data_5TFF # _model_server_result.job_id yqQNzubjS66FVJpMO6Qk7Q _model_server_result.datetime_utc '2025-08-31 09:16:56' _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 5tff # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 5TFF # _exptl.entry_id 5TFF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 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 90 _cell.entry_id 5TFF _cell.length_a 40.183 _cell.length_b 40.183 _cell.length_c 141.794 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TFF _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 OG1 THR 48 A THR 465 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc2 A OE1 GLN 76 A GLN 493 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 B MG MG . A MG 701 1_555 C O2B UTP . A UTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 B MG MG . A MG 701 1_555 C O2G UTP . A UTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc5 B MG MG . A MG 701 1_555 D O HOH . A HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc6 B MG MG . A MG 701 1_555 D O HOH . A HOH 822 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _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 PA O1A UTP doub 358 n n PA O2A UTP sing 359 n n PA O3A UTP sing 360 n n PA O5' UTP sing 361 n n O2A H2A UTP sing 362 n n O3A PB UTP sing 363 n n O5' C5' UTP sing 364 n n PB O1B UTP sing 365 n n PB O2B UTP doub 366 n n PB O3B UTP sing 367 n n O1B H1B UTP sing 368 n n O3B PG UTP sing 369 n n PG O1G UTP sing 370 n n PG O2G UTP doub 371 n n PG O3G UTP sing 372 n n O1G H1G UTP sing 373 n n O3G H3G UTP sing 374 n n C5' C4' UTP sing 375 n n C5' "H5'1" UTP sing 376 n n C5' "H5'2" UTP sing 377 n n C4' O4' UTP sing 378 n n C4' C3' UTP sing 379 n n C4' H4' UTP sing 380 n n O4' C1' UTP sing 381 n n C1' C2' UTP sing 382 n n C1' N1 UTP sing 383 n n C1' H1' UTP sing 384 n n C2' O2' UTP sing 385 n n C2' C3' UTP sing 386 n n C2' H2' UTP sing 387 n n O2' HA UTP sing 388 n n C3' O3' UTP sing 389 n n C3' H3' UTP sing 390 n n O3' HB UTP sing 391 n n N1 C6 UTP sing 392 n y N1 C2 UTP sing 393 n y C6 C5 UTP doub 394 n y C6 H6 UTP sing 395 n n C2 O2 UTP doub 396 n n C2 N3 UTP sing 397 n y N3 C4 UTP sing 398 n y N3 H3 UTP sing 399 n n C4 O4 UTP doub 400 n n C4 C5 UTP sing 401 n y C5 H5 UTP sing 402 n n # _atom_sites.entry_id 5TFF _atom_sites.fract_transf_matrix[1][1] 0.024886 _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] 0.024886 _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] 0.007052 _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 1 701 700 MG MG . C 3 UTP A 1 702 1 UTP UTP . D 4 HOH A 1 801 107 HOH HOH . D 4 HOH A 2 802 98 HOH HOH . D 4 HOH A 3 803 106 HOH HOH . D 4 HOH A 4 804 172 HOH HOH . D 4 HOH A 5 805 63 HOH HOH . D 4 HOH A 6 806 129 HOH HOH . D 4 HOH A 7 807 57 HOH HOH . D 4 HOH A 8 808 10 HOH HOH . D 4 HOH A 9 809 135 HOH HOH . D 4 HOH A 10 810 39 HOH HOH . D 4 HOH A 11 811 49 HOH HOH . D 4 HOH A 12 812 154 HOH HOH . D 4 HOH A 13 813 79 HOH HOH . D 4 HOH A 14 814 159 HOH HOH . D 4 HOH A 15 815 105 HOH HOH . D 4 HOH A 16 816 6 HOH HOH . D 4 HOH A 17 817 81 HOH HOH . D 4 HOH A 18 818 61 HOH HOH . D 4 HOH A 19 819 125 HOH HOH . D 4 HOH A 20 820 60 HOH HOH . D 4 HOH A 21 821 55 HOH HOH . D 4 HOH A 22 822 1 HOH HOH . D 4 HOH A 23 823 23 HOH HOH . D 4 HOH A 24 824 41 HOH HOH . D 4 HOH A 25 825 11 HOH HOH . D 4 HOH A 26 826 101 HOH HOH . D 4 HOH A 27 827 4 HOH HOH . D 4 HOH A 28 828 19 HOH HOH . D 4 HOH A 29 829 104 HOH HOH . D 4 HOH A 30 830 33 HOH HOH . D 4 HOH A 31 831 20 HOH HOH . D 4 HOH A 32 832 27 HOH HOH . D 4 HOH A 33 833 70 HOH HOH . D 4 HOH A 34 834 100 HOH HOH . D 4 HOH A 35 835 13 HOH HOH . D 4 HOH A 36 836 190 HOH HOH . D 4 HOH A 37 837 3 HOH HOH . D 4 HOH A 38 838 139 HOH HOH . D 4 HOH A 39 839 80 HOH HOH . D 4 HOH A 40 840 90 HOH HOH . D 4 HOH A 41 841 29 HOH HOH . D 4 HOH A 42 842 131 HOH HOH . D 4 HOH A 43 843 137 HOH HOH . D 4 HOH A 44 844 162 HOH HOH . D 4 HOH A 45 845 85 HOH HOH . D 4 HOH A 46 846 167 HOH HOH . D 4 HOH A 47 847 72 HOH HOH . D 4 HOH A 48 848 40 HOH HOH . D 4 HOH A 49 849 77 HOH HOH . D 4 HOH A 50 850 155 HOH HOH . D 4 HOH A 51 851 127 HOH HOH . D 4 HOH A 52 852 44 HOH HOH . D 4 HOH A 53 853 102 HOH HOH . D 4 HOH A 54 854 26 HOH HOH . D 4 HOH A 55 855 9 HOH HOH . D 4 HOH A 56 856 168 HOH HOH . D 4 HOH A 57 857 17 HOH HOH . D 4 HOH A 58 858 123 HOH HOH . D 4 HOH A 59 859 56 HOH HOH . D 4 HOH A 60 860 82 HOH HOH . D 4 HOH A 61 861 69 HOH HOH . D 4 HOH A 62 862 87 HOH HOH . D 4 HOH A 63 863 86 HOH HOH . D 4 HOH A 64 864 93 HOH HOH . D 4 HOH A 65 865 180 HOH HOH . D 4 HOH A 66 866 48 HOH HOH . D 4 HOH A 67 867 174 HOH HOH . D 4 HOH A 68 868 88 HOH HOH . D 4 HOH A 69 869 68 HOH HOH . D 4 HOH A 70 870 183 HOH HOH . D 4 HOH A 71 871 7 HOH HOH . D 4 HOH A 72 872 122 HOH HOH . D 4 HOH A 73 873 5 HOH HOH . D 4 HOH A 74 874 59 HOH HOH . D 4 HOH A 75 875 35 HOH HOH . D 4 HOH A 76 876 119 HOH HOH . D 4 HOH A 77 877 187 HOH HOH . D 4 HOH A 78 878 45 HOH HOH . D 4 HOH A 79 879 173 HOH HOH . D 4 HOH A 80 880 24 HOH HOH . D 4 HOH A 81 881 136 HOH HOH . D 4 HOH A 82 882 16 HOH HOH . D 4 HOH A 83 883 91 HOH HOH . D 4 HOH A 84 884 38 HOH HOH . D 4 HOH A 85 885 2 HOH HOH . D 4 HOH A 86 886 78 HOH HOH . D 4 HOH A 87 887 36 HOH HOH . D 4 HOH A 88 888 28 HOH HOH . D 4 HOH A 89 889 148 HOH HOH . D 4 HOH A 90 890 126 HOH HOH . D 4 HOH A 91 891 64 HOH HOH . D 4 HOH A 92 892 144 HOH HOH . D 4 HOH A 93 893 92 HOH HOH . D 4 HOH A 94 894 140 HOH HOH . D 4 HOH A 95 895 47 HOH HOH . D 4 HOH A 96 896 97 HOH HOH . D 4 HOH A 97 897 15 HOH HOH . D 4 HOH A 98 898 147 HOH HOH . D 4 HOH A 99 899 22 HOH HOH . D 4 HOH A 100 900 67 HOH HOH . D 4 HOH A 101 901 121 HOH HOH . D 4 HOH A 102 902 18 HOH HOH . D 4 HOH A 103 903 12 HOH HOH . D 4 HOH A 104 904 117 HOH HOH . D 4 HOH A 105 905 52 HOH HOH . D 4 HOH A 106 906 191 HOH HOH . D 4 HOH A 107 907 94 HOH HOH . D 4 HOH A 108 908 160 HOH HOH . D 4 HOH A 109 909 128 HOH HOH . D 4 HOH A 110 910 32 HOH HOH . D 4 HOH A 111 911 141 HOH HOH . D 4 HOH A 112 912 158 HOH HOH . D 4 HOH A 113 913 120 HOH HOH . D 4 HOH A 114 914 8 HOH HOH . D 4 HOH A 115 915 96 HOH HOH . D 4 HOH A 116 916 116 HOH HOH . D 4 HOH A 117 917 43 HOH HOH . D 4 HOH A 118 918 146 HOH HOH . D 4 HOH A 119 919 109 HOH HOH . D 4 HOH A 120 920 89 HOH HOH . D 4 HOH A 121 921 51 HOH HOH . D 4 HOH A 122 922 65 HOH HOH . D 4 HOH A 123 923 30 HOH HOH . D 4 HOH A 124 924 163 HOH HOH . D 4 HOH A 125 925 176 HOH HOH . D 4 HOH A 126 926 14 HOH HOH . D 4 HOH A 127 927 66 HOH HOH . D 4 HOH A 128 928 54 HOH HOH . D 4 HOH A 129 929 37 HOH HOH . D 4 HOH A 130 930 62 HOH HOH . D 4 HOH A 131 931 84 HOH HOH . D 4 HOH A 132 932 21 HOH HOH . D 4 HOH A 133 933 188 HOH HOH . D 4 HOH A 134 934 76 HOH HOH . D 4 HOH A 135 935 50 HOH HOH . D 4 HOH A 136 936 108 HOH HOH . D 4 HOH A 137 937 73 HOH HOH . D 4 HOH A 138 938 25 HOH HOH . D 4 HOH A 139 939 145 HOH HOH . D 4 HOH A 140 940 192 HOH HOH . D 4 HOH A 141 941 71 HOH HOH . D 4 HOH A 142 942 130 HOH HOH . D 4 HOH A 143 943 115 HOH HOH . D 4 HOH A 144 944 112 HOH HOH . D 4 HOH A 145 945 138 HOH HOH . D 4 HOH A 146 946 177 HOH HOH . D 4 HOH A 147 947 53 HOH HOH . D 4 HOH A 148 948 83 HOH HOH . D 4 HOH A 149 949 113 HOH HOH . D 4 HOH A 150 950 31 HOH HOH . D 4 HOH A 151 951 114 HOH HOH . D 4 HOH A 152 952 75 HOH HOH . D 4 HOH A 153 953 132 HOH HOH . D 4 HOH A 154 954 156 HOH HOH . D 4 HOH A 155 955 165 HOH HOH . D 4 HOH A 156 956 46 HOH HOH . D 4 HOH A 157 957 178 HOH HOH . D 4 HOH A 158 958 34 HOH HOH . D 4 HOH A 159 959 171 HOH HOH . D 4 HOH A 160 960 151 HOH HOH . D 4 HOH A 161 961 189 HOH HOH . D 4 HOH A 162 962 99 HOH HOH . D 4 HOH A 163 963 42 HOH HOH . D 4 HOH A 164 964 152 HOH HOH . D 4 HOH A 165 965 182 HOH HOH . D 4 HOH A 166 966 194 HOH HOH . D 4 HOH A 167 967 157 HOH HOH . D 4 HOH A 168 968 111 HOH HOH . D 4 HOH A 169 969 142 HOH HOH . D 4 HOH A 170 970 150 HOH HOH . D 4 HOH A 171 971 153 HOH HOH . D 4 HOH A 172 972 58 HOH HOH . D 4 HOH A 173 973 181 HOH HOH . D 4 HOH A 174 974 118 HOH HOH . D 4 HOH A 175 975 161 HOH HOH . D 4 HOH A 176 976 133 HOH HOH . D 4 HOH A 177 977 103 HOH HOH . D 4 HOH A 178 978 175 HOH HOH . D 4 HOH A 179 979 164 HOH HOH . D 4 HOH A 180 980 170 HOH HOH . D 4 HOH A 181 981 169 HOH HOH . D 4 HOH A 182 982 95 HOH HOH . D 4 HOH A 183 983 185 HOH HOH . D 4 HOH A 184 984 184 HOH HOH . D 4 HOH A 185 985 124 HOH HOH . D 4 HOH A 186 986 193 HOH HOH . D 4 HOH A 187 987 74 HOH HOH . D 4 HOH A 188 988 110 HOH HOH . D 4 HOH A 189 989 196 HOH HOH . D 4 HOH A 190 990 179 HOH HOH . D 4 HOH A 191 991 166 HOH HOH . D 4 HOH A 192 992 186 HOH HOH . D 4 HOH A 193 993 195 HOH HOH . D 4 HOH A 194 994 143 HOH HOH . D 4 HOH A 195 995 134 HOH HOH . D 4 HOH A 196 996 149 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 PA UTP . . . C 3 3.052 -72.156 11.168 1 14.8 ? PA UTP 702 A 1 HETATM 2 O O1A UTP . . . C 3 3.903 -72.558 9.951 1 14.98 -1 O1A UTP 702 A 1 HETATM 3 O O2A UTP . . . C 3 1.84 -71.328 10.856 1 10.85 ? O2A UTP 702 A 1 HETATM 4 O O3A UTP . . . C 3 3.913 -71.401 12.326 1 14.18 ? O3A UTP 702 A 1 HETATM 5 O O5' UTP . . . C 3 2.557 -73.581 11.934 1 16.92 ? O5' UTP 702 A 1 HETATM 6 P PB UTP . . . C 3 4.874 -70.073 12.132 1 12.22 ? PB UTP 702 A 1 HETATM 7 O O1B UTP . . . C 3 4.34 -69.069 13.172 1 12.73 ? O1B UTP 702 A 1 HETATM 8 O O2B UTP . . . C 3 4.858 -69.568 10.674 1 12.9 -1 O2B UTP 702 A 1 HETATM 9 O O3B UTP . . . C 3 6.284 -70.68 12.566 1 15.91 ? O3B UTP 702 A 1 HETATM 10 P PG UTP . . . C 3 7.74 -70.214 12.012 1 14.08 ? PG UTP 702 A 1 HETATM 11 O O1G UTP . . . C 3 8.17 -68.902 12.7 1 14.99 ? O1G UTP 702 A 1 HETATM 12 O O2G UTP . . . C 3 7.691 -70.049 10.503 1 16.31 -1 O2G UTP 702 A 1 HETATM 13 O O3G UTP . . . C 3 8.688 -71.325 12.472 1 15.13 -1 O3G UTP 702 A 1 HETATM 14 C C5' UTP . . . C 3 1.708 -73.433 13.053 1 17.9 ? C5' UTP 702 A 1 HETATM 15 C C4' UTP . . . C 3 1.228 -74.879 13.35 1 20.9 ? C4' UTP 702 A 1 HETATM 16 O O4' UTP . . . C 3 0.421 -75.326 12.104 1 25.54 ? O4' UTP 702 A 1 HETATM 17 C C1' UTP . . . C 3 0.951 -76.706 11.779 1 29.4 ? C1' UTP 702 A 1 HETATM 18 C C2' UTP . . . C 3 2.212 -76.691 12.193 1 29.19 ? C2' UTP 702 A 1 HETATM 19 O O2' UTP . . . C 3 2.575 -77.996 12.675 1 37.55 ? O2' UTP 702 A 1 HETATM 20 C C3' UTP . . . C 3 2.255 -75.679 13.437 1 26.19 ? C3' UTP 702 A 1 HETATM 21 O O3' UTP . . . C 3 2.165 -76.452 14.7 1 33.84 ? O3' UTP 702 A 1 HETATM 22 N N1 UTP . . . C 3 0.812 -76.834 10.327 1 28.79 ? N1 UTP 702 A 1 HETATM 23 C C6 UTP . . . C 3 1.252 -75.851 9.547 1 30.14 ? C6 UTP 702 A 1 HETATM 24 C C2 UTP . . . C 3 0.202 -77.93 9.787 1 30.73 ? C2 UTP 702 A 1 HETATM 25 O O2 UTP . . . C 3 -0.2 -78.789 10.473 1 37.51 ? O2 UTP 702 A 1 HETATM 26 N N3 UTP . . . C 3 0.06 -78.027 8.435 1 25.96 ? N3 UTP 702 A 1 HETATM 27 C C4 UTP . . . C 3 0.509 -77.052 7.652 1 25.28 ? C4 UTP 702 A 1 HETATM 28 O O4 UTP . . . C 3 0.379 -77.142 6.437 1 39.23 ? O4 UTP 702 A 1 HETATM 29 C C5 UTP . . . C 3 1.108 -75.952 8.186 1 28.4 ? C5 UTP 702 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #