data_1TDU # _model_server_result.job_id sV6nq5vZOVryydB66DiWxg _model_server_result.datetime_utc '2024-10-19 05:27:14' _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 1tdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 1TDU # _exptl.entry_id 1TDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE" _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 120 _cell.entry_id 1TDU _cell.length_a 127.299 _cell.length_b 127.299 _cell.length_c 67.983 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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 _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 G N 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 covale ? covale1 A C FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A O1 FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? covale ? covale3 B C FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B O2 FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id DUR _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1TDU _atom_sites.fract_transf_matrix[1][1] 0.007856 _atom_sites.fract_transf_matrix[1][2] 0.004535 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009071 _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] 0.01471 _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 PO4 A 1 300 300 PO4 PO4 . D 3 DUR A 1 301 301 DUR DUR . E 4 CB3 A 1 302 302 CB3 CB3 . F 2 PO4 B 1 300 300 PO4 PO4 . G 3 DUR B 1 301 301 DUR DUR . H 4 CB3 B 1 302 302 CB3 CB3 . I 5 HOH A 1 750 750 HOH HOH . I 5 HOH A 2 753 753 HOH HOH . I 5 HOH A 3 754 754 HOH HOH . I 5 HOH A 4 755 755 HOH HOH . I 5 HOH A 5 756 756 HOH HOH . I 5 HOH A 6 758 758 HOH HOH . I 5 HOH A 7 763 763 HOH HOH . I 5 HOH A 8 764 764 HOH HOH . I 5 HOH A 9 765 765 HOH HOH . I 5 HOH A 10 766 766 HOH HOH . I 5 HOH A 11 767 767 HOH HOH . I 5 HOH A 12 768 768 HOH HOH . I 5 HOH A 13 769 769 HOH HOH . I 5 HOH A 14 770 770 HOH HOH . I 5 HOH A 15 771 771 HOH HOH . I 5 HOH A 16 772 772 HOH HOH . I 5 HOH A 17 773 773 HOH HOH . I 5 HOH A 18 774 774 HOH HOH . I 5 HOH A 19 775 775 HOH HOH . I 5 HOH A 20 776 776 HOH HOH . I 5 HOH A 21 778 778 HOH HOH . I 5 HOH A 22 779 779 HOH HOH . I 5 HOH A 23 780 780 HOH HOH . I 5 HOH A 24 781 781 HOH HOH . I 5 HOH A 25 782 782 HOH HOH . I 5 HOH A 26 783 783 HOH HOH . I 5 HOH A 27 785 785 HOH HOH . I 5 HOH A 28 786 786 HOH HOH . I 5 HOH A 29 787 787 HOH HOH . I 5 HOH A 30 789 789 HOH HOH . I 5 HOH A 31 790 790 HOH HOH . I 5 HOH A 32 791 791 HOH HOH . I 5 HOH A 33 792 792 HOH HOH . I 5 HOH A 34 793 793 HOH HOH . I 5 HOH A 35 794 794 HOH HOH . I 5 HOH A 36 795 795 HOH HOH . I 5 HOH A 37 796 796 HOH HOH . I 5 HOH A 38 798 798 HOH HOH . I 5 HOH A 39 800 800 HOH HOH . I 5 HOH A 40 802 802 HOH HOH . I 5 HOH A 41 803 803 HOH HOH . I 5 HOH A 42 804 804 HOH HOH . I 5 HOH A 43 805 805 HOH HOH . I 5 HOH A 44 806 806 HOH HOH . I 5 HOH A 45 807 807 HOH HOH . I 5 HOH A 46 808 808 HOH HOH . I 5 HOH A 47 809 809 HOH HOH . I 5 HOH A 48 810 810 HOH HOH . I 5 HOH A 49 811 811 HOH HOH . I 5 HOH A 50 814 814 HOH HOH . I 5 HOH A 51 815 815 HOH HOH . I 5 HOH A 52 816 816 HOH HOH . I 5 HOH A 53 817 817 HOH HOH . I 5 HOH A 54 818 818 HOH HOH . I 5 HOH A 55 825 825 HOH HOH . I 5 HOH A 56 826 826 HOH HOH . I 5 HOH A 57 828 828 HOH HOH . I 5 HOH A 58 836 836 HOH HOH . I 5 HOH A 59 837 837 HOH HOH . I 5 HOH A 60 844 844 HOH HOH . I 5 HOH A 61 846 846 HOH HOH . I 5 HOH A 62 848 848 HOH HOH . I 5 HOH A 63 849 849 HOH HOH . I 5 HOH A 64 853 853 HOH HOH . I 5 HOH A 65 857 857 HOH HOH . I 5 HOH A 66 859 859 HOH HOH . I 5 HOH A 67 860 860 HOH HOH . I 5 HOH A 68 861 861 HOH HOH . I 5 HOH A 69 862 862 HOH HOH . I 5 HOH A 70 867 867 HOH HOH . I 5 HOH A 71 868 868 HOH HOH . I 5 HOH A 72 872 872 HOH HOH . I 5 HOH A 73 873 873 HOH HOH . I 5 HOH A 74 874 874 HOH HOH . I 5 HOH A 75 876 876 HOH HOH . I 5 HOH A 76 877 877 HOH HOH . I 5 HOH A 77 878 878 HOH HOH . I 5 HOH A 78 879 879 HOH HOH . I 5 HOH A 79 880 880 HOH HOH . I 5 HOH A 80 881 881 HOH HOH . I 5 HOH A 81 882 882 HOH HOH . I 5 HOH A 82 885 885 HOH HOH . I 5 HOH A 83 886 886 HOH HOH . I 5 HOH A 84 887 887 HOH HOH . I 5 HOH A 85 889 889 HOH HOH . I 5 HOH A 86 891 891 HOH HOH . I 5 HOH A 87 892 892 HOH HOH . I 5 HOH A 88 896 896 HOH HOH . I 5 HOH A 89 897 897 HOH HOH . I 5 HOH A 90 901 901 HOH HOH . I 5 HOH A 91 902 902 HOH HOH . I 5 HOH A 92 903 903 HOH HOH . I 5 HOH A 93 908 908 HOH HOH . I 5 HOH A 94 909 909 HOH HOH . J 5 HOH B 1 751 751 HOH HOH . J 5 HOH B 2 752 752 HOH HOH . J 5 HOH B 3 757 757 HOH HOH . J 5 HOH B 4 760 760 HOH HOH . J 5 HOH B 5 761 761 HOH HOH . J 5 HOH B 6 762 762 HOH HOH . J 5 HOH B 7 777 777 HOH HOH . J 5 HOH B 8 784 784 HOH HOH . J 5 HOH B 9 788 788 HOH HOH . J 5 HOH B 10 799 799 HOH HOH . J 5 HOH B 11 812 812 HOH HOH . J 5 HOH B 12 813 813 HOH HOH . J 5 HOH B 13 819 819 HOH HOH . J 5 HOH B 14 820 820 HOH HOH . J 5 HOH B 15 821 821 HOH HOH . J 5 HOH B 16 822 822 HOH HOH . J 5 HOH B 17 823 823 HOH HOH . J 5 HOH B 18 824 824 HOH HOH . J 5 HOH B 19 827 827 HOH HOH . J 5 HOH B 20 829 829 HOH HOH . J 5 HOH B 21 830 830 HOH HOH . J 5 HOH B 22 831 831 HOH HOH . J 5 HOH B 23 832 832 HOH HOH . J 5 HOH B 24 834 834 HOH HOH . J 5 HOH B 25 835 835 HOH HOH . J 5 HOH B 26 838 838 HOH HOH . J 5 HOH B 27 839 839 HOH HOH . J 5 HOH B 28 840 840 HOH HOH . J 5 HOH B 29 841 841 HOH HOH . J 5 HOH B 30 842 842 HOH HOH . J 5 HOH B 31 843 843 HOH HOH . J 5 HOH B 32 845 845 HOH HOH . J 5 HOH B 33 850 850 HOH HOH . J 5 HOH B 34 851 851 HOH HOH . J 5 HOH B 35 852 852 HOH HOH . J 5 HOH B 36 854 854 HOH HOH . J 5 HOH B 37 855 855 HOH HOH . J 5 HOH B 38 856 856 HOH HOH . J 5 HOH B 39 858 858 HOH HOH . J 5 HOH B 40 863 863 HOH HOH . J 5 HOH B 41 864 864 HOH HOH . J 5 HOH B 42 865 865 HOH HOH . J 5 HOH B 43 866 866 HOH HOH . J 5 HOH B 44 869 869 HOH HOH . J 5 HOH B 45 870 870 HOH HOH . J 5 HOH B 46 875 875 HOH HOH . J 5 HOH B 47 883 883 HOH HOH . J 5 HOH B 48 884 884 HOH HOH . J 5 HOH B 49 888 888 HOH HOH . J 5 HOH B 50 894 894 HOH HOH . J 5 HOH B 51 895 895 HOH HOH . J 5 HOH B 52 898 898 HOH HOH . J 5 HOH B 53 899 899 HOH HOH . J 5 HOH B 54 900 900 HOH HOH . J 5 HOH B 55 904 904 HOH HOH . J 5 HOH B 56 905 905 HOH HOH . J 5 HOH B 57 906 906 HOH HOH . J 5 HOH B 58 907 907 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 DUR . . . D 3 17.341 19.918 31.602 1 33.88 ? N1 DUR 301 A 1 HETATM 2 C C2 DUR . . . D 3 18.289 20.028 32.616 1 32.68 ? C2 DUR 301 A 1 HETATM 3 N N3 DUR . . . D 3 19.362 19.183 32.513 1 33.68 ? N3 DUR 301 A 1 HETATM 4 C C4 DUR . . . D 3 19.563 18.247 31.52 1 34.39 ? C4 DUR 301 A 1 HETATM 5 C C5 DUR . . . D 3 18.531 18.182 30.506 1 35.58 ? C5 DUR 301 A 1 HETATM 6 C C6 DUR . . . D 3 17.434 19.041 30.608 1 35.01 ? C6 DUR 301 A 1 HETATM 7 O O2 DUR . . . D 3 18.253 20.839 33.536 1 32.27 ? O2 DUR 301 A 1 HETATM 8 O O4 DUR . . . D 3 20.595 17.584 31.493 1 35.78 ? O4 DUR 301 A 1 HETATM 9 C C1' DUR . . . D 3 16.157 20.815 31.571 1 32.06 ? C1' DUR 301 A 1 HETATM 10 C C2' DUR . . . D 3 16.39 22.146 30.843 1 30.52 ? C2' DUR 301 A 1 HETATM 11 C C3' DUR . . . D 3 14.991 22.664 30.479 1 29.02 ? C3' DUR 301 A 1 HETATM 12 C C4' DUR . . . D 3 14.344 21.323 30.064 1 29.34 ? C4' DUR 301 A 1 HETATM 13 O O3' DUR . . . D 3 14.314 23.17 31.652 1 24.68 ? O3' DUR 301 A 1 HETATM 14 O O4' DUR . . . D 3 14.978 20.289 30.891 1 29.67 ? O4' DUR 301 A 1 HETATM 15 C C5' DUR . . . D 3 14.545 20.928 28.562 1 30.19 ? C5' DUR 301 A 1 HETATM 16 O O5' DUR . . . D 3 15.904 20.931 28.104 1 33.04 ? O5' DUR 301 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #