data_6A2P # _model_server_result.job_id V33fuxj3jTInjf4_sFz0PQ _model_server_result.datetime_utc '2024-11-13 03:50:07' _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 6a2p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":702}' # _entry.id 6A2P # _exptl.entry_id 6A2P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 4 _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 6A2P _cell.length_a 59.243 _cell.length_b 158.9 _cell.length_c 167.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A2P _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 _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 ? 4 E N N ? 4 G 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 510 n n N1 C6 UMP sing 511 n n N1 C1' UMP sing 512 n n C2 N3 UMP sing 513 n n C2 O2 UMP doub 514 n n N3 C4 UMP sing 515 n n N3 HN3 UMP sing 516 n n C4 C5 UMP sing 517 n n C4 O4 UMP doub 518 n n C5 C6 UMP doub 519 n n C5 H5 UMP sing 520 n n C6 H6 UMP sing 521 n n C1' C2' UMP sing 522 n n C1' O4' UMP sing 523 n n C1' H1' UMP sing 524 n n C2' C3' UMP sing 525 n n C2' H2' UMP sing 526 n n C2' "H2''" UMP sing 527 n n C3' C4' UMP sing 528 n n C3' O3' UMP sing 529 n n C3' H3' UMP sing 530 n n C4' O4' UMP sing 531 n n C4' C5' UMP sing 532 n n C4' H4' UMP sing 533 n n O3' HO3' UMP sing 534 n n C5' O5' UMP sing 535 n n C5' H5' UMP sing 536 n n C5' "H5''" UMP sing 537 n n O5' P UMP sing 538 n n P OP1 UMP doub 539 n n P OP2 UMP sing 540 n n P OP3 UMP sing 541 n n OP2 HOP2 UMP sing 542 n n OP3 HOP3 UMP sing 543 n n # _atom_sites.entry_id 6A2P _atom_sites.fract_transf_matrix[1][1] 0.01688 _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] 0.006293 _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] 0.005967 _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 9RR A 1 701 701 9RR bt3 . D 3 NAP A 1 702 702 NAP NAP . E 4 UMP A 1 703 703 UMP UMP . F 2 9RR B 1 701 701 9RR bt3 . G 4 UMP B 1 702 703 UMP UMP . H 5 HOH A 1 801 147 HOH HOH . H 5 HOH A 2 802 57 HOH HOH . H 5 HOH A 3 803 59 HOH HOH . H 5 HOH A 4 804 94 HOH HOH . H 5 HOH A 5 805 183 HOH HOH . H 5 HOH A 6 806 185 HOH HOH . H 5 HOH A 7 807 61 HOH HOH . H 5 HOH A 8 808 81 HOH HOH . H 5 HOH A 9 809 85 HOH HOH . H 5 HOH A 10 810 18 HOH HOH . H 5 HOH A 11 811 177 HOH HOH . H 5 HOH A 12 812 51 HOH HOH . H 5 HOH A 13 813 17 HOH HOH . H 5 HOH A 14 814 36 HOH HOH . H 5 HOH A 15 815 192 HOH HOH . H 5 HOH A 16 816 87 HOH HOH . H 5 HOH A 17 817 46 HOH HOH . H 5 HOH A 18 818 156 HOH HOH . H 5 HOH A 19 819 68 HOH HOH . H 5 HOH A 20 820 110 HOH HOH . H 5 HOH A 21 821 40 HOH HOH . H 5 HOH A 22 822 137 HOH HOH . H 5 HOH A 23 823 19 HOH HOH . H 5 HOH A 24 824 180 HOH HOH . H 5 HOH A 25 825 30 HOH HOH . H 5 HOH A 26 826 157 HOH HOH . H 5 HOH A 27 827 92 HOH HOH . H 5 HOH A 28 828 9 HOH HOH . H 5 HOH A 29 829 116 HOH HOH . H 5 HOH A 30 830 11 HOH HOH . H 5 HOH A 31 831 77 HOH HOH . H 5 HOH A 32 832 15 HOH HOH . H 5 HOH A 33 833 101 HOH HOH . H 5 HOH A 34 834 108 HOH HOH . H 5 HOH A 35 835 45 HOH HOH . H 5 HOH A 36 836 5 HOH HOH . H 5 HOH A 37 837 113 HOH HOH . H 5 HOH A 38 838 119 HOH HOH . H 5 HOH A 39 839 170 HOH HOH . H 5 HOH A 40 840 39 HOH HOH . H 5 HOH A 41 841 83 HOH HOH . H 5 HOH A 42 842 63 HOH HOH . H 5 HOH A 43 843 166 HOH HOH . H 5 HOH A 44 844 146 HOH HOH . H 5 HOH A 45 845 190 HOH HOH . H 5 HOH A 46 846 67 HOH HOH . H 5 HOH A 47 847 121 HOH HOH . H 5 HOH A 48 848 142 HOH HOH . H 5 HOH A 49 849 175 HOH HOH . H 5 HOH A 50 850 47 HOH HOH . H 5 HOH A 51 851 163 HOH HOH . H 5 HOH A 52 852 128 HOH HOH . H 5 HOH A 53 853 96 HOH HOH . H 5 HOH A 54 854 178 HOH HOH . H 5 HOH A 55 855 120 HOH HOH . H 5 HOH A 56 856 65 HOH HOH . H 5 HOH A 57 857 144 HOH HOH . H 5 HOH A 58 858 70 HOH HOH . H 5 HOH A 59 859 138 HOH HOH . H 5 HOH A 60 860 50 HOH HOH . H 5 HOH A 61 861 181 HOH HOH . H 5 HOH A 62 862 79 HOH HOH . H 5 HOH A 63 863 86 HOH HOH . H 5 HOH A 64 864 172 HOH HOH . H 5 HOH A 65 865 162 HOH HOH . H 5 HOH A 66 866 129 HOH HOH . H 5 HOH A 67 867 29 HOH HOH . H 5 HOH A 68 868 93 HOH HOH . H 5 HOH A 69 869 14 HOH HOH . H 5 HOH A 70 870 4 HOH HOH . H 5 HOH A 71 871 7 HOH HOH . H 5 HOH A 72 872 174 HOH HOH . H 5 HOH A 73 873 114 HOH HOH . H 5 HOH A 74 874 104 HOH HOH . H 5 HOH A 75 875 6 HOH HOH . H 5 HOH A 76 876 135 HOH HOH . H 5 HOH A 77 877 143 HOH HOH . H 5 HOH A 78 878 98 HOH HOH . H 5 HOH A 79 879 130 HOH HOH . H 5 HOH A 80 880 41 HOH HOH . H 5 HOH A 81 881 76 HOH HOH . H 5 HOH A 82 882 82 HOH HOH . H 5 HOH A 83 883 122 HOH HOH . H 5 HOH A 84 884 10 HOH HOH . H 5 HOH A 85 885 22 HOH HOH . H 5 HOH A 86 886 168 HOH HOH . H 5 HOH A 87 887 49 HOH HOH . H 5 HOH A 88 888 31 HOH HOH . H 5 HOH A 89 889 197 HOH HOH . H 5 HOH A 90 890 71 HOH HOH . H 5 HOH A 91 891 176 HOH HOH . H 5 HOH A 92 892 106 HOH HOH . H 5 HOH A 93 893 107 HOH HOH . H 5 HOH A 94 894 25 HOH HOH . H 5 HOH A 95 895 198 HOH HOH . H 5 HOH A 96 896 33 HOH HOH . H 5 HOH A 97 897 2 HOH HOH . H 5 HOH A 98 898 78 HOH HOH . H 5 HOH A 99 899 184 HOH HOH . H 5 HOH A 100 900 74 HOH HOH . I 5 HOH B 1 801 165 HOH HOH . I 5 HOH B 2 802 55 HOH HOH . I 5 HOH B 3 803 164 HOH HOH . I 5 HOH B 4 804 186 HOH HOH . I 5 HOH B 5 805 95 HOH HOH . I 5 HOH B 6 806 23 HOH HOH . I 5 HOH B 7 807 35 HOH HOH . I 5 HOH B 8 808 127 HOH HOH . I 5 HOH B 9 809 84 HOH HOH . I 5 HOH B 10 810 171 HOH HOH . I 5 HOH B 11 811 44 HOH HOH . I 5 HOH B 12 812 3 HOH HOH . I 5 HOH B 13 813 188 HOH HOH . I 5 HOH B 14 814 24 HOH HOH . I 5 HOH B 15 815 195 HOH HOH . I 5 HOH B 16 816 158 HOH HOH . I 5 HOH B 17 817 139 HOH HOH . I 5 HOH B 18 818 160 HOH HOH . I 5 HOH B 19 819 26 HOH HOH . I 5 HOH B 20 820 73 HOH HOH . I 5 HOH B 21 821 99 HOH HOH . I 5 HOH B 22 822 13 HOH HOH . I 5 HOH B 23 823 151 HOH HOH . I 5 HOH B 24 824 132 HOH HOH . I 5 HOH B 25 825 155 HOH HOH . I 5 HOH B 26 826 150 HOH HOH . I 5 HOH B 27 827 131 HOH HOH . I 5 HOH B 28 828 12 HOH HOH . I 5 HOH B 29 829 56 HOH HOH . I 5 HOH B 30 830 159 HOH HOH . I 5 HOH B 31 831 43 HOH HOH . I 5 HOH B 32 832 169 HOH HOH . I 5 HOH B 33 833 58 HOH HOH . I 5 HOH B 34 834 69 HOH HOH . I 5 HOH B 35 835 60 HOH HOH . I 5 HOH B 36 836 111 HOH HOH . I 5 HOH B 37 837 80 HOH HOH . I 5 HOH B 38 838 189 HOH HOH . I 5 HOH B 39 839 75 HOH HOH . I 5 HOH B 40 840 89 HOH HOH . I 5 HOH B 41 841 112 HOH HOH . I 5 HOH B 42 842 109 HOH HOH . I 5 HOH B 43 843 133 HOH HOH . I 5 HOH B 44 844 54 HOH HOH . I 5 HOH B 45 845 103 HOH HOH . I 5 HOH B 46 846 179 HOH HOH . I 5 HOH B 47 847 126 HOH HOH . I 5 HOH B 48 848 173 HOH HOH . I 5 HOH B 49 849 66 HOH HOH . I 5 HOH B 50 850 64 HOH HOH . I 5 HOH B 51 851 148 HOH HOH . I 5 HOH B 52 852 141 HOH HOH . I 5 HOH B 53 853 187 HOH HOH . I 5 HOH B 54 854 42 HOH HOH . I 5 HOH B 55 855 90 HOH HOH . I 5 HOH B 56 856 20 HOH HOH . I 5 HOH B 57 857 191 HOH HOH . I 5 HOH B 58 858 34 HOH HOH . I 5 HOH B 59 859 194 HOH HOH . I 5 HOH B 60 860 161 HOH HOH . I 5 HOH B 61 861 37 HOH HOH . I 5 HOH B 62 862 118 HOH HOH . I 5 HOH B 63 863 27 HOH HOH . I 5 HOH B 64 864 134 HOH HOH . I 5 HOH B 65 865 145 HOH HOH . I 5 HOH B 66 866 28 HOH HOH . I 5 HOH B 67 867 124 HOH HOH . I 5 HOH B 68 868 48 HOH HOH . I 5 HOH B 69 869 100 HOH HOH . I 5 HOH B 70 870 72 HOH HOH . I 5 HOH B 71 871 91 HOH HOH . I 5 HOH B 72 872 32 HOH HOH . I 5 HOH B 73 873 136 HOH HOH . I 5 HOH B 74 874 38 HOH HOH . I 5 HOH B 75 875 125 HOH HOH . I 5 HOH B 76 876 123 HOH HOH . I 5 HOH B 77 877 193 HOH HOH . I 5 HOH B 78 878 52 HOH HOH . I 5 HOH B 79 879 21 HOH HOH . I 5 HOH B 80 880 182 HOH HOH . I 5 HOH B 81 881 16 HOH HOH . I 5 HOH B 82 882 97 HOH HOH . I 5 HOH B 83 883 115 HOH HOH . I 5 HOH B 84 884 117 HOH HOH . I 5 HOH B 85 885 154 HOH HOH . I 5 HOH B 86 886 8 HOH HOH . I 5 HOH B 87 887 105 HOH HOH . I 5 HOH B 88 888 88 HOH HOH . I 5 HOH B 89 889 62 HOH HOH . I 5 HOH B 90 890 167 HOH HOH . I 5 HOH B 91 891 140 HOH HOH . I 5 HOH B 92 892 1 HOH HOH . I 5 HOH B 93 893 53 HOH HOH . I 5 HOH B 94 894 102 HOH HOH . I 5 HOH B 95 895 149 HOH HOH . I 5 HOH B 96 896 196 HOH HOH . I 5 HOH B 97 897 152 HOH HOH . I 5 HOH B 98 898 153 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 . . . G 4 14.351 15.002 9.778 1 57.63 ? N1 UMP 702 B 1 HETATM 2 C C2 UMP . . . G 4 15.11 13.807 9.818 1 53.7 ? C2 UMP 702 B 1 HETATM 3 N N3 UMP . . . G 4 15.866 13.486 8.78 1 55.71 ? N3 UMP 702 B 1 HETATM 4 C C4 UMP . . . G 4 15.93 14.257 7.699 1 65.76 ? C4 UMP 702 B 1 HETATM 5 C C5 UMP . . . G 4 15.197 15.422 7.594 1 69.89 ? C5 UMP 702 B 1 HETATM 6 C C6 UMP . . . G 4 14.39 15.775 8.658 1 68.04 ? C6 UMP 702 B 1 HETATM 7 O O2 UMP . . . G 4 15.147 13.063 10.802 1 46.91 ? O2 UMP 702 B 1 HETATM 8 O O4 UMP . . . G 4 16.626 13.922 6.74 1 78.39 ? O4 UMP 702 B 1 HETATM 9 C C1' UMP . . . G 4 13.432 15.431 10.823 1 53.46 ? C1' UMP 702 B 1 HETATM 10 C C2' UMP . . . G 4 13.942 15.846 12.186 1 59.23 ? C2' UMP 702 B 1 HETATM 11 C C3' UMP . . . G 4 12.716 16.67 12.651 1 60.44 ? C3' UMP 702 B 1 HETATM 12 C C4' UMP . . . G 4 12.308 17.484 11.412 1 45.36 ? C4' UMP 702 B 1 HETATM 13 O O3' UMP . . . G 4 11.645 15.805 13.131 1 54.95 ? O3' UMP 702 B 1 HETATM 14 O O4' UMP . . . G 4 12.708 16.618 10.376 1 55 ? O4' UMP 702 B 1 HETATM 15 C C5' UMP . . . G 4 13.048 18.834 11.218 1 43.81 ? C5' UMP 702 B 1 HETATM 16 O O5' UMP . . . G 4 12.645 19.66 12.282 1 42.15 ? O5' UMP 702 B 1 HETATM 17 P P UMP . . . G 4 13.46 20.766 12.948 1 47.05 ? P UMP 702 B 1 HETATM 18 O OP1 UMP . . . G 4 12.42 21.501 13.739 1 50.53 ? OP1 UMP 702 B 1 HETATM 19 O OP2 UMP . . . G 4 14.38 19.961 13.818 1 43.69 ? OP2 UMP 702 B 1 HETATM 20 O OP3 UMP . . . G 4 14.061 21.563 11.779 1 45.84 ? OP3 UMP 702 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #