data_2I1V # _model_server_result.job_id 7g5UsRNAhAELFJIV9IiGuw _model_server_result.datetime_utc '2024-11-19 06:35:26' _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 2i1v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":700}' # _entry.id 2I1V # _exptl.entry_id 2I1V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 2I1V _cell.length_a 102.14 _cell.length_b 102.14 _cell.length_c 259.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2I1V _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 51.07 88.455835 43.24 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 2I1V _atom_sites.fract_transf_matrix[1][1] 0.00979 _atom_sites.fract_transf_matrix[1][2] 0.005652 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011305 _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] 0.003854 _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 FDP B 1 710 710 FDP FBP . C 3 F6P B 1 720 720 F6P F6P . D 4 ADP B 1 700 700 ADP ADP . E 5 PHS B 1 730 730 PHS PHS . F 6 HOH B 1 731 1 HOH HOH . F 6 HOH B 2 732 2 HOH HOH . F 6 HOH B 3 733 3 HOH HOH . F 6 HOH B 4 734 4 HOH HOH . F 6 HOH B 5 735 5 HOH HOH . F 6 HOH B 6 736 6 HOH HOH . F 6 HOH B 7 737 7 HOH HOH . F 6 HOH B 8 738 8 HOH HOH . F 6 HOH B 9 739 9 HOH HOH . F 6 HOH B 10 740 10 HOH HOH . F 6 HOH B 11 741 11 HOH HOH . F 6 HOH B 12 742 12 HOH HOH . F 6 HOH B 13 743 13 HOH HOH . F 6 HOH B 14 744 14 HOH HOH . F 6 HOH B 15 745 15 HOH HOH . F 6 HOH B 16 746 16 HOH HOH . F 6 HOH B 17 747 17 HOH HOH . F 6 HOH B 18 748 18 HOH HOH . F 6 HOH B 19 749 19 HOH HOH . F 6 HOH B 20 750 20 HOH HOH . F 6 HOH B 21 751 21 HOH HOH . F 6 HOH B 22 752 22 HOH HOH . F 6 HOH B 23 753 23 HOH HOH . F 6 HOH B 24 754 24 HOH HOH . F 6 HOH B 25 755 25 HOH HOH . F 6 HOH B 26 756 26 HOH HOH . F 6 HOH B 27 757 27 HOH HOH . F 6 HOH B 28 758 28 HOH HOH . F 6 HOH B 29 759 29 HOH HOH . F 6 HOH B 30 760 30 HOH HOH . F 6 HOH B 31 761 31 HOH HOH . F 6 HOH B 32 762 32 HOH HOH . F 6 HOH B 33 763 33 HOH HOH . F 6 HOH B 34 764 34 HOH HOH . F 6 HOH B 35 765 35 HOH HOH . F 6 HOH B 36 766 36 HOH HOH . F 6 HOH B 37 767 37 HOH HOH . F 6 HOH B 38 768 38 HOH HOH . F 6 HOH B 39 769 39 HOH HOH . F 6 HOH B 40 770 40 HOH HOH . F 6 HOH B 41 771 41 HOH HOH . F 6 HOH B 42 772 42 HOH HOH . F 6 HOH B 43 773 43 HOH HOH . F 6 HOH B 44 774 44 HOH HOH . F 6 HOH B 45 775 45 HOH HOH . F 6 HOH B 46 776 46 HOH HOH . F 6 HOH B 47 777 47 HOH HOH . F 6 HOH B 48 778 48 HOH HOH . F 6 HOH B 49 779 49 HOH HOH . F 6 HOH B 50 780 50 HOH HOH . F 6 HOH B 51 781 51 HOH HOH . F 6 HOH B 52 782 52 HOH HOH . F 6 HOH B 53 783 53 HOH HOH . F 6 HOH B 54 784 54 HOH HOH . F 6 HOH B 55 785 55 HOH HOH . F 6 HOH B 56 786 56 HOH HOH . F 6 HOH B 57 787 57 HOH HOH . F 6 HOH B 58 788 58 HOH HOH . F 6 HOH B 59 789 59 HOH HOH . F 6 HOH B 60 790 60 HOH HOH . F 6 HOH B 61 791 61 HOH HOH . F 6 HOH B 62 792 62 HOH HOH . F 6 HOH B 63 793 63 HOH HOH . F 6 HOH B 64 794 64 HOH HOH . F 6 HOH B 65 795 65 HOH HOH . F 6 HOH B 66 796 66 HOH HOH . F 6 HOH B 67 797 67 HOH HOH . F 6 HOH B 68 798 68 HOH HOH . F 6 HOH B 69 799 70 HOH HOH . F 6 HOH B 70 800 71 HOH HOH . F 6 HOH B 71 801 72 HOH HOH . F 6 HOH B 72 802 73 HOH HOH . F 6 HOH B 73 803 74 HOH HOH . F 6 HOH B 74 804 75 HOH HOH . F 6 HOH B 75 805 76 HOH HOH . F 6 HOH B 76 806 78 HOH HOH . F 6 HOH B 77 807 79 HOH HOH . F 6 HOH B 78 808 80 HOH HOH . F 6 HOH B 79 809 81 HOH HOH . F 6 HOH B 80 810 82 HOH HOH . F 6 HOH B 81 811 83 HOH HOH . F 6 HOH B 82 812 84 HOH HOH . F 6 HOH B 83 813 85 HOH HOH . F 6 HOH B 84 814 86 HOH HOH . F 6 HOH B 85 815 87 HOH HOH . F 6 HOH B 86 816 88 HOH HOH . F 6 HOH B 87 817 89 HOH HOH . F 6 HOH B 88 818 90 HOH HOH . F 6 HOH B 89 819 91 HOH HOH . F 6 HOH B 90 820 92 HOH HOH . F 6 HOH B 91 821 93 HOH HOH . F 6 HOH B 92 822 94 HOH HOH . F 6 HOH B 93 823 95 HOH HOH . F 6 HOH B 94 824 96 HOH HOH . F 6 HOH B 95 825 97 HOH HOH . F 6 HOH B 96 826 99 HOH HOH . F 6 HOH B 97 827 100 HOH HOH . F 6 HOH B 98 828 102 HOH HOH . F 6 HOH B 99 829 103 HOH HOH . F 6 HOH B 100 830 104 HOH HOH . F 6 HOH B 101 831 105 HOH HOH . F 6 HOH B 102 832 106 HOH HOH . F 6 HOH B 103 833 107 HOH HOH . F 6 HOH B 104 834 108 HOH HOH . F 6 HOH B 105 835 109 HOH HOH . F 6 HOH B 106 836 110 HOH HOH . F 6 HOH B 107 837 111 HOH HOH . F 6 HOH B 108 838 112 HOH HOH . F 6 HOH B 109 839 113 HOH HOH . F 6 HOH B 110 840 114 HOH HOH . F 6 HOH B 111 841 115 HOH HOH . F 6 HOH B 112 842 116 HOH HOH . F 6 HOH B 113 843 117 HOH HOH . F 6 HOH B 114 844 118 HOH HOH . F 6 HOH B 115 845 119 HOH HOH . F 6 HOH B 116 846 120 HOH HOH . F 6 HOH B 117 847 121 HOH HOH . F 6 HOH B 118 848 122 HOH HOH . F 6 HOH B 119 849 123 HOH HOH . F 6 HOH B 120 850 124 HOH HOH . F 6 HOH B 121 851 126 HOH HOH . F 6 HOH B 122 852 127 HOH HOH . F 6 HOH B 123 853 128 HOH HOH . F 6 HOH B 124 854 129 HOH HOH . F 6 HOH B 125 855 130 HOH HOH . F 6 HOH B 126 856 131 HOH HOH . F 6 HOH B 127 857 132 HOH HOH . F 6 HOH B 128 858 133 HOH HOH . F 6 HOH B 129 859 134 HOH HOH . F 6 HOH B 130 860 136 HOH HOH . F 6 HOH B 131 861 137 HOH HOH . F 6 HOH B 132 862 138 HOH HOH . F 6 HOH B 133 863 139 HOH HOH . F 6 HOH B 134 864 140 HOH HOH . F 6 HOH B 135 865 141 HOH HOH . F 6 HOH B 136 866 143 HOH HOH . F 6 HOH B 137 867 145 HOH HOH . F 6 HOH B 138 868 147 HOH HOH . F 6 HOH B 139 869 148 HOH HOH . F 6 HOH B 140 870 149 HOH HOH . F 6 HOH B 141 871 150 HOH HOH . F 6 HOH B 142 872 151 HOH HOH . F 6 HOH B 143 873 152 HOH HOH . F 6 HOH B 144 874 153 HOH HOH . F 6 HOH B 145 875 155 HOH HOH . F 6 HOH B 146 876 158 HOH HOH . F 6 HOH B 147 877 159 HOH HOH . F 6 HOH B 148 878 161 HOH HOH . F 6 HOH B 149 879 163 HOH HOH . F 6 HOH B 150 880 164 HOH HOH . F 6 HOH B 151 881 168 HOH HOH . F 6 HOH B 152 882 169 HOH HOH . F 6 HOH B 153 883 170 HOH HOH . F 6 HOH B 154 884 172 HOH HOH . F 6 HOH B 155 885 173 HOH HOH . F 6 HOH B 156 886 174 HOH HOH . F 6 HOH B 157 887 176 HOH HOH . F 6 HOH B 158 888 177 HOH HOH . F 6 HOH B 159 889 178 HOH HOH . F 6 HOH B 160 890 179 HOH HOH . F 6 HOH B 161 891 180 HOH HOH . F 6 HOH B 162 892 181 HOH HOH . F 6 HOH B 163 893 182 HOH HOH . F 6 HOH B 164 894 183 HOH HOH . F 6 HOH B 165 895 185 HOH HOH . F 6 HOH B 166 896 186 HOH HOH . F 6 HOH B 167 897 187 HOH HOH . F 6 HOH B 168 898 192 HOH HOH . F 6 HOH B 169 899 193 HOH HOH . F 6 HOH B 170 900 198 HOH HOH . F 6 HOH B 171 901 199 HOH HOH . F 6 HOH B 172 902 200 HOH HOH . F 6 HOH B 173 903 202 HOH HOH . F 6 HOH B 174 904 203 HOH HOH . F 6 HOH B 175 905 204 HOH HOH . F 6 HOH B 176 906 205 HOH HOH . F 6 HOH B 177 907 206 HOH HOH . F 6 HOH B 178 908 208 HOH HOH . F 6 HOH B 179 909 210 HOH HOH . F 6 HOH B 180 910 211 HOH HOH . F 6 HOH B 181 911 212 HOH HOH . F 6 HOH B 182 912 214 HOH HOH . F 6 HOH B 183 913 215 HOH HOH . F 6 HOH B 184 914 217 HOH HOH . F 6 HOH B 185 915 218 HOH HOH . F 6 HOH B 186 916 219 HOH HOH . F 6 HOH B 187 917 220 HOH HOH . F 6 HOH B 188 918 222 HOH HOH . F 6 HOH B 189 919 223 HOH HOH . F 6 HOH B 190 920 225 HOH HOH . F 6 HOH B 191 921 226 HOH HOH . F 6 HOH B 192 922 229 HOH HOH . F 6 HOH B 193 923 230 HOH HOH . F 6 HOH B 194 924 231 HOH HOH . F 6 HOH B 195 925 232 HOH HOH . F 6 HOH B 196 926 233 HOH HOH . F 6 HOH B 197 927 234 HOH HOH . F 6 HOH B 198 928 236 HOH HOH . F 6 HOH B 199 929 238 HOH HOH . F 6 HOH B 200 930 239 HOH HOH . F 6 HOH B 201 931 243 HOH HOH . F 6 HOH B 202 932 244 HOH HOH . F 6 HOH B 203 933 247 HOH HOH . F 6 HOH B 204 934 249 HOH HOH . F 6 HOH B 205 935 252 HOH HOH . F 6 HOH B 206 936 254 HOH HOH . F 6 HOH B 207 937 256 HOH HOH . F 6 HOH B 208 938 258 HOH HOH . F 6 HOH B 209 939 259 HOH HOH . F 6 HOH B 210 940 260 HOH HOH . F 6 HOH B 211 941 264 HOH HOH . F 6 HOH B 212 942 266 HOH HOH . F 6 HOH B 213 943 267 HOH HOH . F 6 HOH B 214 944 268 HOH HOH . F 6 HOH B 215 945 269 HOH HOH . F 6 HOH B 216 946 270 HOH HOH . F 6 HOH B 217 947 272 HOH HOH . F 6 HOH B 218 948 274 HOH HOH . F 6 HOH B 219 949 275 HOH HOH . F 6 HOH B 220 950 277 HOH HOH . F 6 HOH B 221 951 278 HOH HOH . F 6 HOH B 222 952 279 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 4 -7.506 47.923 4.686 1 33.55 ? PB ADP 700 B 1 HETATM 2 O O1B ADP . . . D 4 -6.437 48.297 5.661 1 29.07 ? O1B ADP 700 B 1 HETATM 3 O O2B ADP . . . D 4 -8.105 49.038 3.918 1 31.1 ? O2B ADP 700 B 1 HETATM 4 O O3B ADP . . . D 4 -6.881 46.885 3.668 1 30.26 ? O3B ADP 700 B 1 HETATM 5 P PA ADP . . . D 4 -10.257 47.671 5.563 1 38.86 ? PA ADP 700 B 1 HETATM 6 O O1A ADP . . . D 4 -10.617 49.058 5.93 1 41.46 ? O1A ADP 700 B 1 HETATM 7 O O2A ADP . . . D 4 -10.671 47.081 4.275 1 38.45 ? O2A ADP 700 B 1 HETATM 8 O O3A ADP . . . D 4 -8.605 47.393 5.642 1 33.87 ? O3A ADP 700 B 1 HETATM 9 O O5' ADP . . . D 4 -10.64 46.806 6.841 1 38.33 ? O5' ADP 700 B 1 HETATM 10 C C5' ADP . . . D 4 -11.919 46.883 7.418 1 39.5 ? C5' ADP 700 B 1 HETATM 11 C C4' ADP . . . D 4 -11.873 45.928 8.61 1 40.11 ? C4' ADP 700 B 1 HETATM 12 O O4' ADP . . . D 4 -10.856 46.308 9.518 1 40.09 ? O4' ADP 700 B 1 HETATM 13 C C3' ADP . . . D 4 -13.169 45.815 9.417 1 39.88 ? C3' ADP 700 B 1 HETATM 14 O O3' ADP . . . D 4 -13.405 44.448 9.703 1 42.36 ? O3' ADP 700 B 1 HETATM 15 C C2' ADP . . . D 4 -12.862 46.58 10.705 1 40.36 ? C2' ADP 700 B 1 HETATM 16 O O2' ADP . . . D 4 -13.6 46.156 11.872 1 43.99 ? O2' ADP 700 B 1 HETATM 17 C C1' ADP . . . D 4 -11.336 46.403 10.822 1 40.54 ? C1' ADP 700 B 1 HETATM 18 N N9 ADP . . . D 4 -10.702 47.558 11.518 1 42.2 ? N9 ADP 700 B 1 HETATM 19 C C8 ADP . . . D 4 -11.148 48.853 11.767 1 42.04 ? C8 ADP 700 B 1 HETATM 20 N N7 ADP . . . D 4 -10.366 49.685 12.426 1 41.07 ? N7 ADP 700 B 1 HETATM 21 C C5 ADP . . . D 4 -9.284 48.872 12.654 1 40.48 ? C5 ADP 700 B 1 HETATM 22 C C6 ADP . . . D 4 -8.034 49.08 13.314 1 42.19 ? C6 ADP 700 B 1 HETATM 23 N N6 ADP . . . D 4 -7.727 50.369 13.912 1 42.8 ? N6 ADP 700 B 1 HETATM 24 N N1 ADP . . . D 4 -7.121 48.043 13.383 1 42.48 ? N1 ADP 700 B 1 HETATM 25 C C2 ADP . . . D 4 -7.412 46.815 12.817 1 40.89 ? C2 ADP 700 B 1 HETATM 26 N N3 ADP . . . D 4 -8.56 46.487 12.158 1 38.65 ? N3 ADP 700 B 1 HETATM 27 C C4 ADP . . . D 4 -9.463 47.552 12.108 1 39.83 ? C4 ADP 700 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #