data_7F3Z # _model_server_result.job_id iNq8Ag4NCp_ZpTDHGjJRYA _model_server_result.datetime_utc '2024-11-23 05:23:18' _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 7f3z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 7F3Z # _exptl.entry_id 7F3Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 7F3Z _cell.length_a 56.332 _cell.length_b 153.739 _cell.length_c 164.119 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7F3Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H N 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 493 n n N1 C6 UMP sing 494 n n N1 C1' UMP sing 495 n n C2 N3 UMP sing 496 n n C2 O2 UMP doub 497 n n N3 C4 UMP sing 498 n n N3 HN3 UMP sing 499 n n C4 C5 UMP sing 500 n n C4 O4 UMP doub 501 n n C5 C6 UMP doub 502 n n C5 H5 UMP sing 503 n n C6 H6 UMP sing 504 n n C1' C2' UMP sing 505 n n C1' O4' UMP sing 506 n n C1' H1' UMP sing 507 n n C2' C3' UMP sing 508 n n C2' H2' UMP sing 509 n n C2' "H2''" UMP sing 510 n n C3' C4' UMP sing 511 n n C3' O3' UMP sing 512 n n C3' H3' UMP sing 513 n n C4' O4' UMP sing 514 n n C4' C5' UMP sing 515 n n C4' H4' UMP sing 516 n n O3' HO3' UMP sing 517 n n C5' O5' UMP sing 518 n n C5' H5' UMP sing 519 n n C5' "H5''" UMP sing 520 n n O5' P UMP sing 521 n n P OP1 UMP doub 522 n n P OP2 UMP sing 523 n n P OP3 UMP sing 524 n n OP2 HOP2 UMP sing 525 n n OP3 HOP3 UMP sing 526 n n # _atom_sites.entry_id 7F3Z _atom_sites.fract_transf_matrix[1][1] 0.017752 _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] 0.006505 _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] 0.006093 _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 2 NDP A 1 701 701 NDP NDP . D 3 UMP A 1 702 702 UMP UMP . E 4 TOP A 1 703 703 TOP TOP . F 5 GOL A 1 704 704 GOL GOL . G 2 NDP B 1 701 701 NDP NDP . H 3 UMP B 1 702 702 UMP UMP . I 4 TOP B 1 703 703 TOP TOP . J 5 GOL B 1 704 704 GOL GOL . K 6 HOH A 1 801 185 HOH HOH . K 6 HOH A 2 802 157 HOH HOH . K 6 HOH A 3 803 89 HOH HOH . K 6 HOH A 4 804 63 HOH HOH . K 6 HOH A 5 805 41 HOH HOH . K 6 HOH A 6 806 95 HOH HOH . K 6 HOH A 7 807 144 HOH HOH . K 6 HOH A 8 808 5 HOH HOH . K 6 HOH A 9 809 60 HOH HOH . K 6 HOH A 10 810 168 HOH HOH . K 6 HOH A 11 811 149 HOH HOH . K 6 HOH A 12 812 49 HOH HOH . K 6 HOH A 13 813 53 HOH HOH . K 6 HOH A 14 814 70 HOH HOH . K 6 HOH A 15 815 176 HOH HOH . K 6 HOH A 16 816 73 HOH HOH . K 6 HOH A 17 817 90 HOH HOH . K 6 HOH A 18 818 24 HOH HOH . K 6 HOH A 19 819 43 HOH HOH . K 6 HOH A 20 820 74 HOH HOH . K 6 HOH A 21 821 135 HOH HOH . K 6 HOH A 22 822 195 HOH HOH . K 6 HOH A 23 823 33 HOH HOH . K 6 HOH A 24 824 153 HOH HOH . K 6 HOH A 25 825 94 HOH HOH . K 6 HOH A 26 826 40 HOH HOH . K 6 HOH A 27 827 190 HOH HOH . K 6 HOH A 28 828 148 HOH HOH . K 6 HOH A 29 829 162 HOH HOH . K 6 HOH A 30 830 15 HOH HOH . K 6 HOH A 31 831 4 HOH HOH . K 6 HOH A 32 832 170 HOH HOH . K 6 HOH A 33 833 127 HOH HOH . K 6 HOH A 34 834 75 HOH HOH . K 6 HOH A 35 835 126 HOH HOH . K 6 HOH A 36 836 151 HOH HOH . K 6 HOH A 37 837 50 HOH HOH . K 6 HOH A 38 838 36 HOH HOH . K 6 HOH A 39 839 180 HOH HOH . K 6 HOH A 40 840 160 HOH HOH . K 6 HOH A 41 841 174 HOH HOH . K 6 HOH A 42 842 188 HOH HOH . K 6 HOH A 43 843 12 HOH HOH . K 6 HOH A 44 844 137 HOH HOH . K 6 HOH A 45 845 57 HOH HOH . K 6 HOH A 46 846 19 HOH HOH . K 6 HOH A 47 847 122 HOH HOH . K 6 HOH A 48 848 178 HOH HOH . K 6 HOH A 49 849 146 HOH HOH . K 6 HOH A 50 850 173 HOH HOH . K 6 HOH A 51 851 45 HOH HOH . K 6 HOH A 52 852 3 HOH HOH . K 6 HOH A 53 853 171 HOH HOH . K 6 HOH A 54 854 29 HOH HOH . K 6 HOH A 55 855 102 HOH HOH . K 6 HOH A 56 856 98 HOH HOH . K 6 HOH A 57 857 101 HOH HOH . K 6 HOH A 58 858 21 HOH HOH . K 6 HOH A 59 859 115 HOH HOH . K 6 HOH A 60 860 136 HOH HOH . K 6 HOH A 61 861 169 HOH HOH . K 6 HOH A 62 862 199 HOH HOH . K 6 HOH A 63 863 38 HOH HOH . K 6 HOH A 64 864 147 HOH HOH . K 6 HOH A 65 865 2 HOH HOH . K 6 HOH A 66 866 104 HOH HOH . K 6 HOH A 67 867 161 HOH HOH . K 6 HOH A 68 868 196 HOH HOH . K 6 HOH A 69 869 26 HOH HOH . K 6 HOH A 70 870 100 HOH HOH . K 6 HOH A 71 871 87 HOH HOH . K 6 HOH A 72 872 83 HOH HOH . K 6 HOH A 73 873 107 HOH HOH . K 6 HOH A 74 874 156 HOH HOH . K 6 HOH A 75 875 132 HOH HOH . K 6 HOH A 76 876 175 HOH HOH . K 6 HOH A 77 877 181 HOH HOH . K 6 HOH A 78 878 145 HOH HOH . K 6 HOH A 79 879 72 HOH HOH . K 6 HOH A 80 880 125 HOH HOH . K 6 HOH A 81 881 193 HOH HOH . K 6 HOH A 82 882 48 HOH HOH . K 6 HOH A 83 883 79 HOH HOH . K 6 HOH A 84 884 47 HOH HOH . K 6 HOH A 85 885 109 HOH HOH . K 6 HOH A 86 886 68 HOH HOH . K 6 HOH A 87 887 141 HOH HOH . K 6 HOH A 88 888 117 HOH HOH . K 6 HOH A 89 889 97 HOH HOH . K 6 HOH A 90 890 120 HOH HOH . K 6 HOH A 91 891 99 HOH HOH . K 6 HOH A 92 892 179 HOH HOH . K 6 HOH A 93 893 54 HOH HOH . K 6 HOH A 94 894 124 HOH HOH . K 6 HOH A 95 895 155 HOH HOH . K 6 HOH A 96 896 78 HOH HOH . K 6 HOH A 97 897 177 HOH HOH . K 6 HOH A 98 898 202 HOH HOH . K 6 HOH A 99 899 205 HOH HOH . K 6 HOH A 100 900 167 HOH HOH . K 6 HOH A 101 901 92 HOH HOH . K 6 HOH A 102 902 142 HOH HOH . K 6 HOH A 103 903 140 HOH HOH . K 6 HOH A 104 904 172 HOH HOH . K 6 HOH A 105 905 61 HOH HOH . K 6 HOH A 106 906 197 HOH HOH . L 6 HOH B 1 801 27 HOH HOH . L 6 HOH B 2 802 187 HOH HOH . L 6 HOH B 3 803 128 HOH HOH . L 6 HOH B 4 804 66 HOH HOH . L 6 HOH B 5 805 30 HOH HOH . L 6 HOH B 6 806 59 HOH HOH . L 6 HOH B 7 807 150 HOH HOH . L 6 HOH B 8 808 44 HOH HOH . L 6 HOH B 9 809 131 HOH HOH . L 6 HOH B 10 810 86 HOH HOH . L 6 HOH B 11 811 186 HOH HOH . L 6 HOH B 12 812 32 HOH HOH . L 6 HOH B 13 813 184 HOH HOH . L 6 HOH B 14 814 34 HOH HOH . L 6 HOH B 15 815 96 HOH HOH . L 6 HOH B 16 816 203 HOH HOH . L 6 HOH B 17 817 25 HOH HOH . L 6 HOH B 18 818 14 HOH HOH . L 6 HOH B 19 819 206 HOH HOH . L 6 HOH B 20 820 51 HOH HOH . L 6 HOH B 21 821 39 HOH HOH . L 6 HOH B 22 822 93 HOH HOH . L 6 HOH B 23 823 159 HOH HOH . L 6 HOH B 24 824 76 HOH HOH . L 6 HOH B 25 825 42 HOH HOH . L 6 HOH B 26 826 130 HOH HOH . L 6 HOH B 27 827 52 HOH HOH . L 6 HOH B 28 828 119 HOH HOH . L 6 HOH B 29 829 133 HOH HOH . L 6 HOH B 30 830 192 HOH HOH . L 6 HOH B 31 831 10 HOH HOH . L 6 HOH B 32 832 164 HOH HOH . L 6 HOH B 33 833 1 HOH HOH . L 6 HOH B 34 834 110 HOH HOH . L 6 HOH B 35 835 183 HOH HOH . L 6 HOH B 36 836 121 HOH HOH . L 6 HOH B 37 837 208 HOH HOH . L 6 HOH B 38 838 8 HOH HOH . L 6 HOH B 39 839 165 HOH HOH . L 6 HOH B 40 840 189 HOH HOH . L 6 HOH B 41 841 105 HOH HOH . L 6 HOH B 42 842 55 HOH HOH . L 6 HOH B 43 843 143 HOH HOH . L 6 HOH B 44 844 207 HOH HOH . L 6 HOH B 45 845 7 HOH HOH . L 6 HOH B 46 846 18 HOH HOH . L 6 HOH B 47 847 198 HOH HOH . L 6 HOH B 48 848 82 HOH HOH . L 6 HOH B 49 849 9 HOH HOH . L 6 HOH B 50 850 13 HOH HOH . L 6 HOH B 51 851 111 HOH HOH . L 6 HOH B 52 852 118 HOH HOH . L 6 HOH B 53 853 17 HOH HOH . L 6 HOH B 54 854 16 HOH HOH . L 6 HOH B 55 855 113 HOH HOH . L 6 HOH B 56 856 123 HOH HOH . L 6 HOH B 57 857 103 HOH HOH . L 6 HOH B 58 858 64 HOH HOH . L 6 HOH B 59 859 91 HOH HOH . L 6 HOH B 60 860 163 HOH HOH . L 6 HOH B 61 861 204 HOH HOH . L 6 HOH B 62 862 129 HOH HOH . L 6 HOH B 63 863 77 HOH HOH . L 6 HOH B 64 864 154 HOH HOH . L 6 HOH B 65 865 191 HOH HOH . L 6 HOH B 66 866 6 HOH HOH . L 6 HOH B 67 867 200 HOH HOH . L 6 HOH B 68 868 20 HOH HOH . L 6 HOH B 69 869 71 HOH HOH . L 6 HOH B 70 870 108 HOH HOH . L 6 HOH B 71 871 69 HOH HOH . L 6 HOH B 72 872 80 HOH HOH . L 6 HOH B 73 873 138 HOH HOH . L 6 HOH B 74 874 201 HOH HOH . L 6 HOH B 75 875 35 HOH HOH . L 6 HOH B 76 876 65 HOH HOH . L 6 HOH B 77 877 11 HOH HOH . L 6 HOH B 78 878 62 HOH HOH . L 6 HOH B 79 879 58 HOH HOH . L 6 HOH B 80 880 182 HOH HOH . L 6 HOH B 81 881 67 HOH HOH . L 6 HOH B 82 882 114 HOH HOH . L 6 HOH B 83 883 116 HOH HOH . L 6 HOH B 84 884 139 HOH HOH . L 6 HOH B 85 885 37 HOH HOH . L 6 HOH B 86 886 112 HOH HOH . L 6 HOH B 87 887 194 HOH HOH . L 6 HOH B 88 888 56 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 . . . D 3 -16.509 20.177 -19.501 1 85.57 0 N1 UMP 702 A 1 HETATM 2 C C2 UMP . . . D 3 -15.725 19.611 -20.496 1 83.77 0 C2 UMP 702 A 1 HETATM 3 N N3 UMP . . . D 3 -14.951 20.513 -21.189 1 92.57 0 N3 UMP 702 A 1 HETATM 4 C C4 UMP . . . D 3 -14.888 21.884 -21.005 1 96.54 0 C4 UMP 702 A 1 HETATM 5 C C5 UMP . . . D 3 -15.748 22.391 -19.979 1 98.3 0 C5 UMP 702 A 1 HETATM 6 C C6 UMP . . . D 3 -16.515 21.538 -19.285 1 96.24 0 C6 UMP 702 A 1 HETATM 7 O O2 UMP . . . D 3 -15.688 18.408 -20.738 1 60.68 0 O2 UMP 702 A 1 HETATM 8 O O4 UMP . . . D 3 -14.129 22.559 -21.7 1 99 0 O4 UMP 702 A 1 HETATM 9 C C1' UMP . . . D 3 -17.428 19.307 -18.726 1 82.34 0 C1' UMP 702 A 1 HETATM 10 C C2' UMP . . . D 3 -16.809 18.12 -18.01 1 79.07 0 C2' UMP 702 A 1 HETATM 11 C C3' UMP . . . D 3 -17.884 17.825 -16.973 1 73.01 0 C3' UMP 702 A 1 HETATM 12 C C4' UMP . . . D 3 -18.347 19.23 -16.573 1 72.77 0 C4' UMP 702 A 1 HETATM 13 O O3' UMP . . . D 3 -18.934 17.075 -17.575 1 57.89 0 O3' UMP 702 A 1 HETATM 14 O O4' UMP . . . D 3 -18.008 20.088 -17.686 1 78.04 0 O4' UMP 702 A 1 HETATM 15 C C5' UMP . . . D 3 -17.714 19.804 -15.323 1 76.6 0 C5' UMP 702 A 1 HETATM 16 O O5' UMP . . . D 3 -18.259 19.168 -14.115 1 74.47 0 O5' UMP 702 A 1 HETATM 17 P P UMP . . . D 3 -17.415 19.253 -12.735 1 62.5 0 P UMP 702 A 1 HETATM 18 O OP1 UMP . . . D 3 -18.097 18.445 -11.657 1 71.4 0 OP1 UMP 702 A 1 HETATM 19 O OP2 UMP . . . D 3 -16.108 18.621 -13.121 1 78.81 0 OP2 UMP 702 A 1 HETATM 20 O OP3 UMP . . . D 3 -17.283 20.72 -12.383 1 61.01 0 OP3 UMP 702 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #