data_5M3U # _model_server_result.job_id wa5AYCUxiua0azNqp7iPBA _model_server_result.datetime_utc '2024-11-23 22:43:51' _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 5m3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5M3U # _exptl.entry_id 5M3U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 98.71 _cell.angle_gamma 90 _cell.entry_id 5M3U _cell.length_a 35.65 _cell.length_b 106.031 _cell.length_c 50.097 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M3U _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,E,F,G _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 OD2 ASP 374 A ASP 374 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A O ASP 411 A ASP 411 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc3 A O LEU 413 A LEU 413 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc4 B O2B ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc5 B O1A ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc6 C O2 3PG . A 3PG 502 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc7 D MG MG . A MG 503 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc8 D MG MG . A MG 503 1_555 G O HOH . A HOH 728 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc9 E MG MG . A MG 504 1_555 G O HOH . A HOH 664 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? # _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 18 n n PB O2B ADP sing 19 n n PB O3B ADP sing 20 n n PB O3A ADP sing 21 n n O2B HOB2 ADP sing 22 n n O3B HOB3 ADP sing 23 n n PA O1A ADP doub 24 n n PA O2A ADP sing 25 n n PA O3A ADP sing 26 n n PA O5' ADP sing 27 n n O2A HOA2 ADP sing 28 n n O5' C5' ADP sing 29 n n C5' C4' ADP sing 30 n n C5' "H5'1" ADP sing 31 n n C5' "H5'2" ADP sing 32 n n C4' O4' ADP sing 33 n n C4' C3' ADP sing 34 n n C4' H4' ADP sing 35 n n O4' C1' ADP sing 36 n n C3' O3' ADP sing 37 n n C3' C2' ADP sing 38 n n C3' H3' ADP sing 39 n n O3' HO3' ADP sing 40 n n C2' O2' ADP sing 41 n n C2' C1' ADP sing 42 n n C2' H2' ADP sing 43 n n O2' HO2' ADP sing 44 n n C1' N9 ADP sing 45 n n C1' H1' ADP sing 46 n n N9 C8 ADP sing 47 n y N9 C4 ADP sing 48 n y C8 N7 ADP doub 49 n y C8 H8 ADP sing 50 n n N7 C5 ADP sing 51 n y C5 C6 ADP sing 52 n y C5 C4 ADP doub 53 n y C6 N6 ADP sing 54 n n C6 N1 ADP doub 55 n y N6 HN61 ADP sing 56 n n N6 HN62 ADP sing 57 n n N1 C2 ADP sing 58 n y C2 N3 ADP doub 59 n y C2 H2 ADP sing 60 n n N3 C4 ADP sing 61 n y # _atom_sites.entry_id 5M3U _atom_sites.fract_transf_matrix[1][1] 0.02805 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004295 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009431 _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] 0.020194 _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 ADP A 1 501 1 ADP ADP . C 3 3PG A 1 502 1 3PG 3PG . D 4 MG A 1 503 1 MG MG . E 4 MG A 1 504 2 MG MG . F 4 MG A 1 505 4 MG MG . G 5 HOH A 1 601 115 HOH HOH . G 5 HOH A 2 602 155 HOH HOH . G 5 HOH A 3 603 109 HOH HOH . G 5 HOH A 4 604 124 HOH HOH . G 5 HOH A 5 605 98 HOH HOH . G 5 HOH A 6 606 137 HOH HOH . G 5 HOH A 7 607 159 HOH HOH . G 5 HOH A 8 608 32 HOH HOH . G 5 HOH A 9 609 113 HOH HOH . G 5 HOH A 10 610 102 HOH HOH . G 5 HOH A 11 611 151 HOH HOH . G 5 HOH A 12 612 110 HOH HOH . G 5 HOH A 13 613 53 HOH HOH . G 5 HOH A 14 614 20 HOH HOH . G 5 HOH A 15 615 111 HOH HOH . G 5 HOH A 16 616 76 HOH HOH . G 5 HOH A 17 617 132 HOH HOH . G 5 HOH A 18 618 17 HOH HOH . G 5 HOH A 19 619 97 HOH HOH . G 5 HOH A 20 620 46 HOH HOH . G 5 HOH A 21 621 78 HOH HOH . G 5 HOH A 22 622 121 HOH HOH . G 5 HOH A 23 623 126 HOH HOH . G 5 HOH A 24 624 141 HOH HOH . G 5 HOH A 25 625 23 HOH HOH . G 5 HOH A 26 626 29 HOH HOH . G 5 HOH A 27 627 89 HOH HOH . G 5 HOH A 28 628 85 HOH HOH . G 5 HOH A 29 629 60 HOH HOH . G 5 HOH A 30 630 1 HOH HOH . G 5 HOH A 31 631 5 HOH HOH . G 5 HOH A 32 632 47 HOH HOH . G 5 HOH A 33 633 118 HOH HOH . G 5 HOH A 34 634 39 HOH HOH . G 5 HOH A 35 635 19 HOH HOH . G 5 HOH A 36 636 37 HOH HOH . G 5 HOH A 37 637 135 HOH HOH . G 5 HOH A 38 638 63 HOH HOH . G 5 HOH A 39 639 35 HOH HOH . G 5 HOH A 40 640 130 HOH HOH . G 5 HOH A 41 641 149 HOH HOH . G 5 HOH A 42 642 122 HOH HOH . G 5 HOH A 43 643 66 HOH HOH . G 5 HOH A 44 644 58 HOH HOH . G 5 HOH A 45 645 33 HOH HOH . G 5 HOH A 46 646 136 HOH HOH . G 5 HOH A 47 647 14 HOH HOH . G 5 HOH A 48 648 34 HOH HOH . G 5 HOH A 49 649 48 HOH HOH . G 5 HOH A 50 650 125 HOH HOH . G 5 HOH A 51 651 15 HOH HOH . G 5 HOH A 52 652 9 HOH HOH . G 5 HOH A 53 653 13 HOH HOH . G 5 HOH A 54 654 147 HOH HOH . G 5 HOH A 55 655 11 HOH HOH . G 5 HOH A 56 656 38 HOH HOH . G 5 HOH A 57 657 73 HOH HOH . G 5 HOH A 58 658 21 HOH HOH . G 5 HOH A 59 659 128 HOH HOH . G 5 HOH A 60 660 25 HOH HOH . G 5 HOH A 61 661 3 HOH HOH . G 5 HOH A 62 662 42 HOH HOH . G 5 HOH A 63 663 2 HOH HOH . G 5 HOH A 64 664 156 HOH HOH . G 5 HOH A 65 665 84 HOH HOH . G 5 HOH A 66 666 134 HOH HOH . G 5 HOH A 67 667 27 HOH HOH . G 5 HOH A 68 668 4 HOH HOH . G 5 HOH A 69 669 6 HOH HOH . G 5 HOH A 70 670 138 HOH HOH . G 5 HOH A 71 671 133 HOH HOH . G 5 HOH A 72 672 7 HOH HOH . G 5 HOH A 73 673 152 HOH HOH . G 5 HOH A 74 674 30 HOH HOH . G 5 HOH A 75 675 112 HOH HOH . G 5 HOH A 76 676 12 HOH HOH . G 5 HOH A 77 677 65 HOH HOH . G 5 HOH A 78 678 88 HOH HOH . G 5 HOH A 79 679 140 HOH HOH . G 5 HOH A 80 680 59 HOH HOH . G 5 HOH A 81 681 69 HOH HOH . G 5 HOH A 82 682 24 HOH HOH . G 5 HOH A 83 683 50 HOH HOH . G 5 HOH A 84 684 52 HOH HOH . G 5 HOH A 85 685 154 HOH HOH . G 5 HOH A 86 686 75 HOH HOH . G 5 HOH A 87 687 68 HOH HOH . G 5 HOH A 88 688 43 HOH HOH . G 5 HOH A 89 689 18 HOH HOH . G 5 HOH A 90 690 72 HOH HOH . G 5 HOH A 91 691 127 HOH HOH . G 5 HOH A 92 692 64 HOH HOH . G 5 HOH A 93 693 8 HOH HOH . G 5 HOH A 94 694 129 HOH HOH . G 5 HOH A 95 695 54 HOH HOH . G 5 HOH A 96 696 91 HOH HOH . G 5 HOH A 97 697 82 HOH HOH . G 5 HOH A 98 698 57 HOH HOH . G 5 HOH A 99 699 150 HOH HOH . G 5 HOH A 100 700 10 HOH HOH . G 5 HOH A 101 701 22 HOH HOH . G 5 HOH A 102 702 90 HOH HOH . G 5 HOH A 103 703 116 HOH HOH . G 5 HOH A 104 704 49 HOH HOH . G 5 HOH A 105 705 120 HOH HOH . G 5 HOH A 106 706 44 HOH HOH . G 5 HOH A 107 707 139 HOH HOH . G 5 HOH A 108 708 92 HOH HOH . G 5 HOH A 109 709 123 HOH HOH . G 5 HOH A 110 710 55 HOH HOH . G 5 HOH A 111 711 131 HOH HOH . G 5 HOH A 112 712 83 HOH HOH . G 5 HOH A 113 713 40 HOH HOH . G 5 HOH A 114 714 45 HOH HOH . G 5 HOH A 115 715 41 HOH HOH . G 5 HOH A 116 716 144 HOH HOH . G 5 HOH A 117 717 67 HOH HOH . G 5 HOH A 118 718 146 HOH HOH . G 5 HOH A 119 719 145 HOH HOH . G 5 HOH A 120 720 51 HOH HOH . G 5 HOH A 121 721 119 HOH HOH . G 5 HOH A 122 722 80 HOH HOH . G 5 HOH A 123 723 36 HOH HOH . G 5 HOH A 124 724 143 HOH HOH . G 5 HOH A 125 725 74 HOH HOH . G 5 HOH A 126 726 87 HOH HOH . G 5 HOH A 127 727 28 HOH HOH . G 5 HOH A 128 728 117 HOH HOH . G 5 HOH A 129 729 71 HOH HOH . G 5 HOH A 130 730 81 HOH HOH . G 5 HOH A 131 731 114 HOH HOH . G 5 HOH A 132 732 93 HOH HOH . G 5 HOH A 133 733 153 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 . . . B 2 -10.142 3.668 17.975 1 41.38 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 -11.127 4.376 17.05 1 42.05 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 -10.513 2.226 18.122 1 41.86 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 -8.689 4.012 17.605 1 39.48 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 -9.685 3.646 20.799 1 31.29 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 -9.759 2.158 20.732 1 33.92 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 -8.337 4.222 21.184 1 36.34 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 -10.323 4.309 19.472 1 33.19 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 -10.688 4.167 21.947 1 28.45 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 -12.061 4.126 21.809 1 24.85 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 -12.562 3.887 23.206 1 23 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 -12.232 5.098 23.88 1 22.5 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 -14.072 3.678 23.307 1 24.37 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 -14.367 2.361 23.802 1 25.96 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 -14.507 4.77 24.28 1 20.74 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 -15.44 4.308 25.235 1 22.98 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 -13.211 5.183 24.93 1 21.93 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 -13.246 6.527 25.509 1 18.92 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 -13.453 7.706 24.877 1 17.07 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 -13.395 8.727 25.755 1 18.47 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 -13.178 8.176 26.974 1 18.23 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 -13.055 8.698 28.341 1 18.52 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 -13.114 10.012 28.593 1 20.08 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 -12.79 7.806 29.305 1 20.6 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 -12.715 6.476 29.114 1 20.12 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 -12.854 5.929 27.882 1 19.66 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 -13.091 6.736 26.814 1 19.13 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #