data_1YRS # _model_server_result.job_id VZKOiPNR90lruAvHVDxXlw _model_server_result.datetime_utc '2024-10-13 13:18:03' _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 1yrs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 1YRS # _exptl.entry_id 1YRS _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 2 _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 1YRS _cell.length_a 69.3 _cell.length_b 79.8 _cell.length_c 159.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YRS _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N 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 OG1 THR 112 A THR 112 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc2 D O1B ADP . A ADP 601 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.139 ? metalc ? metalc3 D O3B ADP . A ADP 601 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc4 C MG MG . A MG 603 1_555 I O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc5 C MG MG . A MG 603 1_555 I O HOH . A HOH 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc6 B OG1 THR 112 B THR 112 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc7 G O3B ADP . B ADP 600 1_555 F MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc8 F MG MG . B MG 602 1_555 J O HOH . B HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? # _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 1YRS _atom_sites.fract_transf_matrix[1][1] 0.01443 _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] 0.012531 _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] 0.006266 _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 2 MG A 1 603 603 MG MG . D 3 ADP A 1 601 601 ADP ADP . E 4 L47 A 1 604 2 L47 L47 . F 2 MG B 1 602 602 MG MG . G 3 ADP B 1 600 600 ADP ADP . H 4 L47 B 1 603 1 L47 L47 . I 5 HOH A 1 605 1 HOH HOH . I 5 HOH A 2 606 3 HOH HOH . I 5 HOH A 3 607 4 HOH HOH . I 5 HOH A 4 608 5 HOH HOH . I 5 HOH A 5 609 7 HOH HOH . I 5 HOH A 6 610 10 HOH HOH . I 5 HOH A 7 611 12 HOH HOH . I 5 HOH A 8 612 13 HOH HOH . I 5 HOH A 9 613 21 HOH HOH . I 5 HOH A 10 614 22 HOH HOH . I 5 HOH A 11 615 23 HOH HOH . I 5 HOH A 12 616 24 HOH HOH . I 5 HOH A 13 617 25 HOH HOH . I 5 HOH A 14 618 26 HOH HOH . I 5 HOH A 15 619 27 HOH HOH . I 5 HOH A 16 620 28 HOH HOH . I 5 HOH A 17 621 29 HOH HOH . I 5 HOH A 18 622 30 HOH HOH . I 5 HOH A 19 623 32 HOH HOH . I 5 HOH A 20 624 33 HOH HOH . I 5 HOH A 21 625 34 HOH HOH . I 5 HOH A 22 626 38 HOH HOH . I 5 HOH A 23 627 39 HOH HOH . I 5 HOH A 24 628 41 HOH HOH . I 5 HOH A 25 629 42 HOH HOH . I 5 HOH A 26 630 45 HOH HOH . I 5 HOH A 27 631 49 HOH HOH . I 5 HOH A 28 632 50 HOH HOH . I 5 HOH A 29 633 52 HOH HOH . I 5 HOH A 30 634 53 HOH HOH . I 5 HOH A 31 635 54 HOH HOH . I 5 HOH A 32 636 57 HOH HOH . I 5 HOH A 33 637 58 HOH HOH . I 5 HOH A 34 638 59 HOH HOH . I 5 HOH A 35 639 60 HOH HOH . I 5 HOH A 36 640 65 HOH HOH . I 5 HOH A 37 641 66 HOH HOH . I 5 HOH A 38 642 67 HOH HOH . I 5 HOH A 39 643 70 HOH HOH . I 5 HOH A 40 644 71 HOH HOH . I 5 HOH A 41 645 75 HOH HOH . I 5 HOH A 42 646 76 HOH HOH . I 5 HOH A 43 647 77 HOH HOH . I 5 HOH A 44 648 79 HOH HOH . I 5 HOH A 45 649 83 HOH HOH . I 5 HOH A 46 650 84 HOH HOH . I 5 HOH A 47 651 88 HOH HOH . I 5 HOH A 48 652 89 HOH HOH . I 5 HOH A 49 653 90 HOH HOH . I 5 HOH A 50 654 91 HOH HOH . I 5 HOH A 51 655 92 HOH HOH . I 5 HOH A 52 656 93 HOH HOH . I 5 HOH A 53 657 95 HOH HOH . I 5 HOH A 54 658 99 HOH HOH . I 5 HOH A 55 659 100 HOH HOH . I 5 HOH A 56 660 101 HOH HOH . I 5 HOH A 57 661 102 HOH HOH . I 5 HOH A 58 662 105 HOH HOH . I 5 HOH A 59 663 107 HOH HOH . I 5 HOH A 60 664 108 HOH HOH . I 5 HOH A 61 665 109 HOH HOH . I 5 HOH A 62 666 110 HOH HOH . I 5 HOH A 63 667 111 HOH HOH . I 5 HOH A 64 668 113 HOH HOH . I 5 HOH A 65 669 114 HOH HOH . I 5 HOH A 66 670 120 HOH HOH . I 5 HOH A 67 671 122 HOH HOH . I 5 HOH A 68 672 123 HOH HOH . I 5 HOH A 69 673 125 HOH HOH . I 5 HOH A 70 674 126 HOH HOH . I 5 HOH A 71 675 127 HOH HOH . I 5 HOH A 72 676 130 HOH HOH . I 5 HOH A 73 677 131 HOH HOH . I 5 HOH A 74 678 132 HOH HOH . I 5 HOH A 75 679 133 HOH HOH . I 5 HOH A 76 680 134 HOH HOH . I 5 HOH A 77 681 136 HOH HOH . I 5 HOH A 78 682 137 HOH HOH . I 5 HOH A 79 683 139 HOH HOH . I 5 HOH A 80 684 142 HOH HOH . I 5 HOH A 81 685 143 HOH HOH . I 5 HOH A 82 686 144 HOH HOH . I 5 HOH A 83 687 145 HOH HOH . I 5 HOH A 84 688 147 HOH HOH . I 5 HOH A 85 689 150 HOH HOH . I 5 HOH A 86 690 151 HOH HOH . I 5 HOH A 87 691 152 HOH HOH . I 5 HOH A 88 692 153 HOH HOH . I 5 HOH A 89 693 154 HOH HOH . I 5 HOH A 90 694 155 HOH HOH . I 5 HOH A 91 695 156 HOH HOH . I 5 HOH A 92 696 159 HOH HOH . I 5 HOH A 93 697 160 HOH HOH . I 5 HOH A 94 698 161 HOH HOH . I 5 HOH A 95 699 162 HOH HOH . I 5 HOH A 96 700 165 HOH HOH . I 5 HOH A 97 701 166 HOH HOH . J 5 HOH B 1 604 2 HOH HOH . J 5 HOH B 2 605 6 HOH HOH . J 5 HOH B 3 606 8 HOH HOH . J 5 HOH B 4 607 9 HOH HOH . J 5 HOH B 5 608 11 HOH HOH . J 5 HOH B 6 609 14 HOH HOH . J 5 HOH B 7 610 15 HOH HOH . J 5 HOH B 8 611 16 HOH HOH . J 5 HOH B 9 612 17 HOH HOH . J 5 HOH B 10 613 18 HOH HOH . J 5 HOH B 11 614 19 HOH HOH . J 5 HOH B 12 615 20 HOH HOH . J 5 HOH B 13 616 31 HOH HOH . J 5 HOH B 14 617 35 HOH HOH . J 5 HOH B 15 618 36 HOH HOH . J 5 HOH B 16 619 37 HOH HOH . J 5 HOH B 17 620 40 HOH HOH . J 5 HOH B 18 621 43 HOH HOH . J 5 HOH B 19 622 44 HOH HOH . J 5 HOH B 20 623 46 HOH HOH . J 5 HOH B 21 624 47 HOH HOH . J 5 HOH B 22 625 48 HOH HOH . J 5 HOH B 23 626 51 HOH HOH . J 5 HOH B 24 627 55 HOH HOH . J 5 HOH B 25 628 56 HOH HOH . J 5 HOH B 26 629 61 HOH HOH . J 5 HOH B 27 630 62 HOH HOH . J 5 HOH B 28 631 63 HOH HOH . J 5 HOH B 29 632 64 HOH HOH . J 5 HOH B 30 633 68 HOH HOH . J 5 HOH B 31 634 69 HOH HOH . J 5 HOH B 32 635 72 HOH HOH . J 5 HOH B 33 636 73 HOH HOH . J 5 HOH B 34 637 74 HOH HOH . J 5 HOH B 35 638 78 HOH HOH . J 5 HOH B 36 639 80 HOH HOH . J 5 HOH B 37 640 81 HOH HOH . J 5 HOH B 38 641 82 HOH HOH . J 5 HOH B 39 642 85 HOH HOH . J 5 HOH B 40 643 86 HOH HOH . J 5 HOH B 41 644 87 HOH HOH . J 5 HOH B 42 645 94 HOH HOH . J 5 HOH B 43 646 96 HOH HOH . J 5 HOH B 44 647 97 HOH HOH . J 5 HOH B 45 648 98 HOH HOH . J 5 HOH B 46 649 103 HOH HOH . J 5 HOH B 47 650 104 HOH HOH . J 5 HOH B 48 651 106 HOH HOH . J 5 HOH B 49 652 112 HOH HOH . J 5 HOH B 50 653 115 HOH HOH . J 5 HOH B 51 654 116 HOH HOH . J 5 HOH B 52 655 117 HOH HOH . J 5 HOH B 53 656 118 HOH HOH . J 5 HOH B 54 657 119 HOH HOH . J 5 HOH B 55 658 121 HOH HOH . J 5 HOH B 56 659 124 HOH HOH . J 5 HOH B 57 660 128 HOH HOH . J 5 HOH B 58 661 129 HOH HOH . J 5 HOH B 59 662 135 HOH HOH . J 5 HOH B 60 663 138 HOH HOH . J 5 HOH B 61 664 140 HOH HOH . J 5 HOH B 62 665 141 HOH HOH . J 5 HOH B 63 666 146 HOH HOH . J 5 HOH B 64 667 148 HOH HOH . J 5 HOH B 65 668 149 HOH HOH . J 5 HOH B 66 669 157 HOH HOH . J 5 HOH B 67 670 158 HOH HOH . J 5 HOH B 68 671 163 HOH HOH . J 5 HOH B 69 672 164 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 . . . D 3 14.868 6.451 99.354 1 18.55 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . D 3 14.362 7.095 98.123 1 21.18 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . D 3 15.359 4.958 99.046 1 26.72 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . D 3 15.982 7.206 99.966 1 20.3 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . D 3 13.335 7.108 101.659 1 27.89 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . D 3 14.291 6.821 102.736 1 29.18 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . D 3 13.334 8.538 101.359 1 31.47 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . D 3 13.714 6.295 100.377 1 25.91 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . D 3 11.873 6.754 102.089 1 30.59 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . D 3 10.914 5.884 101.497 1 30.94 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . D 3 9.667 5.951 102.453 1 33.26 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . D 3 9.706 4.702 103.141 1 32.32 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . D 3 9.725 7.031 103.575 1 33.39 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . D 3 8.458 7.683 103.77 1 36.35 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . D 3 10.191 6.316 104.838 1 33.8 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . D 3 9.66 6.881 106.045 1 35.13 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . D 3 9.802 4.868 104.575 1 34.18 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . D 3 10.812 3.851 105.084 1 35.73 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . D 3 11.876 3.371 104.376 1 35.26 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . D 3 12.547 2.497 105.107 1 34.64 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . D 3 11.959 2.39 106.269 1 35.67 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . D 3 12.181 1.647 107.438 1 35.67 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . D 3 13.213 0.808 107.505 1 35.98 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . D 3 11.331 1.78 108.527 1 36.51 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . D 3 10.256 2.626 108.513 1 36.56 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . D 3 10.023 3.354 107.383 1 35.75 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . D 3 10.83 3.269 106.266 1 35.72 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #