data_4WBD # _model_server_result.job_id SYWAyd_6mtORFH9HMaoM1g _model_server_result.datetime_utc '2025-02-05 15:05:23' _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 4wbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4WBD # _exptl.entry_id 4WBD _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 116.83 _cell.angle_gamma 90 _cell.entry_id 4WBD _cell.length_a 82.53 _cell.length_b 92.16 _cell.length_c 87.377 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 125.622842 0 77.970833 # _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 # _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 4WBD _atom_sites.fract_transf_matrix[1][1] 0.012117 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006128 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010851 _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] 0.012825 _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 1 601 601 ADP ADP . C 3 CIT A 1 602 602 CIT CIT . D 4 GOL A 1 603 231 GOL GOL . E 5 HOH A 1 701 218 HOH HOH . E 5 HOH A 2 702 130 HOH HOH . E 5 HOH A 3 703 119 HOH HOH . E 5 HOH A 4 704 196 HOH HOH . E 5 HOH A 5 705 121 HOH HOH . E 5 HOH A 6 706 166 HOH HOH . E 5 HOH A 7 707 39 HOH HOH . E 5 HOH A 8 708 164 HOH HOH . E 5 HOH A 9 709 158 HOH HOH . E 5 HOH A 10 710 80 HOH HOH . E 5 HOH A 11 711 63 HOH HOH . E 5 HOH A 12 712 52 HOH HOH . E 5 HOH A 13 713 141 HOH HOH . E 5 HOH A 14 714 163 HOH HOH . E 5 HOH A 15 715 61 HOH HOH . E 5 HOH A 16 716 97 HOH HOH . E 5 HOH A 17 717 221 HOH HOH . E 5 HOH A 18 718 176 HOH HOH . E 5 HOH A 19 719 100 HOH HOH . E 5 HOH A 20 720 178 HOH HOH . E 5 HOH A 21 721 109 HOH HOH . E 5 HOH A 22 722 165 HOH HOH . E 5 HOH A 23 723 198 HOH HOH . E 5 HOH A 24 724 51 HOH HOH . E 5 HOH A 25 725 212 HOH HOH . E 5 HOH A 26 726 108 HOH HOH . E 5 HOH A 27 727 220 HOH HOH . E 5 HOH A 28 728 82 HOH HOH . E 5 HOH A 29 729 18 HOH HOH . E 5 HOH A 30 730 93 HOH HOH . E 5 HOH A 31 731 70 HOH HOH . E 5 HOH A 32 732 197 HOH HOH . E 5 HOH A 33 733 128 HOH HOH . E 5 HOH A 34 734 37 HOH HOH . E 5 HOH A 35 735 30 HOH HOH . E 5 HOH A 36 736 32 HOH HOH . E 5 HOH A 37 737 60 HOH HOH . E 5 HOH A 38 738 202 HOH HOH . E 5 HOH A 39 739 14 HOH HOH . E 5 HOH A 40 740 192 HOH HOH . E 5 HOH A 41 741 129 HOH HOH . E 5 HOH A 42 742 66 HOH HOH . E 5 HOH A 43 743 84 HOH HOH . E 5 HOH A 44 744 34 HOH HOH . E 5 HOH A 45 745 43 HOH HOH . E 5 HOH A 46 746 226 HOH HOH . E 5 HOH A 47 747 205 HOH HOH . E 5 HOH A 48 748 161 HOH HOH . E 5 HOH A 49 749 189 HOH HOH . E 5 HOH A 50 750 160 HOH HOH . E 5 HOH A 51 751 49 HOH HOH . E 5 HOH A 52 752 207 HOH HOH . E 5 HOH A 53 753 115 HOH HOH . E 5 HOH A 54 754 177 HOH HOH . E 5 HOH A 55 755 123 HOH HOH . E 5 HOH A 56 756 201 HOH HOH . E 5 HOH A 57 757 169 HOH HOH . E 5 HOH A 58 758 179 HOH HOH . E 5 HOH A 59 759 65 HOH HOH . E 5 HOH A 60 760 145 HOH HOH . E 5 HOH A 61 761 170 HOH HOH . E 5 HOH A 62 762 131 HOH HOH . E 5 HOH A 63 763 1 HOH HOH . E 5 HOH A 64 764 2 HOH HOH . E 5 HOH A 65 765 3 HOH HOH . E 5 HOH A 66 766 4 HOH HOH . E 5 HOH A 67 767 5 HOH HOH . E 5 HOH A 68 768 6 HOH HOH . E 5 HOH A 69 769 7 HOH HOH . E 5 HOH A 70 770 8 HOH HOH . E 5 HOH A 71 771 9 HOH HOH . E 5 HOH A 72 772 10 HOH HOH . E 5 HOH A 73 773 11 HOH HOH . E 5 HOH A 74 774 12 HOH HOH . E 5 HOH A 75 775 13 HOH HOH . E 5 HOH A 76 776 15 HOH HOH . E 5 HOH A 77 777 16 HOH HOH . E 5 HOH A 78 778 17 HOH HOH . E 5 HOH A 79 779 19 HOH HOH . E 5 HOH A 80 780 20 HOH HOH . E 5 HOH A 81 781 21 HOH HOH . E 5 HOH A 82 782 22 HOH HOH . E 5 HOH A 83 783 23 HOH HOH . E 5 HOH A 84 784 24 HOH HOH . E 5 HOH A 85 785 25 HOH HOH . E 5 HOH A 86 786 26 HOH HOH . E 5 HOH A 87 787 27 HOH HOH . E 5 HOH A 88 788 28 HOH HOH . E 5 HOH A 89 789 29 HOH HOH . E 5 HOH A 90 790 31 HOH HOH . E 5 HOH A 91 791 33 HOH HOH . E 5 HOH A 92 792 35 HOH HOH . E 5 HOH A 93 793 36 HOH HOH . E 5 HOH A 94 794 38 HOH HOH . E 5 HOH A 95 795 40 HOH HOH . E 5 HOH A 96 796 41 HOH HOH . E 5 HOH A 97 797 42 HOH HOH . E 5 HOH A 98 798 44 HOH HOH . E 5 HOH A 99 799 45 HOH HOH . E 5 HOH A 100 800 46 HOH HOH . E 5 HOH A 101 801 47 HOH HOH . E 5 HOH A 102 802 48 HOH HOH . E 5 HOH A 103 803 50 HOH HOH . E 5 HOH A 104 804 53 HOH HOH . E 5 HOH A 105 805 54 HOH HOH . E 5 HOH A 106 806 55 HOH HOH . E 5 HOH A 107 807 56 HOH HOH . E 5 HOH A 108 808 57 HOH HOH . E 5 HOH A 109 809 58 HOH HOH . E 5 HOH A 110 810 59 HOH HOH . E 5 HOH A 111 811 62 HOH HOH . E 5 HOH A 112 812 64 HOH HOH . E 5 HOH A 113 813 67 HOH HOH . E 5 HOH A 114 814 68 HOH HOH . E 5 HOH A 115 815 69 HOH HOH . E 5 HOH A 116 816 71 HOH HOH . E 5 HOH A 117 817 72 HOH HOH . E 5 HOH A 118 818 73 HOH HOH . E 5 HOH A 119 819 74 HOH HOH . E 5 HOH A 120 820 75 HOH HOH . E 5 HOH A 121 821 76 HOH HOH . E 5 HOH A 122 822 77 HOH HOH . E 5 HOH A 123 823 78 HOH HOH . E 5 HOH A 124 824 79 HOH HOH . E 5 HOH A 125 825 81 HOH HOH . E 5 HOH A 126 826 83 HOH HOH . E 5 HOH A 127 827 85 HOH HOH . E 5 HOH A 128 828 86 HOH HOH . E 5 HOH A 129 829 87 HOH HOH . E 5 HOH A 130 830 88 HOH HOH . E 5 HOH A 131 831 89 HOH HOH . E 5 HOH A 132 832 90 HOH HOH . E 5 HOH A 133 833 91 HOH HOH . E 5 HOH A 134 834 92 HOH HOH . E 5 HOH A 135 835 94 HOH HOH . E 5 HOH A 136 836 95 HOH HOH . E 5 HOH A 137 837 96 HOH HOH . E 5 HOH A 138 838 98 HOH HOH . E 5 HOH A 139 839 99 HOH HOH . E 5 HOH A 140 840 101 HOH HOH . E 5 HOH A 141 841 102 HOH HOH . E 5 HOH A 142 842 103 HOH HOH . E 5 HOH A 143 843 104 HOH HOH . E 5 HOH A 144 844 105 HOH HOH . E 5 HOH A 145 845 106 HOH HOH . E 5 HOH A 146 846 107 HOH HOH . E 5 HOH A 147 847 110 HOH HOH . E 5 HOH A 148 848 111 HOH HOH . E 5 HOH A 149 849 112 HOH HOH . E 5 HOH A 150 850 113 HOH HOH . E 5 HOH A 151 851 114 HOH HOH . E 5 HOH A 152 852 116 HOH HOH . E 5 HOH A 153 853 117 HOH HOH . E 5 HOH A 154 854 118 HOH HOH . E 5 HOH A 155 855 120 HOH HOH . E 5 HOH A 156 856 122 HOH HOH . E 5 HOH A 157 857 124 HOH HOH . E 5 HOH A 158 858 125 HOH HOH . E 5 HOH A 159 859 126 HOH HOH . E 5 HOH A 160 860 127 HOH HOH . E 5 HOH A 161 861 132 HOH HOH . E 5 HOH A 162 862 133 HOH HOH . E 5 HOH A 163 863 134 HOH HOH . E 5 HOH A 164 864 135 HOH HOH . E 5 HOH A 165 865 136 HOH HOH . E 5 HOH A 166 866 137 HOH HOH . E 5 HOH A 167 867 138 HOH HOH . E 5 HOH A 168 868 139 HOH HOH . E 5 HOH A 169 869 140 HOH HOH . E 5 HOH A 170 870 142 HOH HOH . E 5 HOH A 171 871 143 HOH HOH . E 5 HOH A 172 872 144 HOH HOH . E 5 HOH A 173 873 146 HOH HOH . E 5 HOH A 174 874 147 HOH HOH . E 5 HOH A 175 875 148 HOH HOH . E 5 HOH A 176 876 149 HOH HOH . E 5 HOH A 177 877 150 HOH HOH . E 5 HOH A 178 878 151 HOH HOH . E 5 HOH A 179 879 152 HOH HOH . E 5 HOH A 180 880 153 HOH HOH . E 5 HOH A 181 881 154 HOH HOH . E 5 HOH A 182 882 155 HOH HOH . E 5 HOH A 183 883 156 HOH HOH . E 5 HOH A 184 884 157 HOH HOH . E 5 HOH A 185 885 159 HOH HOH . E 5 HOH A 186 886 162 HOH HOH . E 5 HOH A 187 887 167 HOH HOH . E 5 HOH A 188 888 168 HOH HOH . E 5 HOH A 189 889 171 HOH HOH . E 5 HOH A 190 890 172 HOH HOH . E 5 HOH A 191 891 173 HOH HOH . E 5 HOH A 192 892 174 HOH HOH . E 5 HOH A 193 893 175 HOH HOH . E 5 HOH A 194 894 180 HOH HOH . E 5 HOH A 195 895 181 HOH HOH . E 5 HOH A 196 896 182 HOH HOH . E 5 HOH A 197 897 183 HOH HOH . E 5 HOH A 198 898 184 HOH HOH . E 5 HOH A 199 899 185 HOH HOH . E 5 HOH A 200 900 186 HOH HOH . E 5 HOH A 201 901 187 HOH HOH . E 5 HOH A 202 902 188 HOH HOH . E 5 HOH A 203 903 190 HOH HOH . E 5 HOH A 204 904 191 HOH HOH . E 5 HOH A 205 905 193 HOH HOH . E 5 HOH A 206 906 194 HOH HOH . E 5 HOH A 207 907 195 HOH HOH . E 5 HOH A 208 908 199 HOH HOH . E 5 HOH A 209 909 200 HOH HOH . E 5 HOH A 210 910 203 HOH HOH . E 5 HOH A 211 911 204 HOH HOH . E 5 HOH A 212 912 206 HOH HOH . E 5 HOH A 213 913 208 HOH HOH . E 5 HOH A 214 914 209 HOH HOH . E 5 HOH A 215 915 210 HOH HOH . E 5 HOH A 216 916 211 HOH HOH . E 5 HOH A 217 917 213 HOH HOH . E 5 HOH A 218 918 214 HOH HOH . E 5 HOH A 219 919 215 HOH HOH . E 5 HOH A 220 920 216 HOH HOH . E 5 HOH A 221 921 217 HOH HOH . E 5 HOH A 222 922 219 HOH HOH . E 5 HOH A 223 923 222 HOH HOH . E 5 HOH A 224 924 223 HOH HOH . E 5 HOH A 225 925 224 HOH HOH . E 5 HOH A 226 926 225 HOH HOH . E 5 HOH A 227 927 227 HOH HOH . E 5 HOH A 228 928 228 HOH HOH . E 5 HOH A 229 929 229 HOH HOH . E 5 HOH A 230 930 230 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 33.544 -5.6 13.127 1 47.85 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . B 2 33.127 -4.671 12.072 1 46 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . B 2 32.635 -6.745 13.102 1 50.52 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . B 2 34.948 -5.858 13.238 1 44.49 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . B 2 32.674 -4.929 15.764 1 28.59 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . B 2 32.532 -3.545 16.171 1 26.18 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . B 2 33.432 -5.816 16.551 1 31.04 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . B 2 33.331 -4.699 14.397 1 37.45 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . B 2 31.217 -5.48 15.578 1 22.06 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . B 2 30.876 -6.823 15.576 1 18.47 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . B 2 29.462 -6.96 15.004 1 18.35 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . B 2 28.53 -6.361 15.836 1 17.71 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . B 2 29.264 -6.261 13.681 1 18.18 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . B 2 29.781 -7.011 12.614 1 17.15 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . B 2 27.782 -6.005 13.647 1 15.64 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . B 2 27.112 -7.171 13.233 1 15.63 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . B 2 27.533 -5.701 15.113 1 17.68 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . B 2 27.559 -4.247 15.42 1 19.07 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . B 2 28.584 -3.422 15.354 1 19.78 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . B 2 28.216 -2.189 15.713 1 18.81 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . B 2 26.933 -2.221 16.017 1 15.09 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . B 2 25.921 -1.267 16.444 1 15.59 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . B 2 26.259 -0.003 16.648 1 14.95 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . B 2 24.701 -1.724 16.609 1 14.37 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . B 2 24.385 -2.983 16.423 1 14.03 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . B 2 25.231 -3.907 16.034 1 13.62 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . B 2 26.494 -3.59 15.827 1 16.49 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #