data_1SEH # _model_server_result.job_id b98BOdLZMVfDbePTJJq7HQ _model_server_result.datetime_utc '2024-11-25 08:23:28' _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 1seh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":777}' # _entry.id 1SEH # _exptl.entry_id 1SEH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 1SEH _cell.length_a 75.257 _cell.length_b 75.257 _cell.length_c 100.532 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SEH _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 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 PISA trimeric 3 author_and_software_defined_assembly 1 PQS hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1,2,3 A,B,C,D 2 1,2,3,4,5,6 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 37.6285 65.174474 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -37.6285 65.174474 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 37.6285 65.174474 50.266 5 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 50.266 6 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -37.6285 65.174474 50.266 # _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 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 377 n n N1 C6 UMP sing 378 n n N1 C1' UMP sing 379 n n C2 N3 UMP sing 380 n n C2 O2 UMP doub 381 n n N3 C4 UMP sing 382 n n N3 HN3 UMP sing 383 n n C4 C5 UMP sing 384 n n C4 O4 UMP doub 385 n n C5 C6 UMP doub 386 n n C5 H5 UMP sing 387 n n C6 H6 UMP sing 388 n n C1' C2' UMP sing 389 n n C1' O4' UMP sing 390 n n C1' H1' UMP sing 391 n n C2' C3' UMP sing 392 n n C2' H2' UMP sing 393 n n C2' "H2''" UMP sing 394 n n C3' C4' UMP sing 395 n n C3' O3' UMP sing 396 n n C3' H3' UMP sing 397 n n C4' O4' UMP sing 398 n n C4' C5' UMP sing 399 n n C4' H4' UMP sing 400 n n O3' HO3' UMP sing 401 n n C5' O5' UMP sing 402 n n C5' H5' UMP sing 403 n n C5' "H5''" UMP sing 404 n n O5' P UMP sing 405 n n P OP1 UMP doub 406 n n P OP2 UMP sing 407 n n P OP3 UMP sing 408 n n OP2 HOP2 UMP sing 409 n n OP3 HOP3 UMP sing 410 n n # _atom_sites.entry_id 1SEH _atom_sites.fract_transf_matrix[1][1] 0.013288 _atom_sites.fract_transf_matrix[1][2] 0.007672 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015343 _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] 0.009947 _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 UMP A 1 777 777 UMP UMP . C 3 TRS A 1 501 501 TRS TRS . D 4 HOH A 1 778 94 HOH HOH . D 4 HOH A 2 779 2 HOH HOH . D 4 HOH A 3 780 3 HOH HOH . D 4 HOH A 4 781 13 HOH HOH . D 4 HOH A 5 782 5 HOH HOH . D 4 HOH A 6 783 6 HOH HOH . D 4 HOH A 7 784 7 HOH HOH . D 4 HOH A 8 785 8 HOH HOH . D 4 HOH A 9 786 9 HOH HOH . D 4 HOH A 10 787 10 HOH HOH . D 4 HOH A 11 788 11 HOH HOH . D 4 HOH A 12 789 12 HOH HOH . D 4 HOH A 13 790 4 HOH HOH . D 4 HOH A 14 791 14 HOH HOH . D 4 HOH A 15 792 15 HOH HOH . D 4 HOH A 16 793 16 HOH HOH . D 4 HOH A 17 794 17 HOH HOH . D 4 HOH A 18 795 18 HOH HOH . D 4 HOH A 19 796 19 HOH HOH . D 4 HOH A 20 797 20 HOH HOH . D 4 HOH A 21 798 21 HOH HOH . D 4 HOH A 22 799 22 HOH HOH . D 4 HOH A 23 800 23 HOH HOH . D 4 HOH A 24 801 24 HOH HOH . D 4 HOH A 25 802 25 HOH HOH . D 4 HOH A 26 803 26 HOH HOH . D 4 HOH A 27 804 27 HOH HOH . D 4 HOH A 28 805 28 HOH HOH . D 4 HOH A 29 806 29 HOH HOH . D 4 HOH A 30 807 30 HOH HOH . D 4 HOH A 31 808 31 HOH HOH . D 4 HOH A 32 809 32 HOH HOH . D 4 HOH A 33 810 33 HOH HOH . D 4 HOH A 34 811 34 HOH HOH . D 4 HOH A 35 812 35 HOH HOH . D 4 HOH A 36 813 36 HOH HOH . D 4 HOH A 37 814 37 HOH HOH . D 4 HOH A 38 815 38 HOH HOH . D 4 HOH A 39 816 39 HOH HOH . D 4 HOH A 40 817 40 HOH HOH . D 4 HOH A 41 818 41 HOH HOH . D 4 HOH A 42 819 42 HOH HOH . D 4 HOH A 43 820 43 HOH HOH . D 4 HOH A 44 821 44 HOH HOH . D 4 HOH A 45 822 45 HOH HOH . D 4 HOH A 46 823 46 HOH HOH . D 4 HOH A 47 824 47 HOH HOH . D 4 HOH A 48 825 48 HOH HOH . D 4 HOH A 49 826 49 HOH HOH . D 4 HOH A 50 827 50 HOH HOH . D 4 HOH A 51 828 51 HOH HOH . D 4 HOH A 52 829 52 HOH HOH . D 4 HOH A 53 830 53 HOH HOH . D 4 HOH A 54 831 54 HOH HOH . D 4 HOH A 55 832 55 HOH HOH . D 4 HOH A 56 833 56 HOH HOH . D 4 HOH A 57 834 57 HOH HOH . D 4 HOH A 58 835 58 HOH HOH . D 4 HOH A 59 836 59 HOH HOH . D 4 HOH A 60 837 60 HOH HOH . D 4 HOH A 61 838 61 HOH HOH . D 4 HOH A 62 839 62 HOH HOH . D 4 HOH A 63 840 63 HOH HOH . D 4 HOH A 64 841 64 HOH HOH . D 4 HOH A 65 842 65 HOH HOH . D 4 HOH A 66 843 66 HOH HOH . D 4 HOH A 67 844 67 HOH HOH . D 4 HOH A 68 845 68 HOH HOH . D 4 HOH A 69 846 69 HOH HOH . D 4 HOH A 70 847 70 HOH HOH . D 4 HOH A 71 848 71 HOH HOH . D 4 HOH A 72 849 72 HOH HOH . D 4 HOH A 73 850 73 HOH HOH . D 4 HOH A 74 851 74 HOH HOH . D 4 HOH A 75 852 75 HOH HOH . D 4 HOH A 76 853 76 HOH HOH . D 4 HOH A 77 854 77 HOH HOH . D 4 HOH A 78 855 78 HOH HOH . D 4 HOH A 79 856 79 HOH HOH . D 4 HOH A 80 857 80 HOH HOH . D 4 HOH A 81 858 81 HOH HOH . D 4 HOH A 82 859 82 HOH HOH . D 4 HOH A 83 860 83 HOH HOH . D 4 HOH A 84 861 84 HOH HOH . D 4 HOH A 85 862 85 HOH HOH . D 4 HOH A 86 863 86 HOH HOH . D 4 HOH A 87 864 87 HOH HOH . D 4 HOH A 88 865 88 HOH HOH . D 4 HOH A 89 866 90 HOH HOH . D 4 HOH A 90 867 91 HOH HOH . D 4 HOH A 91 868 92 HOH HOH . D 4 HOH A 92 869 93 HOH HOH . D 4 HOH A 93 870 1 HOH HOH . D 4 HOH A 94 871 95 HOH HOH . D 4 HOH A 95 872 96 HOH HOH . D 4 HOH A 96 873 97 HOH HOH . D 4 HOH A 97 874 98 HOH HOH . D 4 HOH A 98 875 99 HOH HOH . D 4 HOH A 99 876 100 HOH HOH . D 4 HOH A 100 877 101 HOH HOH . D 4 HOH A 101 878 102 HOH HOH . D 4 HOH A 102 879 103 HOH HOH . D 4 HOH A 103 880 104 HOH HOH . D 4 HOH A 104 881 105 HOH HOH . D 4 HOH A 105 882 106 HOH HOH . D 4 HOH A 106 883 107 HOH HOH . D 4 HOH A 107 884 108 HOH HOH . D 4 HOH A 108 885 109 HOH HOH . D 4 HOH A 109 886 110 HOH HOH . D 4 HOH A 110 887 111 HOH HOH . D 4 HOH A 111 888 112 HOH HOH . D 4 HOH A 112 889 113 HOH HOH . D 4 HOH A 113 890 114 HOH HOH . D 4 HOH A 114 891 115 HOH HOH . D 4 HOH A 115 892 116 HOH HOH . D 4 HOH A 116 893 117 HOH HOH . D 4 HOH A 117 894 118 HOH HOH . D 4 HOH A 118 895 119 HOH HOH . D 4 HOH A 119 896 120 HOH HOH . D 4 HOH A 120 897 121 HOH HOH . D 4 HOH A 121 898 122 HOH HOH . D 4 HOH A 122 899 123 HOH HOH . D 4 HOH A 123 900 124 HOH HOH . D 4 HOH A 124 901 125 HOH HOH . D 4 HOH A 125 902 126 HOH HOH . D 4 HOH A 126 903 127 HOH HOH . D 4 HOH A 127 904 128 HOH HOH . D 4 HOH A 128 905 129 HOH HOH . D 4 HOH A 129 906 130 HOH HOH . D 4 HOH A 130 907 131 HOH HOH . D 4 HOH A 131 908 132 HOH HOH . D 4 HOH A 132 909 133 HOH HOH . D 4 HOH A 133 910 134 HOH HOH . D 4 HOH A 134 911 135 HOH HOH . D 4 HOH A 135 912 136 HOH HOH . D 4 HOH A 136 913 137 HOH HOH . D 4 HOH A 137 914 138 HOH HOH . D 4 HOH A 138 915 139 HOH HOH . D 4 HOH A 139 916 140 HOH HOH . D 4 HOH A 140 917 141 HOH HOH . D 4 HOH A 141 918 142 HOH HOH . D 4 HOH A 142 919 143 HOH HOH . D 4 HOH A 143 920 144 HOH HOH . D 4 HOH A 144 921 145 HOH HOH . D 4 HOH A 145 922 146 HOH HOH . D 4 HOH A 146 923 147 HOH HOH . D 4 HOH A 147 924 148 HOH HOH . D 4 HOH A 148 925 149 HOH HOH . D 4 HOH A 149 926 150 HOH HOH . D 4 HOH A 150 927 151 HOH HOH . D 4 HOH A 151 928 152 HOH HOH . D 4 HOH A 152 929 153 HOH HOH . D 4 HOH A 153 930 154 HOH HOH . D 4 HOH A 154 931 155 HOH HOH . D 4 HOH A 155 932 156 HOH HOH . D 4 HOH A 156 933 157 HOH HOH . D 4 HOH A 157 934 158 HOH HOH . D 4 HOH A 158 935 159 HOH HOH . D 4 HOH A 159 936 160 HOH HOH . D 4 HOH A 160 937 161 HOH HOH . D 4 HOH A 161 938 162 HOH HOH . D 4 HOH A 162 939 163 HOH HOH . D 4 HOH A 163 940 164 HOH HOH . D 4 HOH A 164 941 166 HOH HOH . D 4 HOH A 165 942 167 HOH HOH . D 4 HOH A 166 943 168 HOH HOH . D 4 HOH A 167 944 169 HOH HOH . D 4 HOH A 168 945 170 HOH HOH . D 4 HOH A 169 946 171 HOH HOH . D 4 HOH A 170 947 172 HOH HOH . D 4 HOH A 171 948 173 HOH HOH . D 4 HOH A 172 949 174 HOH HOH . D 4 HOH A 173 950 175 HOH HOH . D 4 HOH A 174 951 176 HOH HOH . D 4 HOH A 175 952 177 HOH HOH . D 4 HOH A 176 953 179 HOH HOH . D 4 HOH A 177 954 180 HOH HOH . D 4 HOH A 178 955 181 HOH HOH . D 4 HOH A 179 956 182 HOH HOH . D 4 HOH A 180 957 183 HOH HOH . D 4 HOH A 181 958 184 HOH HOH . D 4 HOH A 182 959 185 HOH HOH . D 4 HOH A 183 960 187 HOH HOH . D 4 HOH A 184 961 188 HOH HOH . D 4 HOH A 185 962 189 HOH HOH . D 4 HOH A 186 963 190 HOH HOH . D 4 HOH A 187 964 191 HOH HOH . D 4 HOH A 188 965 192 HOH HOH . D 4 HOH A 189 966 193 HOH HOH . D 4 HOH A 190 967 195 HOH HOH . D 4 HOH A 191 968 196 HOH HOH . D 4 HOH A 192 969 197 HOH HOH . D 4 HOH A 193 970 198 HOH HOH . D 4 HOH A 194 971 199 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 N N1 UMP . . . B 2 -7.439 31.543 4.811 1 22.51 ? N1 UMP 777 A 1 HETATM 2 C C2 UMP . . . B 2 -6.421 30.809 4.251 1 23.62 ? C2 UMP 777 A 1 HETATM 3 N N3 UMP . . . B 2 -5.512 31.469 3.446 1 23.95 ? N3 UMP 777 A 1 HETATM 4 C C4 UMP . . . B 2 -5.603 32.819 3.179 1 25.19 ? C4 UMP 777 A 1 HETATM 5 C C5 UMP . . . B 2 -6.623 33.56 3.752 1 24.95 ? C5 UMP 777 A 1 HETATM 6 C C6 UMP . . . B 2 -7.529 32.896 4.56 1 23.26 ? C6 UMP 777 A 1 HETATM 7 O O2 UMP . . . B 2 -6.307 29.585 4.446 1 21.88 ? O2 UMP 777 A 1 HETATM 8 O O4 UMP . . . B 2 -4.773 33.356 2.463 1 26.03 ? O4 UMP 777 A 1 HETATM 9 C C1' UMP . . . B 2 -8.421 30.901 5.711 1 24.34 ? C1' UMP 777 A 1 HETATM 10 C C2' UMP . . . B 2 -8.246 31.499 7.11 1 24.69 ? C2' UMP 777 A 1 HETATM 11 C C3' UMP . . . B 2 -9.479 32.332 7.337 1 27.08 ? C3' UMP 777 A 1 HETATM 12 C C4' UMP . . . B 2 -10.472 31.568 6.488 1 27.02 ? C4' UMP 777 A 1 HETATM 13 O O3' UMP . . . B 2 -9.87 32.411 8.696 1 25.45 ? O3' UMP 777 A 1 HETATM 14 O O4' UMP . . . B 2 -9.74 31.19 5.323 1 30.47 ? O4' UMP 777 A 1 HETATM 15 C C5' UMP . . . B 2 -11.727 32.345 6.172 1 41.09 ? C5' UMP 777 A 1 HETATM 16 O O5' UMP . . . B 2 -11.409 33.335 5.251 1 39.67 ? O5' UMP 777 A 1 HETATM 17 P P UMP . . . B 2 -12.615 34.222 4.698 1 43.62 ? P UMP 777 A 1 HETATM 18 O OP1 UMP . . . B 2 -11.932 35.312 3.947 1 46.68 ? OP1 UMP 777 A 1 HETATM 19 O OP2 UMP . . . B 2 -13.431 34.789 5.884 1 44.69 ? OP2 UMP 777 A 1 HETATM 20 O OP3 UMP . . . B 2 -13.534 33.376 3.791 1 52.42 ? OP3 UMP 777 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #