data_1Y56 # _model_server_result.job_id dcP4Itb75bDYcGHBskWdHg _model_server_result.datetime_utc '2024-11-05 00:38:06' _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 1y56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 1Y56 # _exptl.entry_id 1Y56 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 1Y56 _cell.length_a 172.219 _cell.length_b 172.219 _cell.length_c 175.398 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y56 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? octameric 8 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PQS monomeric 1 software_defined_assembly 3 PQS monomeric 1 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 1,2,3,4 A,B,C,D,E,F,G,H,I,J,K 2 1 A,C,D,E,F,G,J 3 1 B,H,I,K 4 1 # 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' 4_765 -x+2,-y+1,z -1 0 0 0 -1 0 0 0 1 258.3285 149.146029 0 3 'crystal symmetry operation' 9_765 -x+2,-x+y+1,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 258.3285 149.146029 116.932 4 'crystal symmetry operation' 12_555 x,x-y,-z+2/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 116.932 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 415 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 413 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 454 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 452 _struct_conn.ptnr2_symmetry 1_555 _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 2.066 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1Y56 _atom_sites.fract_transf_matrix[1][1] 0.005807 _atom_sites.fract_transf_matrix[1][2] 0.003352 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006705 _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] 0.005701 _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 3 FE A 1 805 805 FE FE . D 4 SO4 A 1 806 806 SO4 SO4 . E 5 FMN A 1 802 802 FMN FMN . F 6 ATP A 1 801 801 ATP ATP . G 7 CXS A 1 803 803 CXS CXS . H 8 CL B 1 804 804 CL CL . I 9 FAD B 1 800 800 FAD FAD . J 10 HOH A 1 807 2 HOH HOH . J 10 HOH A 2 808 3 HOH HOH . J 10 HOH A 3 809 4 HOH HOH . J 10 HOH A 4 810 5 HOH HOH . J 10 HOH A 5 811 6 HOH HOH . J 10 HOH A 6 812 8 HOH HOH . J 10 HOH A 7 813 9 HOH HOH . J 10 HOH A 8 814 10 HOH HOH . J 10 HOH A 9 815 12 HOH HOH . J 10 HOH A 10 816 15 HOH HOH . J 10 HOH A 11 817 20 HOH HOH . J 10 HOH A 12 818 24 HOH HOH . J 10 HOH A 13 819 25 HOH HOH . J 10 HOH A 14 820 26 HOH HOH . J 10 HOH A 15 821 29 HOH HOH . J 10 HOH A 16 822 32 HOH HOH . J 10 HOH A 17 823 34 HOH HOH . J 10 HOH A 18 824 36 HOH HOH . J 10 HOH A 19 825 37 HOH HOH . J 10 HOH A 20 826 38 HOH HOH . J 10 HOH A 21 827 39 HOH HOH . J 10 HOH A 22 828 46 HOH HOH . J 10 HOH A 23 829 47 HOH HOH . J 10 HOH A 24 830 48 HOH HOH . J 10 HOH A 25 831 49 HOH HOH . J 10 HOH A 26 832 52 HOH HOH . J 10 HOH A 27 833 54 HOH HOH . J 10 HOH A 28 834 56 HOH HOH . J 10 HOH A 29 835 58 HOH HOH . J 10 HOH A 30 836 61 HOH HOH . J 10 HOH A 31 837 66 HOH HOH . J 10 HOH A 32 838 67 HOH HOH . J 10 HOH A 33 839 70 HOH HOH . J 10 HOH A 34 840 71 HOH HOH . J 10 HOH A 35 841 72 HOH HOH . J 10 HOH A 36 842 73 HOH HOH . J 10 HOH A 37 843 74 HOH HOH . J 10 HOH A 38 844 75 HOH HOH . J 10 HOH A 39 845 76 HOH HOH . J 10 HOH A 40 846 80 HOH HOH . J 10 HOH A 41 847 81 HOH HOH . J 10 HOH A 42 848 82 HOH HOH . J 10 HOH A 43 849 83 HOH HOH . J 10 HOH A 44 850 84 HOH HOH . J 10 HOH A 45 851 85 HOH HOH . J 10 HOH A 46 852 87 HOH HOH . J 10 HOH A 47 853 88 HOH HOH . J 10 HOH A 48 854 89 HOH HOH . J 10 HOH A 49 855 90 HOH HOH . J 10 HOH A 50 856 93 HOH HOH . J 10 HOH A 51 857 94 HOH HOH . J 10 HOH A 52 858 95 HOH HOH . J 10 HOH A 53 859 97 HOH HOH . J 10 HOH A 54 860 100 HOH HOH . J 10 HOH A 55 861 101 HOH HOH . J 10 HOH A 56 862 103 HOH HOH . J 10 HOH A 57 863 104 HOH HOH . J 10 HOH A 58 864 107 HOH HOH . J 10 HOH A 59 865 108 HOH HOH . J 10 HOH A 60 866 109 HOH HOH . J 10 HOH A 61 867 110 HOH HOH . J 10 HOH A 62 868 113 HOH HOH . J 10 HOH A 63 869 114 HOH HOH . J 10 HOH A 64 870 116 HOH HOH . J 10 HOH A 65 871 117 HOH HOH . J 10 HOH A 66 872 118 HOH HOH . J 10 HOH A 67 873 119 HOH HOH . J 10 HOH A 68 874 120 HOH HOH . J 10 HOH A 69 875 122 HOH HOH . J 10 HOH A 70 876 123 HOH HOH . J 10 HOH A 71 877 124 HOH HOH . J 10 HOH A 72 878 126 HOH HOH . J 10 HOH A 73 879 127 HOH HOH . J 10 HOH A 74 880 128 HOH HOH . J 10 HOH A 75 881 130 HOH HOH . J 10 HOH A 76 882 131 HOH HOH . J 10 HOH A 77 883 132 HOH HOH . J 10 HOH A 78 884 133 HOH HOH . J 10 HOH A 79 885 134 HOH HOH . J 10 HOH A 80 886 136 HOH HOH . J 10 HOH A 81 887 137 HOH HOH . J 10 HOH A 82 888 138 HOH HOH . J 10 HOH A 83 889 139 HOH HOH . J 10 HOH A 84 890 140 HOH HOH . J 10 HOH A 85 891 142 HOH HOH . J 10 HOH A 86 892 144 HOH HOH . J 10 HOH A 87 893 145 HOH HOH . J 10 HOH A 88 894 146 HOH HOH . J 10 HOH A 89 895 147 HOH HOH . J 10 HOH A 90 896 148 HOH HOH . J 10 HOH A 91 897 152 HOH HOH . J 10 HOH A 92 898 153 HOH HOH . J 10 HOH A 93 899 154 HOH HOH . J 10 HOH A 94 900 155 HOH HOH . J 10 HOH A 95 901 156 HOH HOH . J 10 HOH A 96 902 157 HOH HOH . J 10 HOH A 97 903 158 HOH HOH . J 10 HOH A 98 904 160 HOH HOH . J 10 HOH A 99 905 161 HOH HOH . J 10 HOH A 100 906 162 HOH HOH . J 10 HOH A 101 907 163 HOH HOH . J 10 HOH A 102 908 165 HOH HOH . J 10 HOH A 103 909 166 HOH HOH . J 10 HOH A 104 910 167 HOH HOH . J 10 HOH A 105 911 168 HOH HOH . J 10 HOH A 106 912 170 HOH HOH . J 10 HOH A 107 913 171 HOH HOH . J 10 HOH A 108 914 172 HOH HOH . J 10 HOH A 109 915 173 HOH HOH . J 10 HOH A 110 916 174 HOH HOH . J 10 HOH A 111 917 175 HOH HOH . J 10 HOH A 112 918 177 HOH HOH . J 10 HOH A 113 919 178 HOH HOH . J 10 HOH A 114 920 183 HOH HOH . J 10 HOH A 115 921 185 HOH HOH . J 10 HOH A 116 922 187 HOH HOH . J 10 HOH A 117 923 188 HOH HOH . J 10 HOH A 118 924 189 HOH HOH . J 10 HOH A 119 925 190 HOH HOH . J 10 HOH A 120 926 191 HOH HOH . J 10 HOH A 121 927 192 HOH HOH . J 10 HOH A 122 928 194 HOH HOH . J 10 HOH A 123 929 196 HOH HOH . J 10 HOH A 124 930 198 HOH HOH . J 10 HOH A 125 931 199 HOH HOH . J 10 HOH A 126 932 200 HOH HOH . J 10 HOH A 127 933 201 HOH HOH . J 10 HOH A 128 934 202 HOH HOH . J 10 HOH A 129 935 205 HOH HOH . K 10 HOH B 1 805 1 HOH HOH . K 10 HOH B 2 806 7 HOH HOH . K 10 HOH B 3 807 11 HOH HOH . K 10 HOH B 4 808 13 HOH HOH . K 10 HOH B 5 809 14 HOH HOH . K 10 HOH B 6 810 16 HOH HOH . K 10 HOH B 7 811 17 HOH HOH . K 10 HOH B 8 812 18 HOH HOH . K 10 HOH B 9 813 19 HOH HOH . K 10 HOH B 10 814 21 HOH HOH . K 10 HOH B 11 815 22 HOH HOH . K 10 HOH B 12 816 23 HOH HOH . K 10 HOH B 13 817 27 HOH HOH . K 10 HOH B 14 818 28 HOH HOH . K 10 HOH B 15 819 30 HOH HOH . K 10 HOH B 16 820 31 HOH HOH . K 10 HOH B 17 821 33 HOH HOH . K 10 HOH B 18 822 35 HOH HOH . K 10 HOH B 19 823 40 HOH HOH . K 10 HOH B 20 824 41 HOH HOH . K 10 HOH B 21 825 42 HOH HOH . K 10 HOH B 22 826 43 HOH HOH . K 10 HOH B 23 827 44 HOH HOH . K 10 HOH B 24 828 45 HOH HOH . K 10 HOH B 25 829 50 HOH HOH . K 10 HOH B 26 830 51 HOH HOH . K 10 HOH B 27 831 53 HOH HOH . K 10 HOH B 28 832 55 HOH HOH . K 10 HOH B 29 833 57 HOH HOH . K 10 HOH B 30 834 59 HOH HOH . K 10 HOH B 31 835 60 HOH HOH . K 10 HOH B 32 836 62 HOH HOH . K 10 HOH B 33 837 63 HOH HOH . K 10 HOH B 34 838 64 HOH HOH . K 10 HOH B 35 839 65 HOH HOH . K 10 HOH B 36 840 68 HOH HOH . K 10 HOH B 37 841 69 HOH HOH . K 10 HOH B 38 842 77 HOH HOH . K 10 HOH B 39 843 78 HOH HOH . K 10 HOH B 40 844 79 HOH HOH . K 10 HOH B 41 845 86 HOH HOH . K 10 HOH B 42 846 91 HOH HOH . K 10 HOH B 43 847 92 HOH HOH . K 10 HOH B 44 848 96 HOH HOH . K 10 HOH B 45 849 98 HOH HOH . K 10 HOH B 46 850 99 HOH HOH . K 10 HOH B 47 851 102 HOH HOH . K 10 HOH B 48 852 105 HOH HOH . K 10 HOH B 49 853 106 HOH HOH . K 10 HOH B 50 854 111 HOH HOH . K 10 HOH B 51 855 112 HOH HOH . K 10 HOH B 52 856 115 HOH HOH . K 10 HOH B 53 857 121 HOH HOH . K 10 HOH B 54 858 125 HOH HOH . K 10 HOH B 55 859 129 HOH HOH . K 10 HOH B 56 860 135 HOH HOH . K 10 HOH B 57 861 141 HOH HOH . K 10 HOH B 58 862 143 HOH HOH . K 10 HOH B 59 863 149 HOH HOH . K 10 HOH B 60 864 150 HOH HOH . K 10 HOH B 61 865 151 HOH HOH . K 10 HOH B 62 866 159 HOH HOH . K 10 HOH B 63 867 164 HOH HOH . K 10 HOH B 64 868 169 HOH HOH . K 10 HOH B 65 869 176 HOH HOH . K 10 HOH B 66 870 179 HOH HOH . K 10 HOH B 67 871 180 HOH HOH . K 10 HOH B 68 872 181 HOH HOH . K 10 HOH B 69 873 182 HOH HOH . K 10 HOH B 70 874 184 HOH HOH . K 10 HOH B 71 875 186 HOH HOH . K 10 HOH B 72 876 193 HOH HOH . K 10 HOH B 73 877 195 HOH HOH . K 10 HOH B 74 878 197 HOH HOH . K 10 HOH B 75 879 203 HOH HOH . K 10 HOH B 76 880 204 HOH HOH . K 10 HOH B 77 881 206 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 PG ATP . . . F 6 103.206 77.477 48.21 1 21.26 ? PG ATP 801 A 1 HETATM 2 O O1G ATP . . . F 6 103.668 76.175 47.629 1 19.7 ? O1G ATP 801 A 1 HETATM 3 O O2G ATP . . . F 6 103.308 77.545 49.721 1 22.06 ? O2G ATP 801 A 1 HETATM 4 O O3G ATP . . . F 6 101.882 77.989 47.7 1 21.3 ? O3G ATP 801 A 1 HETATM 5 P PB ATP . . . F 6 105.014 78.556 46.22 1 19.75 ? PB ATP 801 A 1 HETATM 6 O O1B ATP . . . F 6 106.436 78.086 46.429 1 17.53 ? O1B ATP 801 A 1 HETATM 7 O O2B ATP . . . F 6 104.702 79.875 45.568 1 17.96 ? O2B ATP 801 A 1 HETATM 8 O O3B ATP . . . F 6 104.277 78.571 47.659 1 21.33 ? O3B ATP 801 A 1 HETATM 9 P PA ATP . . . F 6 102.927 77.371 44.595 1 23.01 ? PA ATP 801 A 1 HETATM 10 O O1A ATP . . . F 6 101.9 78.138 45.376 1 22.07 ? O1A ATP 801 A 1 HETATM 11 O O2A ATP . . . F 6 102.679 75.916 44.256 1 23.04 ? O2A ATP 801 A 1 HETATM 12 O O3A ATP . . . F 6 104.335 77.36 45.379 1 22.12 ? O3A ATP 801 A 1 HETATM 13 O O5' ATP . . . F 6 103.189 78.215 43.251 1 23.42 ? O5' ATP 801 A 1 HETATM 14 C C5' ATP . . . F 6 103.757 77.596 42.1 1 24.64 ? C5' ATP 801 A 1 HETATM 15 C C4' ATP . . . F 6 103.175 78.2 40.833 1 25.04 ? C4' ATP 801 A 1 HETATM 16 O O4' ATP . . . F 6 104.091 78.038 39.748 1 25.52 ? O4' ATP 801 A 1 HETATM 17 C C3' ATP . . . F 6 101.925 77.448 40.443 1 25.59 ? C3' ATP 801 A 1 HETATM 18 O O3' ATP . . . F 6 100.911 78.434 40.341 1 24.77 ? O3' ATP 801 A 1 HETATM 19 C C2' ATP . . . F 6 102.237 76.821 39.093 1 26.41 ? C2' ATP 801 A 1 HETATM 20 O O2' ATP . . . F 6 101.142 76.864 38.168 1 27.74 ? O2' ATP 801 A 1 HETATM 21 C C1' ATP . . . F 6 103.348 77.71 38.584 1 26.11 ? C1' ATP 801 A 1 HETATM 22 N N9 ATP . . . F 6 104.177 77.062 37.541 1 26.61 ? N9 ATP 801 A 1 HETATM 23 C C8 ATP . . . F 6 104.877 75.92 37.638 1 26.25 ? C8 ATP 801 A 1 HETATM 24 N N7 ATP . . . F 6 105.487 75.672 36.451 1 26.01 ? N7 ATP 801 A 1 HETATM 25 C C5 ATP . . . F 6 105.174 76.679 35.604 1 26.35 ? C5 ATP 801 A 1 HETATM 26 C C6 ATP . . . F 6 105.508 76.976 34.283 1 25.37 ? C6 ATP 801 A 1 HETATM 27 N N6 ATP . . . F 6 106.319 76.166 33.562 1 23.71 ? N6 ATP 801 A 1 HETATM 28 N N1 ATP . . . F 6 105.005 78.083 33.726 1 25.5 ? N1 ATP 801 A 1 HETATM 29 C C2 ATP . . . F 6 104.194 78.909 34.411 1 26.32 ? C2 ATP 801 A 1 HETATM 30 N N3 ATP . . . F 6 103.847 78.661 35.682 1 26.29 ? N3 ATP 801 A 1 HETATM 31 C C4 ATP . . . F 6 104.336 77.552 36.301 1 26.96 ? C4 ATP 801 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #