data_3UKD # _model_server_result.job_id VkVWS-VHbiiUrUmWOC4rjQ _model_server_result.datetime_utc '2024-11-23 07:03:42' _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 3ukd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":195}' # _entry.id 3UKD # _exptl.entry_id 3UKD _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 3UKD _cell.length_a 78.8 _cell.length_b 78.8 _cell.length_c 100.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # 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 NH2 ARG 148 A ARG 148 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.405 ? metalc ? metalc2 C O2B ADP . A ADP 195 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc3 C O3B ADP . A ADP 195 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc4 C O2B ADP . A ADP 195 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.648 ? metalc ? metalc5 D O3P C5P . A C5P 196 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 D O2P C5P . A C5P 196 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.698 ? metalc ? metalc7 F O HOH . A HOH 198 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc8 F O HOH . A HOH 198 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.458 ? metalc ? metalc9 F O HOH . A HOH 215 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc10 F O HOH . A HOH 220 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc11 F O HOH . A HOH 227 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc12 B MG MG . A MG 500 1_555 E F3 AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc13 B MG MG . A MG 500 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.595 ? # _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 3UKD _atom_sites.fract_transf_matrix[1][1] 0.01269 _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] 0.01269 _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] 0.00993 _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 MG A 1 500 500 MG MG . C 3 ADP A 1 195 195 ADP ADP . D 4 C5P A 1 196 196 C5P C5P . E 5 AF3 A 1 501 501 AF3 AF3 . F 6 HOH A 1 197 197 HOH HOH . F 6 HOH A 2 198 198 HOH HOH . F 6 HOH A 3 200 200 HOH HOH . F 6 HOH A 4 201 201 HOH HOH . F 6 HOH A 5 202 202 HOH HOH . F 6 HOH A 6 203 203 HOH HOH . F 6 HOH A 7 204 204 HOH HOH . F 6 HOH A 8 206 206 HOH HOH . F 6 HOH A 9 207 207 HOH HOH . F 6 HOH A 10 208 208 HOH HOH . F 6 HOH A 11 209 209 HOH HOH . F 6 HOH A 12 210 210 HOH HOH . F 6 HOH A 13 211 211 HOH HOH . F 6 HOH A 14 212 212 HOH HOH . F 6 HOH A 15 214 214 HOH HOH . F 6 HOH A 16 215 215 HOH HOH . F 6 HOH A 17 216 216 HOH HOH . F 6 HOH A 18 218 218 HOH HOH . F 6 HOH A 19 220 220 HOH HOH . F 6 HOH A 20 221 221 HOH HOH . F 6 HOH A 21 222 222 HOH HOH . F 6 HOH A 22 223 223 HOH HOH . F 6 HOH A 23 226 226 HOH HOH . F 6 HOH A 24 227 227 HOH HOH . F 6 HOH A 25 228 228 HOH HOH . F 6 HOH A 26 229 229 HOH HOH . F 6 HOH A 27 231 231 HOH HOH . F 6 HOH A 28 232 232 HOH HOH . F 6 HOH A 29 233 233 HOH HOH . F 6 HOH A 30 234 234 HOH HOH . F 6 HOH A 31 236 236 HOH HOH . F 6 HOH A 32 238 238 HOH HOH . F 6 HOH A 33 239 239 HOH HOH . F 6 HOH A 34 242 242 HOH HOH . F 6 HOH A 35 244 244 HOH HOH . F 6 HOH A 36 245 245 HOH HOH . F 6 HOH A 37 509 509 HOH HOH . F 6 HOH A 38 512 512 HOH HOH . F 6 HOH A 39 528 528 HOH HOH . F 6 HOH A 40 531 531 HOH HOH . F 6 HOH A 41 532 532 HOH HOH . F 6 HOH A 42 533 533 HOH HOH . F 6 HOH A 43 536 536 HOH HOH . F 6 HOH A 44 538 538 HOH HOH . F 6 HOH A 45 543 543 HOH HOH . F 6 HOH A 46 553 553 HOH HOH . F 6 HOH A 47 558 558 HOH HOH . F 6 HOH A 48 559 559 HOH HOH . F 6 HOH A 49 562 562 HOH HOH . F 6 HOH A 50 563 563 HOH HOH . F 6 HOH A 51 564 564 HOH HOH . F 6 HOH A 52 565 565 HOH HOH . F 6 HOH A 53 566 566 HOH HOH . F 6 HOH A 54 568 568 HOH HOH . F 6 HOH A 55 569 569 HOH HOH . F 6 HOH A 56 577 577 HOH HOH . F 6 HOH A 57 580 580 HOH HOH . F 6 HOH A 58 582 582 HOH HOH . F 6 HOH A 59 591 591 HOH HOH . F 6 HOH A 60 592 592 HOH HOH . F 6 HOH A 61 597 597 HOH HOH . F 6 HOH A 62 599 599 HOH HOH . F 6 HOH A 63 601 601 HOH HOH . F 6 HOH A 64 602 602 HOH HOH . F 6 HOH A 65 603 603 HOH HOH . F 6 HOH A 66 604 604 HOH HOH . F 6 HOH A 67 605 605 HOH HOH . F 6 HOH A 68 606 606 HOH HOH . F 6 HOH A 69 608 608 HOH HOH . F 6 HOH A 70 616 616 HOH HOH . F 6 HOH A 71 640 640 HOH HOH . F 6 HOH A 72 646 646 HOH HOH . F 6 HOH A 73 650 650 HOH HOH . F 6 HOH A 74 664 664 HOH HOH . F 6 HOH A 75 670 670 HOH HOH . F 6 HOH A 76 712 712 HOH HOH . F 6 HOH A 77 717 717 HOH HOH . F 6 HOH A 78 727 727 HOH HOH . F 6 HOH A 79 732 732 HOH HOH . F 6 HOH A 80 734 734 HOH HOH . F 6 HOH A 81 737 737 HOH HOH . F 6 HOH A 82 739 739 HOH HOH . F 6 HOH A 83 741 741 HOH HOH . F 6 HOH A 84 744 744 HOH HOH . F 6 HOH A 85 746 746 HOH HOH . F 6 HOH A 86 747 747 HOH HOH . F 6 HOH A 87 750 750 HOH HOH . F 6 HOH A 88 751 751 HOH HOH . F 6 HOH A 89 752 752 HOH HOH . F 6 HOH A 90 753 753 HOH HOH . F 6 HOH A 91 759 759 HOH HOH . F 6 HOH A 92 767 767 HOH HOH . F 6 HOH A 93 769 769 HOH HOH . F 6 HOH A 94 771 771 HOH HOH . F 6 HOH A 95 774 774 HOH HOH . F 6 HOH A 96 778 778 HOH HOH . F 6 HOH A 97 779 779 HOH HOH . F 6 HOH A 98 781 781 HOH HOH . F 6 HOH A 99 786 786 HOH HOH . F 6 HOH A 100 793 793 HOH HOH . F 6 HOH A 101 797 797 HOH HOH . F 6 HOH A 102 801 801 HOH HOH . F 6 HOH A 103 809 809 HOH HOH . F 6 HOH A 104 810 810 HOH HOH . F 6 HOH A 105 814 814 HOH HOH . F 6 HOH A 106 816 816 HOH HOH . F 6 HOH A 107 817 817 HOH HOH . F 6 HOH A 108 818 818 HOH HOH . F 6 HOH A 109 819 819 HOH HOH . F 6 HOH A 110 822 822 HOH HOH . F 6 HOH A 111 823 823 HOH HOH . F 6 HOH A 112 824 824 HOH HOH . F 6 HOH A 113 826 826 HOH HOH . F 6 HOH A 114 827 827 HOH HOH . F 6 HOH A 115 828 828 HOH HOH . F 6 HOH A 116 829 829 HOH HOH . F 6 HOH A 117 833 833 HOH HOH . F 6 HOH A 118 838 838 HOH HOH . F 6 HOH A 119 839 839 HOH HOH . F 6 HOH A 120 840 840 HOH HOH . F 6 HOH A 121 843 843 HOH HOH . F 6 HOH A 122 844 844 HOH HOH . F 6 HOH A 123 845 845 HOH HOH . F 6 HOH A 124 848 848 HOH HOH . F 6 HOH A 125 849 849 HOH HOH . F 6 HOH A 126 853 853 HOH HOH . F 6 HOH A 127 855 855 HOH HOH . F 6 HOH A 128 856 856 HOH HOH . F 6 HOH A 129 857 857 HOH HOH . F 6 HOH A 130 858 858 HOH HOH . F 6 HOH A 131 861 861 HOH HOH . F 6 HOH A 132 862 862 HOH HOH . F 6 HOH A 133 863 863 HOH HOH . F 6 HOH A 134 864 864 HOH HOH . F 6 HOH A 135 865 865 HOH HOH . F 6 HOH A 136 868 868 HOH HOH . F 6 HOH A 137 869 869 HOH HOH . F 6 HOH A 138 870 870 HOH HOH . F 6 HOH A 139 871 871 HOH HOH . F 6 HOH A 140 872 872 HOH HOH . F 6 HOH A 141 873 873 HOH HOH . F 6 HOH A 142 874 874 HOH HOH . F 6 HOH A 143 877 877 HOH HOH . F 6 HOH A 144 878 878 HOH HOH . F 6 HOH A 145 879 879 HOH HOH . F 6 HOH A 146 880 880 HOH HOH . F 6 HOH A 147 881 881 HOH HOH . F 6 HOH A 148 882 882 HOH HOH . F 6 HOH A 149 883 883 HOH HOH . F 6 HOH A 150 890 890 HOH HOH . F 6 HOH A 151 891 891 HOH HOH . F 6 HOH A 152 892 892 HOH HOH . F 6 HOH A 153 893 893 HOH HOH . F 6 HOH A 154 894 894 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 38.333 65.71 -11.741 1 17.04 ? PB ADP 195 A 1 HETATM 2 O O1B ADP . . . C 3 38.74 64.702 -12.693 1 17.99 ? O1B ADP 195 A 1 HETATM 3 O O2B ADP . . . C 3 39.387 66.446 -11.131 1 17.06 ? O2B ADP 195 A 1 HETATM 4 O O3B ADP . . . C 3 37.347 66.697 -12.434 1 14.78 ? O3B ADP 195 A 1 HETATM 5 P PA ADP . . . C 3 37.443 64.966 -9.024 1 18.59 ? PA ADP 195 A 1 HETATM 6 O O1A ADP . . . C 3 38.689 64.358 -8.58 1 18.01 ? O1A ADP 195 A 1 HETATM 7 O O2A ADP . . . C 3 37.138 66.262 -8.5 1 17.73 ? O2A ADP 195 A 1 HETATM 8 O O3A ADP . . . C 3 37.472 65.038 -10.611 1 18.31 ? O3A ADP 195 A 1 HETATM 9 O O5' ADP . . . C 3 36.239 64.016 -8.674 1 18.06 ? O5' ADP 195 A 1 HETATM 10 C C5' ADP . . . C 3 34.932 64.181 -9.217 1 17.56 ? C5' ADP 195 A 1 HETATM 11 C C4' ADP . . . C 3 33.924 63.786 -8.188 1 18.7 ? C4' ADP 195 A 1 HETATM 12 O O4' ADP . . . C 3 33.937 62.383 -8.166 1 18.73 ? O4' ADP 195 A 1 HETATM 13 C C3' ADP . . . C 3 34.246 64.323 -6.814 1 20.61 ? C3' ADP 195 A 1 HETATM 14 O O3' ADP . . . C 3 33.062 64.643 -6.089 1 22.86 ? O3' ADP 195 A 1 HETATM 15 C C2' ADP . . . C 3 34.927 63.129 -6.22 1 21.86 ? C2' ADP 195 A 1 HETATM 16 O O2' ADP . . . C 3 34.807 63.12 -4.792 1 22.33 ? O2' ADP 195 A 1 HETATM 17 C C1' ADP . . . C 3 34.22 61.947 -6.864 1 20.47 ? C1' ADP 195 A 1 HETATM 18 N N9 ADP . . . C 3 35.1 60.824 -7.052 1 19.4 ? N9 ADP 195 A 1 HETATM 19 C C8 ADP . . . C 3 36.403 60.815 -7.487 1 20.17 ? C8 ADP 195 A 1 HETATM 20 N N7 ADP . . . C 3 36.869 59.626 -7.816 1 21.35 ? N7 ADP 195 A 1 HETATM 21 C C5 ADP . . . C 3 35.801 58.799 -7.535 1 20.23 ? C5 ADP 195 A 1 HETATM 22 C C6 ADP . . . C 3 35.64 57.38 -7.593 1 20.51 ? C6 ADP 195 A 1 HETATM 23 N N6 ADP . . . C 3 36.627 56.532 -7.873 1 20.61 ? N6 ADP 195 A 1 HETATM 24 N N1 ADP . . . C 3 34.431 56.865 -7.287 1 22.94 ? N1 ADP 195 A 1 HETATM 25 C C2 ADP . . . C 3 33.455 57.706 -6.885 1 22.22 ? C2 ADP 195 A 1 HETATM 26 N N3 ADP . . . C 3 33.556 59.046 -6.667 1 21.58 ? N3 ADP 195 A 1 HETATM 27 C C4 ADP . . . C 3 34.734 59.531 -7.051 1 21.21 ? C4 ADP 195 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #