data_1DNA
#
_model_server_result.job_id            bl6Aq8GlIY0Hq_FaGFLXNA 
_model_server_result.datetime_utc      '2024-10-24 04:21:56' 
_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          1dna 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":604}' 
#
_entry.id    1DNA 
#
_exptl.entry_id    1DNA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_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         120 
_cell.entry_id            1DNA 
_cell.length_a            127.221 
_cell.length_b            127.221 
_cell.length_c            68.178 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DNA 
_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 
_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
? 2 C N N 
? 2 E 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 CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? 
covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 UMP . B UMP 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.824 ? 
#
_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 
#
_atom_sites.entry_id                     1DNA 
_atom_sites.fract_transf_matrix[1][1]    0.00786 
_atom_sites.fract_transf_matrix[1][2]    0.004538 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009076 
_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]    0.014667 
_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 UMP A 1 603 603 UMP UMP . 
D 3 CB3 A 1 601 601 CB3 CB3 . 
E 2 UMP B 1 604 604 UMP UMP . 
F 3 CB3 B 1 602 602 CB3 CB3 . 
G 4 HOH A 1 702 702 HOH HOH . 
G 4 HOH A 2 703 703 HOH HOH . 
G 4 HOH A 3 704 704 HOH HOH . 
G 4 HOH A 4 705 705 HOH HOH . 
G 4 HOH A 5 706 706 HOH HOH . 
G 4 HOH A 6 707 707 HOH HOH . 
G 4 HOH A 7 708 708 HOH HOH . 
G 4 HOH A 8 709 709 HOH HOH . 
G 4 HOH A 9 713 713 HOH HOH . 
G 4 HOH A 10 714 714 HOH HOH . 
G 4 HOH A 11 715 715 HOH HOH . 
G 4 HOH A 12 716 716 HOH HOH . 
G 4 HOH A 13 717 717 HOH HOH . 
G 4 HOH A 14 718 718 HOH HOH . 
G 4 HOH A 15 719 719 HOH HOH . 
G 4 HOH A 16 720 720 HOH HOH . 
G 4 HOH A 17 721 721 HOH HOH . 
G 4 HOH A 18 722 722 HOH HOH . 
G 4 HOH A 19 724 724 HOH HOH . 
G 4 HOH A 20 725 725 HOH HOH . 
G 4 HOH A 21 726 726 HOH HOH . 
G 4 HOH A 22 727 727 HOH HOH . 
G 4 HOH A 23 729 729 HOH HOH . 
G 4 HOH A 24 730 730 HOH HOH . 
G 4 HOH A 25 731 731 HOH HOH . 
G 4 HOH A 26 732 732 HOH HOH . 
G 4 HOH A 27 733 733 HOH HOH . 
G 4 HOH A 28 735 735 HOH HOH . 
G 4 HOH A 29 736 736 HOH HOH . 
G 4 HOH A 30 737 737 HOH HOH . 
G 4 HOH A 31 738 738 HOH HOH . 
G 4 HOH A 32 739 739 HOH HOH . 
G 4 HOH A 33 740 740 HOH HOH . 
G 4 HOH A 34 741 741 HOH HOH . 
G 4 HOH A 35 742 742 HOH HOH . 
G 4 HOH A 36 743 743 HOH HOH . 
G 4 HOH A 37 745 745 HOH HOH . 
G 4 HOH A 38 746 746 HOH HOH . 
G 4 HOH A 39 747 747 HOH HOH . 
G 4 HOH A 40 751 751 HOH HOH . 
G 4 HOH A 41 752 752 HOH HOH . 
G 4 HOH A 42 756 756 HOH HOH . 
G 4 HOH A 43 759 759 HOH HOH . 
G 4 HOH A 44 760 760 HOH HOH . 
G 4 HOH A 45 766 766 HOH HOH . 
G 4 HOH A 46 771 771 HOH HOH . 
G 4 HOH A 47 772 772 HOH HOH . 
G 4 HOH A 48 773 773 HOH HOH . 
G 4 HOH A 49 775 775 HOH HOH . 
G 4 HOH A 50 776 776 HOH HOH . 
G 4 HOH A 51 780 780 HOH HOH . 
G 4 HOH A 52 783 783 HOH HOH . 
G 4 HOH A 53 784 784 HOH HOH . 
G 4 HOH A 54 785 785 HOH HOH . 
G 4 HOH A 55 786 786 HOH HOH . 
G 4 HOH A 56 788 788 HOH HOH . 
G 4 HOH A 57 789 789 HOH HOH . 
G 4 HOH A 58 790 790 HOH HOH . 
G 4 HOH A 59 791 791 HOH HOH . 
G 4 HOH A 60 801 801 HOH HOH . 
G 4 HOH A 61 802 802 HOH HOH . 
G 4 HOH A 62 804 804 HOH HOH . 
G 4 HOH A 63 807 807 HOH HOH . 
G 4 HOH A 64 809 809 HOH HOH . 
G 4 HOH A 65 810 810 HOH HOH . 
G 4 HOH A 66 811 811 HOH HOH . 
G 4 HOH A 67 813 813 HOH HOH . 
G 4 HOH A 68 814 814 HOH HOH . 
G 4 HOH A 69 818 818 HOH HOH . 
G 4 HOH A 70 819 819 HOH HOH . 
G 4 HOH A 71 820 820 HOH HOH . 
G 4 HOH A 72 821 821 HOH HOH . 
G 4 HOH A 73 822 822 HOH HOH . 
G 4 HOH A 74 823 823 HOH HOH . 
G 4 HOH A 75 828 828 HOH HOH . 
G 4 HOH A 76 829 829 HOH HOH . 
G 4 HOH A 77 830 830 HOH HOH . 
G 4 HOH A 78 835 835 HOH HOH . 
G 4 HOH A 79 836 836 HOH HOH . 
G 4 HOH A 80 837 837 HOH HOH . 
G 4 HOH A 81 838 838 HOH HOH . 
G 4 HOH A 82 839 839 HOH HOH . 
G 4 HOH A 83 840 840 HOH HOH . 
G 4 HOH A 84 841 841 HOH HOH . 
G 4 HOH A 85 842 842 HOH HOH . 
G 4 HOH A 86 843 843 HOH HOH . 
G 4 HOH A 87 844 844 HOH HOH . 
G 4 HOH A 88 845 845 HOH HOH . 
G 4 HOH A 89 846 846 HOH HOH . 
G 4 HOH A 90 847 847 HOH HOH . 
G 4 HOH A 91 848 848 HOH HOH . 
G 4 HOH A 92 849 849 HOH HOH . 
G 4 HOH A 93 852 852 HOH HOH . 
G 4 HOH A 94 854 854 HOH HOH . 
G 4 HOH A 95 855 855 HOH HOH . 
G 4 HOH A 96 856 856 HOH HOH . 
G 4 HOH A 97 857 857 HOH HOH . 
G 4 HOH A 98 858 858 HOH HOH . 
G 4 HOH A 99 859 859 HOH HOH . 
G 4 HOH A 100 860 860 HOH HOH . 
G 4 HOH A 101 862 862 HOH HOH . 
G 4 HOH A 102 863 863 HOH HOH . 
G 4 HOH A 103 864 864 HOH HOH . 
G 4 HOH A 104 865 865 HOH HOH . 
G 4 HOH A 105 866 866 HOH HOH . 
G 4 HOH A 106 867 867 HOH HOH . 
G 4 HOH A 107 869 869 HOH HOH . 
G 4 HOH A 108 870 870 HOH HOH . 
G 4 HOH A 109 871 871 HOH HOH . 
G 4 HOH A 110 872 872 HOH HOH . 
G 4 HOH A 111 873 873 HOH HOH . 
G 4 HOH A 112 874 874 HOH HOH . 
G 4 HOH A 113 875 875 HOH HOH . 
G 4 HOH A 114 876 876 HOH HOH . 
G 4 HOH A 115 885 885 HOH HOH . 
G 4 HOH A 116 886 886 HOH HOH . 
G 4 HOH A 117 888 888 HOH HOH . 
G 4 HOH A 118 894 894 HOH HOH . 
G 4 HOH A 119 897 897 HOH HOH . 
G 4 HOH A 120 899 899 HOH HOH . 
G 4 HOH A 121 901 901 HOH HOH . 
G 4 HOH A 122 902 902 HOH HOH . 
G 4 HOH A 123 904 904 HOH HOH . 
G 4 HOH A 124 907 907 HOH HOH . 
G 4 HOH A 125 908 908 HOH HOH . 
G 4 HOH A 126 910 910 HOH HOH . 
G 4 HOH A 127 911 911 HOH HOH . 
G 4 HOH A 128 912 912 HOH HOH . 
G 4 HOH A 129 915 915 HOH HOH . 
G 4 HOH A 130 917 917 HOH HOH . 
H 4 HOH B 1 701 701 HOH HOH . 
H 4 HOH B 2 710 710 HOH HOH . 
H 4 HOH B 3 711 711 HOH HOH . 
H 4 HOH B 4 712 712 HOH HOH . 
H 4 HOH B 5 723 723 HOH HOH . 
H 4 HOH B 6 728 728 HOH HOH . 
H 4 HOH B 7 734 734 HOH HOH . 
H 4 HOH B 8 744 744 HOH HOH . 
H 4 HOH B 9 748 748 HOH HOH . 
H 4 HOH B 10 749 749 HOH HOH . 
H 4 HOH B 11 750 750 HOH HOH . 
H 4 HOH B 12 753 753 HOH HOH . 
H 4 HOH B 13 754 754 HOH HOH . 
H 4 HOH B 14 755 755 HOH HOH . 
H 4 HOH B 15 757 757 HOH HOH . 
H 4 HOH B 16 758 758 HOH HOH . 
H 4 HOH B 17 761 761 HOH HOH . 
H 4 HOH B 18 762 762 HOH HOH . 
H 4 HOH B 19 763 763 HOH HOH . 
H 4 HOH B 20 764 764 HOH HOH . 
H 4 HOH B 21 765 765 HOH HOH . 
H 4 HOH B 22 767 767 HOH HOH . 
H 4 HOH B 23 768 768 HOH HOH . 
H 4 HOH B 24 769 769 HOH HOH . 
H 4 HOH B 25 770 770 HOH HOH . 
H 4 HOH B 26 774 774 HOH HOH . 
H 4 HOH B 27 777 777 HOH HOH . 
H 4 HOH B 28 778 778 HOH HOH . 
H 4 HOH B 29 779 779 HOH HOH . 
H 4 HOH B 30 781 781 HOH HOH . 
H 4 HOH B 31 782 782 HOH HOH . 
H 4 HOH B 32 787 787 HOH HOH . 
H 4 HOH B 33 792 792 HOH HOH . 
H 4 HOH B 34 793 793 HOH HOH . 
H 4 HOH B 35 794 794 HOH HOH . 
H 4 HOH B 36 795 795 HOH HOH . 
H 4 HOH B 37 796 796 HOH HOH . 
H 4 HOH B 38 797 797 HOH HOH . 
H 4 HOH B 39 798 798 HOH HOH . 
H 4 HOH B 40 799 799 HOH HOH . 
H 4 HOH B 41 800 800 HOH HOH . 
H 4 HOH B 42 803 803 HOH HOH . 
H 4 HOH B 43 805 805 HOH HOH . 
H 4 HOH B 44 806 806 HOH HOH . 
H 4 HOH B 45 808 808 HOH HOH . 
H 4 HOH B 46 812 812 HOH HOH . 
H 4 HOH B 47 815 815 HOH HOH . 
H 4 HOH B 48 816 816 HOH HOH . 
H 4 HOH B 49 817 817 HOH HOH . 
H 4 HOH B 50 824 824 HOH HOH . 
H 4 HOH B 51 825 825 HOH HOH . 
H 4 HOH B 52 826 826 HOH HOH . 
H 4 HOH B 53 827 827 HOH HOH . 
H 4 HOH B 54 831 831 HOH HOH . 
H 4 HOH B 55 832 832 HOH HOH . 
H 4 HOH B 56 833 833 HOH HOH . 
H 4 HOH B 57 834 834 HOH HOH . 
H 4 HOH B 58 850 850 HOH HOH . 
H 4 HOH B 59 851 851 HOH HOH . 
H 4 HOH B 60 853 853 HOH HOH . 
H 4 HOH B 61 861 861 HOH HOH . 
H 4 HOH B 62 868 868 HOH HOH . 
H 4 HOH B 63 877 877 HOH HOH . 
H 4 HOH B 64 878 878 HOH HOH . 
H 4 HOH B 65 879 879 HOH HOH . 
H 4 HOH B 66 880 880 HOH HOH . 
H 4 HOH B 67 881 881 HOH HOH . 
H 4 HOH B 68 882 882 HOH HOH . 
H 4 HOH B 69 883 883 HOH HOH . 
H 4 HOH B 70 884 884 HOH HOH . 
H 4 HOH B 71 887 887 HOH HOH . 
H 4 HOH B 72 889 889 HOH HOH . 
H 4 HOH B 73 890 890 HOH HOH . 
H 4 HOH B 74 891 891 HOH HOH . 
H 4 HOH B 75 892 892 HOH HOH . 
H 4 HOH B 76 893 893 HOH HOH . 
H 4 HOH B 77 895 895 HOH HOH . 
H 4 HOH B 78 896 896 HOH HOH . 
H 4 HOH B 79 898 898 HOH HOH . 
H 4 HOH B 80 900 900 HOH HOH . 
H 4 HOH B 81 903 903 HOH HOH . 
H 4 HOH B 82 905 905 HOH HOH . 
H 4 HOH B 83 906 906 HOH HOH . 
H 4 HOH B 84 913 913 HOH HOH . 
H 4 HOH B 85 914 914 HOH HOH . 
H 4 HOH B 86 916 916 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 . . . E 2 43.983 34.089 24.662 1 48.92 ? N1 UMP 604 B 1 
HETATM 2 C C2 UMP . . . E 2 43.27 35.075 25.333 1 46.39 ? C2 UMP 604 B 1 
HETATM 3 N N3 UMP . . . E 2 42.344 35.782 24.609 1 46.9 ? N3 UMP 604 B 1 
HETATM 4 C C4 UMP . . . E 2 42.099 35.595 23.271 1 47.59 ? C4 UMP 604 B 1 
HETATM 5 C C5 UMP . . . E 2 42.873 34.583 22.43 1 49.83 ? C5 UMP 604 B 1 
HETATM 6 C C6 UMP . . . E 2 43.625 33.555 23.329 1 47.87 ? C6 UMP 604 B 1 
HETATM 7 O O2 UMP . . . E 2 43.448 35.331 26.524 1 42.4 ? O2 UMP 604 B 1 
HETATM 8 O O4 UMP . . . E 2 41.24 36.292 22.725 1 51.55 ? O4 UMP 604 B 1 
HETATM 9 C C1' UMP . . . E 2 45.222 33.505 25.206 1 47.92 ? C1' UMP 604 B 1 
HETATM 10 C C2' UMP . . . E 2 45.075 32.464 26.309 1 50.43 ? C2' UMP 604 B 1 
HETATM 11 C C3' UMP . . . E 2 46.521 32.076 26.571 1 51.51 ? C3' UMP 604 B 1 
HETATM 12 C C4' UMP . . . E 2 47.197 31.974 25.198 1 51.98 ? C4' UMP 604 B 1 
HETATM 13 O O3' UMP . . . E 2 47.092 33.213 27.255 1 54.87 ? O3' UMP 604 B 1 
HETATM 14 O O4' UMP . . . E 2 46.198 32.743 24.358 1 48.42 ? O4' UMP 604 B 1 
HETATM 15 C C5' UMP . . . E 2 47.358 30.506 24.774 1 50.25 ? C5' UMP 604 B 1 
HETATM 16 O O5' UMP . . . E 2 46.23 29.571 24.888 1 47.49 ? O5' UMP 604 B 1 
HETATM 17 P P UMP . . . E 2 46.507 27.987 24.639 1 40.06 ? P UMP 604 B 1 
HETATM 18 O OP1 UMP . . . E 2 45.685 27.134 25.505 1 47.37 ? OP1 UMP 604 B 1 
HETATM 19 O OP2 UMP . . . E 2 46.255 27.605 23.234 1 39.68 ? OP2 UMP 604 B 1 
HETATM 20 O OP3 UMP . . . E 2 47.884 27.589 24.989 1 47.8 ? OP3 UMP 604 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           20 
#