data_5IDO # _model_server_result.job_id flfYOvOL63YljKDse_RsGg _model_server_result.datetime_utc '2025-06-19 18:20:35' _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 5ido # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5IDO # _exptl.entry_id 5IDO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 2 _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 5IDO _cell.length_a 59.35 _cell.length_b 66.34 _cell.length_c 128.91 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IDO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 # _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 2 _struct_asym.id B _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 SG CYS 8 A CYS 195 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc2 A SG CYS 11 A CYS 198 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc3 A NE2 HIS 25 A HIS 212 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc4 A NE2 HIS 30 A HIS 217 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc5 B O2A UTP . A UTP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 B O1B UTP . A UTP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc7 B O1G UTP . A UTP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc8 D MG MG . A MG 703 1_555 E O HOH . A HOH 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc9 D MG MG . A MG 703 1_555 E O HOH . A HOH 949 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc10 D MG MG . A MG 703 1_555 E O HOH . A HOH 952 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _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 5IDO _atom_sites.fract_transf_matrix[1][1] 0.016849 _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] 0.015074 _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] 0.007757 _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 UTP A 1 701 401 UTP UTP . C 3 ZN A 1 702 1 ZN Zn . D 4 MG A 1 703 1 MG MG . E 5 HOH A 1 801 73 HOH HOH . E 5 HOH A 2 802 86 HOH HOH . E 5 HOH A 3 803 104 HOH HOH . E 5 HOH A 4 804 30 HOH HOH . E 5 HOH A 5 805 101 HOH HOH . E 5 HOH A 6 806 76 HOH HOH . E 5 HOH A 7 807 143 HOH HOH . E 5 HOH A 8 808 150 HOH HOH . E 5 HOH A 9 809 44 HOH HOH . E 5 HOH A 10 810 153 HOH HOH . E 5 HOH A 11 811 97 HOH HOH . E 5 HOH A 12 812 100 HOH HOH . E 5 HOH A 13 813 166 HOH HOH . E 5 HOH A 14 814 18 HOH HOH . E 5 HOH A 15 815 72 HOH HOH . E 5 HOH A 16 816 50 HOH HOH . E 5 HOH A 17 817 3 HOH HOH . E 5 HOH A 18 818 94 HOH HOH . E 5 HOH A 19 819 5 HOH HOH . E 5 HOH A 20 820 77 HOH HOH . E 5 HOH A 21 821 38 HOH HOH . E 5 HOH A 22 822 39 HOH HOH . E 5 HOH A 23 823 82 HOH HOH . E 5 HOH A 24 824 8 HOH HOH . E 5 HOH A 25 825 65 HOH HOH . E 5 HOH A 26 826 67 HOH HOH . E 5 HOH A 27 827 53 HOH HOH . E 5 HOH A 28 828 130 HOH HOH . E 5 HOH A 29 829 136 HOH HOH . E 5 HOH A 30 830 47 HOH HOH . E 5 HOH A 31 831 23 HOH HOH . E 5 HOH A 32 832 56 HOH HOH . E 5 HOH A 33 833 7 HOH HOH . E 5 HOH A 34 834 11 HOH HOH . E 5 HOH A 35 835 98 HOH HOH . E 5 HOH A 36 836 9 HOH HOH . E 5 HOH A 37 837 51 HOH HOH . E 5 HOH A 38 838 28 HOH HOH . E 5 HOH A 39 839 64 HOH HOH . E 5 HOH A 40 840 1 HOH HOH . E 5 HOH A 41 841 43 HOH HOH . E 5 HOH A 42 842 55 HOH HOH . E 5 HOH A 43 843 126 HOH HOH . E 5 HOH A 44 844 17 HOH HOH . E 5 HOH A 45 845 93 HOH HOH . E 5 HOH A 46 846 14 HOH HOH . E 5 HOH A 47 847 34 HOH HOH . E 5 HOH A 48 848 19 HOH HOH . E 5 HOH A 49 849 66 HOH HOH . E 5 HOH A 50 850 91 HOH HOH . E 5 HOH A 51 851 89 HOH HOH . E 5 HOH A 52 852 20 HOH HOH . E 5 HOH A 53 853 61 HOH HOH . E 5 HOH A 54 854 21 HOH HOH . E 5 HOH A 55 855 16 HOH HOH . E 5 HOH A 56 856 32 HOH HOH . E 5 HOH A 57 857 119 HOH HOH . E 5 HOH A 58 858 79 HOH HOH . E 5 HOH A 59 859 114 HOH HOH . E 5 HOH A 60 860 54 HOH HOH . E 5 HOH A 61 861 147 HOH HOH . E 5 HOH A 62 862 145 HOH HOH . E 5 HOH A 63 863 141 HOH HOH . E 5 HOH A 64 864 22 HOH HOH . E 5 HOH A 65 865 35 HOH HOH . E 5 HOH A 66 866 167 HOH HOH . E 5 HOH A 67 867 57 HOH HOH . E 5 HOH A 68 868 74 HOH HOH . E 5 HOH A 69 869 106 HOH HOH . E 5 HOH A 70 870 59 HOH HOH . E 5 HOH A 71 871 58 HOH HOH . E 5 HOH A 72 872 154 HOH HOH . E 5 HOH A 73 873 75 HOH HOH . E 5 HOH A 74 874 132 HOH HOH . E 5 HOH A 75 875 2 HOH HOH . E 5 HOH A 76 876 62 HOH HOH . E 5 HOH A 77 877 148 HOH HOH . E 5 HOH A 78 878 52 HOH HOH . E 5 HOH A 79 879 113 HOH HOH . E 5 HOH A 80 880 111 HOH HOH . E 5 HOH A 81 881 42 HOH HOH . E 5 HOH A 82 882 142 HOH HOH . E 5 HOH A 83 883 146 HOH HOH . E 5 HOH A 84 884 33 HOH HOH . E 5 HOH A 85 885 49 HOH HOH . E 5 HOH A 86 886 123 HOH HOH . E 5 HOH A 87 887 80 HOH HOH . E 5 HOH A 88 888 107 HOH HOH . E 5 HOH A 89 889 68 HOH HOH . E 5 HOH A 90 890 37 HOH HOH . E 5 HOH A 91 891 6 HOH HOH . E 5 HOH A 92 892 137 HOH HOH . E 5 HOH A 93 893 159 HOH HOH . E 5 HOH A 94 894 163 HOH HOH . E 5 HOH A 95 895 10 HOH HOH . E 5 HOH A 96 896 63 HOH HOH . E 5 HOH A 97 897 115 HOH HOH . E 5 HOH A 98 898 29 HOH HOH . E 5 HOH A 99 899 99 HOH HOH . E 5 HOH A 100 900 90 HOH HOH . E 5 HOH A 101 901 36 HOH HOH . E 5 HOH A 102 902 27 HOH HOH . E 5 HOH A 103 903 81 HOH HOH . E 5 HOH A 104 904 31 HOH HOH . E 5 HOH A 105 905 157 HOH HOH . E 5 HOH A 106 906 24 HOH HOH . E 5 HOH A 107 907 102 HOH HOH . E 5 HOH A 108 908 87 HOH HOH . E 5 HOH A 109 909 78 HOH HOH . E 5 HOH A 110 910 26 HOH HOH . E 5 HOH A 111 911 85 HOH HOH . E 5 HOH A 112 912 84 HOH HOH . E 5 HOH A 113 913 46 HOH HOH . E 5 HOH A 114 914 161 HOH HOH . E 5 HOH A 115 915 4 HOH HOH . E 5 HOH A 116 916 69 HOH HOH . E 5 HOH A 117 917 118 HOH HOH . E 5 HOH A 118 918 15 HOH HOH . E 5 HOH A 119 919 45 HOH HOH . E 5 HOH A 120 920 120 HOH HOH . E 5 HOH A 121 921 71 HOH HOH . E 5 HOH A 122 922 83 HOH HOH . E 5 HOH A 123 923 121 HOH HOH . E 5 HOH A 124 924 162 HOH HOH . E 5 HOH A 125 925 134 HOH HOH . E 5 HOH A 126 926 13 HOH HOH . E 5 HOH A 127 927 133 HOH HOH . E 5 HOH A 128 928 155 HOH HOH . E 5 HOH A 129 929 41 HOH HOH . E 5 HOH A 130 930 60 HOH HOH . E 5 HOH A 131 931 169 HOH HOH . E 5 HOH A 132 932 12 HOH HOH . E 5 HOH A 133 933 70 HOH HOH . E 5 HOH A 134 934 40 HOH HOH . E 5 HOH A 135 935 112 HOH HOH . E 5 HOH A 136 936 48 HOH HOH . E 5 HOH A 137 937 140 HOH HOH . E 5 HOH A 138 938 88 HOH HOH . E 5 HOH A 139 939 116 HOH HOH . E 5 HOH A 140 940 95 HOH HOH . E 5 HOH A 141 941 144 HOH HOH . E 5 HOH A 142 942 129 HOH HOH . E 5 HOH A 143 943 156 HOH HOH . E 5 HOH A 144 944 128 HOH HOH . E 5 HOH A 145 945 110 HOH HOH . E 5 HOH A 146 946 138 HOH HOH . E 5 HOH A 147 947 122 HOH HOH . E 5 HOH A 148 948 96 HOH HOH . E 5 HOH A 149 949 25 HOH HOH . E 5 HOH A 150 950 92 HOH HOH . E 5 HOH A 151 951 103 HOH HOH . E 5 HOH A 152 952 171 HOH HOH . E 5 HOH A 153 953 149 HOH HOH . E 5 HOH A 154 954 170 HOH HOH . E 5 HOH A 155 955 109 HOH HOH . E 5 HOH A 156 956 135 HOH HOH . E 5 HOH A 157 957 158 HOH HOH . E 5 HOH A 158 958 127 HOH HOH . E 5 HOH A 159 959 168 HOH HOH . E 5 HOH A 160 960 125 HOH HOH . E 5 HOH A 161 961 131 HOH HOH . E 5 HOH A 162 962 108 HOH HOH . E 5 HOH A 163 963 105 HOH HOH . E 5 HOH A 164 964 151 HOH HOH . E 5 HOH A 165 965 124 HOH HOH . E 5 HOH A 166 966 160 HOH HOH . E 5 HOH A 167 967 164 HOH HOH . E 5 HOH A 168 968 117 HOH HOH . E 5 HOH A 169 969 139 HOH HOH . E 5 HOH A 170 970 165 HOH HOH . E 5 HOH A 171 971 152 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 . . . B 2 138.255 86.446 26.946 1 44.81 ? PA UTP 701 A 1 HETATM 2 O O1A UTP . . . B 2 137.809 87.318 25.79 1 46.82 ? O1A UTP 701 A 1 HETATM 3 O O2A UTP . . . B 2 137.278 86.148 28.062 1 40.96 ? O2A UTP 701 A 1 HETATM 4 O O3A UTP . . . B 2 139.638 87.052 27.518 1 54.35 ? O3A UTP 701 A 1 HETATM 5 O O5' UTP . . . B 2 138.765 85.056 26.321 1 53.71 ? O5' UTP 701 A 1 HETATM 6 P PB UTP . . . B 2 140.136 86.921 29.049 1 40.2 ? PB UTP 701 A 1 HETATM 7 O O1B UTP . . . B 2 139.277 85.944 29.821 1 41.19 ? O1B UTP 701 A 1 HETATM 8 O O2B UTP . . . B 2 141.632 86.693 29.012 1 41.54 ? O2B UTP 701 A 1 HETATM 9 O O3B UTP . . . B 2 139.942 88.438 29.551 1 46.05 ? O3B UTP 701 A 1 HETATM 10 P PG UTP . . . B 2 138.617 89.02 30.256 1 46.59 ? PG UTP 701 A 1 HETATM 11 O O1G UTP . . . B 2 137.576 87.93 30.222 1 48.26 ? O1G UTP 701 A 1 HETATM 12 O O2G UTP . . . B 2 138.292 90.19 29.356 1 38.64 ? O2G UTP 701 A 1 HETATM 13 O O3G UTP . . . B 2 139.076 89.388 31.648 1 50.59 ? O3G UTP 701 A 1 HETATM 14 C C5' UTP . . . B 2 138.86 83.919 27.172 1 52.51 ? C5' UTP 701 A 1 HETATM 15 C C4' UTP . . . B 2 138.762 82.662 26.33 1 50.68 ? C4' UTP 701 A 1 HETATM 16 O O4' UTP . . . B 2 137.396 82.428 25.98 1 51.45 ? O4' UTP 701 A 1 HETATM 17 C C1' UTP . . . B 2 137.313 81.912 24.65 1 50.71 ? C1' UTP 701 A 1 HETATM 18 C C2' UTP . . . B 2 138.727 81.893 24.091 1 49.71 ? C2' UTP 701 A 1 HETATM 19 O O2' UTP . . . B 2 139.24 80.563 24.189 1 44.12 ? O2' UTP 701 A 1 HETATM 20 C C3' UTP . . . B 2 139.513 82.794 25.016 1 49.74 ? C3' UTP 701 A 1 HETATM 21 O O3' UTP . . . B 2 140.877 82.378 25.133 1 49.52 ? O3' UTP 701 A 1 HETATM 22 N N1 UTP . . . B 2 136.46 82.775 23.825 1 53.89 ? N1 UTP 701 A 1 HETATM 23 C C6 UTP . . . B 2 136.178 84.022 24.225 1 53.21 ? C6 UTP 701 A 1 HETATM 24 C C2 UTP . . . B 2 135.952 82.298 22.596 1 53.65 ? C2 UTP 701 A 1 HETATM 25 O O2 UTP . . . B 2 136.218 81.132 22.23 1 49.65 ? O2 UTP 701 A 1 HETATM 26 N N3 UTP . . . B 2 135.178 83.08 21.833 1 52.55 ? N3 UTP 701 A 1 HETATM 27 C C4 UTP . . . B 2 134.879 84.327 22.219 1 54.14 ? C4 UTP 701 A 1 HETATM 28 O O4 UTP . . . B 2 134.156 85.044 21.494 1 53.28 ? O4 UTP 701 A 1 HETATM 29 C C5 UTP . . . B 2 135.374 84.825 23.423 1 55.21 ? C5 UTP 701 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #