data_5M04 # _model_server_result.job_id lLcyYzK6MuZYe7_w3himiA _model_server_result.datetime_utc '2025-08-31 19:12:06' _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 5m04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5M04 # _exptl.entry_id 5M04 _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 5M04 _cell.length_a 64.59 _cell.length_b 83 _cell.length_c 177.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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 # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id O1B _struct_conn.ptnr1_label_comp_id GDP _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GDP _struct_conn.ptnr1_auth_seq_id 401 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 402 _struct_conn.ptnr2_symmetry 1_555 _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 2.805 _struct_conn.pdbx_value_order ? # _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 5M04 _atom_sites.fract_transf_matrix[1][1] 0.015482 _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] 0.012048 _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] 0.005635 _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 MG A 1 402 2 MG MG . D 4 HOH A 1 501 61 HOH HOH . D 4 HOH A 2 502 13 HOH HOH . D 4 HOH A 3 503 122 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 76 HOH HOH . D 4 HOH A 6 506 17 HOH HOH . D 4 HOH A 7 507 153 HOH HOH . D 4 HOH A 8 508 108 HOH HOH . D 4 HOH A 9 509 37 HOH HOH . D 4 HOH A 10 510 165 HOH HOH . D 4 HOH A 11 511 157 HOH HOH . D 4 HOH A 12 512 53 HOH HOH . D 4 HOH A 13 513 47 HOH HOH . D 4 HOH A 14 514 39 HOH HOH . D 4 HOH A 15 515 69 HOH HOH . D 4 HOH A 16 516 50 HOH HOH . D 4 HOH A 17 517 112 HOH HOH . D 4 HOH A 18 518 136 HOH HOH . D 4 HOH A 19 519 86 HOH HOH . D 4 HOH A 20 520 88 HOH HOH . D 4 HOH A 21 521 12 HOH HOH . D 4 HOH A 22 522 33 HOH HOH . D 4 HOH A 23 523 100 HOH HOH . D 4 HOH A 24 524 92 HOH HOH . D 4 HOH A 25 525 70 HOH HOH . D 4 HOH A 26 526 63 HOH HOH . D 4 HOH A 27 527 121 HOH HOH . D 4 HOH A 28 528 43 HOH HOH . D 4 HOH A 29 529 151 HOH HOH . D 4 HOH A 30 530 160 HOH HOH . D 4 HOH A 31 531 98 HOH HOH . D 4 HOH A 32 532 87 HOH HOH . D 4 HOH A 33 533 144 HOH HOH . D 4 HOH A 34 534 14 HOH HOH . D 4 HOH A 35 535 20 HOH HOH . D 4 HOH A 36 536 107 HOH HOH . D 4 HOH A 37 537 44 HOH HOH . D 4 HOH A 38 538 55 HOH HOH . D 4 HOH A 39 539 35 HOH HOH . D 4 HOH A 40 540 49 HOH HOH . D 4 HOH A 41 541 96 HOH HOH . D 4 HOH A 42 542 3 HOH HOH . D 4 HOH A 43 543 90 HOH HOH . D 4 HOH A 44 544 123 HOH HOH . D 4 HOH A 45 545 64 HOH HOH . D 4 HOH A 46 546 101 HOH HOH . D 4 HOH A 47 547 142 HOH HOH . D 4 HOH A 48 548 45 HOH HOH . D 4 HOH A 49 549 1 HOH HOH . D 4 HOH A 50 550 137 HOH HOH . D 4 HOH A 51 551 26 HOH HOH . D 4 HOH A 52 552 34 HOH HOH . D 4 HOH A 53 553 51 HOH HOH . D 4 HOH A 54 554 83 HOH HOH . D 4 HOH A 55 555 11 HOH HOH . D 4 HOH A 56 556 10 HOH HOH . D 4 HOH A 57 557 54 HOH HOH . D 4 HOH A 58 558 18 HOH HOH . D 4 HOH A 59 559 117 HOH HOH . D 4 HOH A 60 560 6 HOH HOH . D 4 HOH A 61 561 99 HOH HOH . D 4 HOH A 62 562 75 HOH HOH . D 4 HOH A 63 563 36 HOH HOH . D 4 HOH A 64 564 30 HOH HOH . D 4 HOH A 65 565 32 HOH HOH . D 4 HOH A 66 566 52 HOH HOH . D 4 HOH A 67 567 68 HOH HOH . D 4 HOH A 68 568 5 HOH HOH . D 4 HOH A 69 569 152 HOH HOH . D 4 HOH A 70 570 145 HOH HOH . D 4 HOH A 71 571 97 HOH HOH . D 4 HOH A 72 572 8 HOH HOH . D 4 HOH A 73 573 89 HOH HOH . D 4 HOH A 74 574 156 HOH HOH . D 4 HOH A 75 575 169 HOH HOH . D 4 HOH A 76 576 31 HOH HOH . D 4 HOH A 77 577 106 HOH HOH . D 4 HOH A 78 578 19 HOH HOH . D 4 HOH A 79 579 60 HOH HOH . D 4 HOH A 80 580 139 HOH HOH . D 4 HOH A 81 581 58 HOH HOH . D 4 HOH A 82 582 72 HOH HOH . D 4 HOH A 83 583 27 HOH HOH . D 4 HOH A 84 584 40 HOH HOH . D 4 HOH A 85 585 23 HOH HOH . D 4 HOH A 86 586 109 HOH HOH . D 4 HOH A 87 587 62 HOH HOH . D 4 HOH A 88 588 155 HOH HOH . D 4 HOH A 89 589 126 HOH HOH . D 4 HOH A 90 590 16 HOH HOH . D 4 HOH A 91 591 73 HOH HOH . D 4 HOH A 92 592 81 HOH HOH . D 4 HOH A 93 593 133 HOH HOH . D 4 HOH A 94 594 21 HOH HOH . D 4 HOH A 95 595 22 HOH HOH . D 4 HOH A 96 596 148 HOH HOH . D 4 HOH A 97 597 124 HOH HOH . D 4 HOH A 98 598 111 HOH HOH . D 4 HOH A 99 599 41 HOH HOH . D 4 HOH A 100 600 28 HOH HOH . D 4 HOH A 101 601 46 HOH HOH . D 4 HOH A 102 602 164 HOH HOH . D 4 HOH A 103 603 138 HOH HOH . D 4 HOH A 104 604 128 HOH HOH . D 4 HOH A 105 605 79 HOH HOH . D 4 HOH A 106 606 104 HOH HOH . D 4 HOH A 107 607 67 HOH HOH . D 4 HOH A 108 608 2 HOH HOH . D 4 HOH A 109 609 119 HOH HOH . D 4 HOH A 110 610 71 HOH HOH . D 4 HOH A 111 611 25 HOH HOH . D 4 HOH A 112 612 116 HOH HOH . D 4 HOH A 113 613 118 HOH HOH . D 4 HOH A 114 614 38 HOH HOH . D 4 HOH A 115 615 150 HOH HOH . D 4 HOH A 116 616 24 HOH HOH . D 4 HOH A 117 617 57 HOH HOH . D 4 HOH A 118 618 168 HOH HOH . D 4 HOH A 119 619 163 HOH HOH . D 4 HOH A 120 620 120 HOH HOH . D 4 HOH A 121 621 125 HOH HOH . D 4 HOH A 122 622 84 HOH HOH . D 4 HOH A 123 623 59 HOH HOH . D 4 HOH A 124 624 95 HOH HOH . D 4 HOH A 125 625 91 HOH HOH . D 4 HOH A 126 626 15 HOH HOH . D 4 HOH A 127 627 143 HOH HOH . D 4 HOH A 128 628 115 HOH HOH . D 4 HOH A 129 629 9 HOH HOH . D 4 HOH A 130 630 48 HOH HOH . D 4 HOH A 131 631 154 HOH HOH . D 4 HOH A 132 632 29 HOH HOH . D 4 HOH A 133 633 7 HOH HOH . D 4 HOH A 134 634 166 HOH HOH . D 4 HOH A 135 635 94 HOH HOH . D 4 HOH A 136 636 80 HOH HOH . D 4 HOH A 137 637 82 HOH HOH . D 4 HOH A 138 638 105 HOH HOH . D 4 HOH A 139 639 147 HOH HOH . D 4 HOH A 140 640 127 HOH HOH . D 4 HOH A 141 641 65 HOH HOH . D 4 HOH A 142 642 141 HOH HOH . D 4 HOH A 143 643 103 HOH HOH . D 4 HOH A 144 644 149 HOH HOH . D 4 HOH A 145 645 42 HOH HOH . D 4 HOH A 146 646 110 HOH HOH . D 4 HOH A 147 647 167 HOH HOH . D 4 HOH A 148 648 159 HOH HOH . D 4 HOH A 149 649 77 HOH HOH . D 4 HOH A 150 650 161 HOH HOH . D 4 HOH A 151 651 56 HOH HOH . D 4 HOH A 152 652 113 HOH HOH . D 4 HOH A 153 653 66 HOH HOH . D 4 HOH A 154 654 158 HOH HOH . D 4 HOH A 155 655 74 HOH HOH . D 4 HOH A 156 656 135 HOH HOH . D 4 HOH A 157 657 78 HOH HOH . D 4 HOH A 158 658 102 HOH HOH . D 4 HOH A 159 659 134 HOH HOH . D 4 HOH A 160 660 93 HOH HOH . D 4 HOH A 161 661 162 HOH HOH . D 4 HOH A 162 662 146 HOH HOH . D 4 HOH A 163 663 132 HOH HOH . D 4 HOH A 164 664 140 HOH HOH . D 4 HOH A 165 665 129 HOH HOH . D 4 HOH A 166 666 131 HOH HOH . D 4 HOH A 167 667 130 HOH HOH . D 4 HOH A 168 668 85 HOH HOH . D 4 HOH A 169 669 114 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 -5.934 38.809 7.847 1 39.29 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 -5.984 38.647 6.355 1 41.89 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 -5.748 37.522 8.622 1 41.06 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 -7.033 39.677 8.313 1 43.39 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 -4.631 39.723 8.185 1 40.75 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 -3.619 40.509 7.159 1 43.65 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 -2.796 39.665 6.193 1 41.72 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 -4.393 41.664 6.646 1 46.17 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 -2.545 41.044 8.156 1 40.68 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 -2.969 41.955 9.17 1 44.76 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 -1.946 43.031 9.415 1 41.15 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 -0.859 42.418 10.105 1 40.34 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 -1.392 43.657 8.167 1 44.8 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 -1.086 45.043 8.407 1 46.6 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 -0.056 42.967 7.982 1 43.52 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 0.911 43.762 7.247 1 43.75 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 0.353 42.607 9.407 1 40.23 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 1.162 41.331 9.404 1 43.03 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 0.819 40.128 8.864 1 40.39 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 1.791 39.209 9.014 1 38.27 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 2.776 39.829 9.684 1 41.28 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 4.079 39.481 10.215 1 40.86 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 4.625 38.341 10.068 1 39.92 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 4.748 40.475 10.848 1 45.8 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 4.29 41.742 11.034 1 47.2 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 5.036 42.661 11.705 1 49.18 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 3.088 42.123 10.607 1 44.92 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 2.328 41.225 9.946 1 42.86 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #