HOH HOH . D 4 HOH A 106 606 16 HOH HOH . D 4 HOH A 107 607 104 HOH HOH . D 4 HOH A 108 608 132 HOH HOH . D 4 HOH A 109 609 170 HOH HOH . D 4 HOH A 110 610 62 HOH HOH . D 4 HOH A 111 611 27 HOH HOH . D 4 HOH A 112 612 167 HOH HOH . D 4 HOH A 113 613 97 HOH HOH . D 4 HOH A 114 614 107 HOH HOH . D 4 HOH A 115 615 68 HOH HOH . D 4 HOH A 116 616 161 HOH HOH . D 4 HOH A 117 617 87 HOH HOH . D 4 HOH A 118 618 118 HOH HOH . D 4 HOH A 119 619 24 HOH HOH . D 4 HOH A 120 620 110 HOH HOH . D 4 HOH A 121 621 148 HOH HOH . D 4 HOH A 122 622 116 HOH HOH . D 4 HOH A 123 623 174 HOH HOH . D 4 HOH A 124 624 91 HOH HOH . D 4 HOH A 125 625 89 HOH HOH . D 4 HOH A 126 626 151 HOH HOH . D 4 HOH A 127 627 79 HOH HOH . D 4 HOH A 128 628 70 HOH HOH . D 4 HOH A 129 629 190 HOH HOH . D 4 HOH A 130 630 11 HOH HOH . D 4 HOH A 131 631 10 HOH HOH . D 4 HOH A 132 632 122 HOH HOH . D 4 HOH A 133 633 188 HOH HOH . D 4 HOH A 134 634 103 HOH HOH . D 4 HOH A 135 635 53 HOH HOH . D 4 HOH A 136 636 121 HOH HOH . D 4 HOH A 137 637 48 HOH HOH . D 4 HOH A 138 638 138 HOH HOH . D 4 HOH A 139 639 130 HOH HOH . D 4 HOH A 140 640 101 HOH HOH . D 4 HOH A 141 641 52 HOH HOH . D 4 HOH A 142 642 159 HOH HOH . D 4 HOH A 143 643 33 HOH HOH . D 4 HOH A 144 644 15 HOH HOH . D 4 HOH A 145 645 75 HOH HOH . D 4 HOH A 146 646 85 HOH HOH . D 4 HOH A 147 647 34 HOH HOH . D 4 HOH A 148 648 98 HOH HOH . D 4 HOH A 149 649 56 HOH HOH . D 4 HOH A 150 650 156 HOH HOH . D 4 HOH A 151 651 1 HOH HOH . D 4 HOH A 152 652 186 HOH HOH . D 4 HOH A 153 653 181 HOH HOH . D 4 HOH A 154 654 189 HOH HOH . D 4 HOH A 155 655 169 HOH HOH . D 4 HOH A 156 656 185 HOH HOH . D 4 HOH A 157 657 180 HOH HOH . D 4 HOH A 158 658 28 HOH HOH . D 4 HOH A 159 659 158 HOH HOH . D 4 HOH A 160 660 39 HOH HOH . D 4 HOH A 161 661 184 HOH HOH . D 4 HOH A 162 662 187 HOH HOH . D 4 HOH A 163 663 197 HOH HOH . D 4 HOH A 164 664 162 HOH HOH . D 4 HOH A 165 665 195 HOH HOH . D 4 HOH A 166 666 192 HOH HOH . D 4 HOH A 167 667 131 HOH HOH . D 4 HOH A 168 668 141 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 46.148 -9.386 109.588 1 17.13 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 46.962 -8.127 109.66 1 16.08 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 44.716 -9.16 109.97 1 20.04 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 46.746 -10.608 110.199 1 18.01 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 46.063 -9.822 108.037 1 16.84 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 45.924 -8.806 106.811 1 16.6 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 47.276 -8.31 106.41 1 15.88 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 44.851 -7.794 107.088 1 15.65 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 45.389 -9.774 105.647 1 16.2 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 44.167 -10.475 105.749 1 15.82 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 43.539 -10.481 104.359 1 15.92 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 43.192 -9.173 103.92 1 16.06 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 44.493 -11.014 103.305 1 16.32 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 44.386 -12.442 103.349 1 16.66 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 44.02 -10.342 102.029 1 16.55 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 42.881 -11.006 101.473 1 18.03 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 43.449 -9.031 102.503 1 15.84 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 44.25 -7.81 102.387 1 15.5 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 45.357 -7.441 103.076 1 15.07 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 45.74 -6.189 102.728 1 14.7 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 44.835 -5.75 101.824 1 15.5 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 44.614 -4.51 101.059 1 15.62 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 45.412 -3.549 101.196 1 17.09 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 43.569 -4.436 100.235 1 15.53 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 42.699 -5.472 100.06 1 15.75 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 41.669 -5.337 99.198 1 14.47 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 42.822 -6.651 100.736 1 15.41 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 43.855 -6.811 101.614 1 15.76 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #