data_5ODT
#
_model_server_result.job_id            XwKd8BU3fpPWw7d3f1gRMQ 
_model_server_result.datetime_utc      '2025-04-11 16:00:35' 
_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          5odt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5ODT 
#
_exptl.entry_id    5ODT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-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            5ODT 
_cell.length_a            137.04 
_cell.length_b            137.04 
_cell.length_c            137.04 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ODT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        197 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,I,J,K,L 
_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 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     5ODT 
_atom_sites.fract_transf_matrix[1][1]    0.007297 
_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]    0.007297 
_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]    0.007297 
_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
C 3 ADP A 1 501 1 ADP ADP . 
D 4 GOL A 1 502 2 GOL GOL . 
E 4 GOL A 1 503 3 GOL GOL . 
F 4 GOL A 1 504 4 GOL GOL . 
G 5 SO4 A 1 505 5 SO4 SO4 . 
H 5 SO4 A 1 506 7 SO4 SO4 . 
I 5 SO4 A 1 507 8 SO4 SO4 . 
J 5 SO4 B 1 601 6 SO4 SO4 . 
K 6 HOH A 1 601 126 HOH HOH . 
K 6 HOH A 2 602 72 HOH HOH . 
K 6 HOH A 3 603 97 HOH HOH . 
K 6 HOH A 4 604 92 HOH HOH . 
K 6 HOH A 5 605 42 HOH HOH . 
K 6 HOH A 6 606 106 HOH HOH . 
K 6 HOH A 7 607 43 HOH HOH . 
K 6 HOH A 8 608 68 HOH HOH . 
K 6 HOH A 9 609 49 HOH HOH . 
K 6 HOH A 10 610 36 HOH HOH . 
K 6 HOH A 11 611 70 HOH HOH . 
K 6 HOH A 12 612 23 HOH HOH . 
K 6 HOH A 13 613 111 HOH HOH . 
K 6 HOH A 14 614 25 HOH HOH . 
K 6 HOH A 15 615 45 HOH HOH . 
K 6 HOH A 16 616 9 HOH HOH . 
K 6 HOH A 17 617 79 HOH HOH . 
K 6 HOH A 18 618 85 HOH HOH . 
K 6 HOH A 19 619 52 HOH HOH . 
K 6 HOH A 20 620 44 HOH HOH . 
K 6 HOH A 21 621 57 HOH HOH . 
K 6 HOH A 22 622 133 HOH HOH . 
K 6 HOH A 23 623 109 HOH HOH . 
K 6 HOH A 24 624 31 HOH HOH . 
K 6 HOH A 25 625 33 HOH HOH . 
K 6 HOH A 26 626 128 HOH HOH . 
K 6 HOH A 27 627 54 HOH HOH . 
K 6 HOH A 28 628 17 HOH HOH . 
K 6 HOH A 29 629 21 HOH HOH . 
K 6 HOH A 30 630 63 HOH HOH . 
K 6 HOH A 31 631 119 HOH HOH . 
K 6 HOH A 32 632 90 HOH HOH . 
K 6 HOH A 33 633 41 HOH HOH . 
K 6 HOH A 34 634 1 HOH HOH . 
K 6 HOH A 35 635 12 HOH HOH . 
K 6 HOH A 36 636 22 HOH HOH . 
K 6 HOH A 37 637 19 HOH HOH . 
K 6 HOH A 38 638 2 HOH HOH . 
K 6 HOH A 39 639 35 HOH HOH . 
K 6 HOH A 40 640 29 HOH HOH . 
K 6 HOH A 41 641 6 HOH HOH . 
K 6 HOH A 42 642 13 HOH HOH . 
K 6 HOH A 43 643 88 HOH HOH . 
K 6 HOH A 44 644 104 HOH HOH . 
K 6 HOH A 45 645 15 HOH HOH . 
K 6 HOH A 46 646 20 HOH HOH . 
K 6 HOH A 47 647 74 HOH HOH . 
K 6 HOH A 48 648 5 HOH HOH . 
K 6 HOH A 49 649 4 HOH HOH . 
K 6 HOH A 50 650 101 HOH HOH . 
K 6 HOH A 51 651 55 HOH HOH . 
K 6 HOH A 52 652 73 HOH HOH . 
K 6 HOH A 53 653 48 HOH HOH . 
K 6 HOH A 54 654 18 HOH HOH . 
K 6 HOH A 55 655 16 HOH HOH . 
K 6 HOH A 56 656 30 HOH HOH . 
K 6 HOH A 57 657 32 HOH HOH . 
K 6 HOH A 58 658 34 HOH HOH . 
K 6 HOH A 59 659 8 HOH HOH . 
K 6 HOH A 60 660 59 HOH HOH . 
K 6 HOH A 61 661 39 HOH HOH . 
K 6 HOH A 62 662 78 HOH HOH . 
K 6 HOH A 63 663 7 HOH HOH . 
K 6 HOH A 64 664 26 HOH HOH . 
K 6 HOH A 65 665 46 HOH HOH . 
K 6 HOH A 66 666 124 HOH HOH . 
K 6 HOH A 67 667 37 HOH HOH . 
K 6 HOH A 68 668 123 HOH HOH . 
K 6 HOH A 69 669 3 HOH HOH . 
K 6 HOH A 70 670 47 HOH HOH . 
K 6 HOH A 71 671 38 HOH HOH . 
K 6 HOH A 72 672 86 HOH HOH . 
K 6 HOH A 73 673 62 HOH HOH . 
K 6 HOH A 74 674 28 HOH HOH . 
K 6 HOH A 75 675 11 HOH HOH . 
K 6 HOH A 76 676 80 HOH HOH . 
K 6 HOH A 77 677 103 HOH HOH . 
K 6 HOH A 78 678 99 HOH HOH . 
K 6 HOH A 79 679 69 HOH HOH . 
K 6 HOH A 80 680 118 HOH HOH . 
K 6 HOH A 81 681 50 HOH HOH . 
K 6 HOH A 82 682 27 HOH HOH . 
K 6 HOH A 83 683 51 HOH HOH . 
K 6 HOH A 84 684 93 HOH HOH . 
K 6 HOH A 85 685 96 HOH HOH . 
K 6 HOH A 86 686 83 HOH HOH . 
K 6 HOH A 87 687 40 HOH HOH . 
K 6 HOH A 88 688 66 HOH HOH . 
K 6 HOH A 89 689 100 HOH HOH . 
K 6 HOH A 90 690 64 HOH HOH . 
K 6 HOH A 91 691 71 HOH HOH . 
K 6 HOH A 92 692 113 HOH HOH . 
K 6 HOH A 93 693 56 HOH HOH . 
K 6 HOH A 94 694 77 HOH HOH . 
K 6 HOH A 95 695 117 HOH HOH . 
K 6 HOH A 96 696 122 HOH HOH . 
K 6 HOH A 97 697 24 HOH HOH . 
K 6 HOH A 98 698 107 HOH HOH . 
K 6 HOH A 99 699 58 HOH HOH . 
K 6 HOH A 100 700 91 HOH HOH . 
K 6 HOH A 101 701 98 HOH HOH . 
K 6 HOH A 102 702 115 HOH HOH . 
K 6 HOH A 103 703 134 HOH HOH . 
K 6 HOH A 104 704 65 HOH HOH . 
K 6 HOH A 105 705 138 HOH HOH . 
K 6 HOH A 106 706 67 HOH HOH . 
K 6 HOH A 107 707 136 HOH HOH . 
K 6 HOH A 108 708 114 HOH HOH . 
K 6 HOH A 109 709 95 HOH HOH . 
K 6 HOH A 110 710 110 HOH HOH . 
K 6 HOH A 111 711 129 HOH HOH . 
K 6 HOH A 112 712 81 HOH HOH . 
K 6 HOH A 113 713 121 HOH HOH . 
K 6 HOH A 114 714 140 HOH HOH . 
K 6 HOH A 115 715 127 HOH HOH . 
K 6 HOH A 116 716 139 HOH HOH . 
K 6 HOH A 117 717 75 HOH HOH . 
K 6 HOH A 118 718 125 HOH HOH . 
K 6 HOH A 119 719 137 HOH HOH . 
K 6 HOH A 120 720 131 HOH HOH . 
K 6 HOH A 121 721 135 HOH HOH . 
K 6 HOH A 122 722 116 HOH HOH . 
K 6 HOH A 123 723 76 HOH HOH . 
K 6 HOH A 124 724 82 HOH HOH . 
K 6 HOH A 125 725 132 HOH HOH . 
K 6 HOH A 126 726 61 HOH HOH . 
K 6 HOH A 127 727 105 HOH HOH . 
K 6 HOH A 128 728 112 HOH HOH . 
L 6 HOH B 1 701 102 HOH HOH . 
L 6 HOH B 2 702 87 HOH HOH . 
L 6 HOH B 3 703 53 HOH HOH . 
L 6 HOH B 4 704 108 HOH HOH . 
L 6 HOH B 5 705 14 HOH HOH . 
L 6 HOH B 6 706 10 HOH HOH . 
L 6 HOH B 7 707 84 HOH HOH . 
L 6 HOH B 8 708 89 HOH HOH . 
L 6 HOH B 9 709 130 HOH HOH . 
L 6 HOH B 10 710 60 HOH HOH . 
L 6 HOH B 11 711 94 HOH HOH . 
L 6 HOH B 12 712 120 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 ADP . . . C 3 17.648 177.298 36.567 1 90.82 ? PB ADP 501 A 1 
HETATM 2 O O1B ADP . . . C 3 18.394 178.178 35.588 1 78.17 ? O1B ADP 501 A 1 
HETATM 3 O O2B ADP . . . C 3 16.147 177.51 36.533 1 70.87 ? O2B ADP 501 A 1 
HETATM 4 O O3B ADP . . . C 3 18.047 175.835 36.5 1 63.58 ? O3B ADP 501 A 1 
HETATM 5 P PA ADP . . . C 3 17.144 178.411 39.169 1 41.6 ? PA ADP 501 A 1 
HETATM 6 O O1A ADP . . . C 3 16.249 179.5 38.617 1 44.49 ? O1A ADP 501 A 1 
HETATM 7 O O2A ADP . . . C 3 17.902 178.68 40.453 1 45.59 ? O2A ADP 501 A 1 
HETATM 8 O O3A ADP . . . C 3 18.133 177.805 38.042 1 54.96 ? O3A ADP 501 A 1 
HETATM 9 O O5' ADP . . . C 3 16.212 177.119 39.4 1 43.58 ? O5' ADP 501 A 1 
HETATM 10 C C5' ADP . . . C 3 16.677 175.889 39.959 1 40.48 ? C5' ADP 501 A 1 
HETATM 11 C C4' ADP . . . C 3 15.601 174.818 39.815 1 40.83 ? C4' ADP 501 A 1 
HETATM 12 O O4' ADP . . . C 3 14.517 175.099 40.711 1 38.99 ? O4' ADP 501 A 1 
HETATM 13 C C3' ADP . . . C 3 15.007 174.777 38.412 1 44.81 ? C3' ADP 501 A 1 
HETATM 14 O O3' ADP . . . C 3 14.55 173.442 38.177 1 43.54 ? O3' ADP 501 A 1 
HETATM 15 C C2' ADP . . . C 3 13.785 175.656 38.525 1 37.61 ? C2' ADP 501 A 1 
HETATM 16 O O2' ADP . . . C 3 12.793 175.314 37.56 1 37.55 ? O2' ADP 501 A 1 
HETATM 17 C C1' ADP . . . C 3 13.333 175.384 39.957 1 38.03 ? C1' ADP 501 A 1 
HETATM 18 N N9 ADP . . . C 3 12.73 176.605 40.512 1 36.79 ? N9 ADP 501 A 1 
HETATM 19 C C8 ADP . . . C 3 13.379 177.765 40.67 1 36.09 ? C8 ADP 501 A 1 
HETATM 20 N N7 ADP . . . C 3 12.573 178.692 41.203 1 34.8 ? N7 ADP 501 A 1 
HETATM 21 C C5 ADP . . . C 3 11.375 178.111 41.384 1 34.35 ? C5 ADP 501 A 1 
HETATM 22 C C6 ADP . . . C 3 10.069 178.559 41.895 1 31.71 ? C6 ADP 501 A 1 
HETATM 23 N N6 ADP . . . C 3 9.919 179.841 42.338 1 33.29 ? N6 ADP 501 A 1 
HETATM 24 N N1 ADP . . . C 3 9.067 177.654 41.902 1 30.32 ? N1 ADP 501 A 1 
HETATM 25 C C2 ADP . . . C 3 9.239 176.388 41.461 1 29.96 ? C2 ADP 501 A 1 
HETATM 26 N N3 ADP . . . C 3 10.402 175.92 40.975 1 30.64 ? N3 ADP 501 A 1 
HETATM 27 C C4 ADP . . . C 3 11.48 176.733 40.919 1 30.64 ? C4 ADP 501 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#