data_1DNA # _model_server_result.job_id 5Mykb2owY_DqChIbhjEkoA _model_server_result.datetime_utc '2024-10-24 04:27:40' _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":"F","auth_seq_id":602}' # _entry.id 1DNA # _exptl.entry_id 1DNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.469 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '10-PROPARGYL-5,8-DIDEAZAFOLIC ACID' _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 ? 3 D N N ? 3 F 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 'C24 H23 N5 O6' _chem_comp.formula_weight 477.469 _chem_comp.id CB3 _chem_comp.mon_nstd_flag . _chem_comp.name '10-PROPARGYL-5,8-DIDEAZAFOLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _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 CB3 . . . F 3 48.32 34.519 23.098 1 58.9 ? N1 CB3 602 B 1 HETATM 2 C C2 CB3 . . . F 3 48.727 34.856 24.343 1 54.81 ? C2 CB3 602 B 1 HETATM 3 N NA2 CB3 . . . F 3 49.693 34.194 24.98 1 50.36 ? NA2 CB3 602 B 1 HETATM 4 N N3 CB3 . . . F 3 48.154 35.896 24.977 1 56.87 ? N3 CB3 602 B 1 HETATM 5 C C4 CB3 . . . F 3 47.202 36.649 24.399 1 56.34 ? C4 CB3 602 B 1 HETATM 6 O O4 CB3 . . . F 3 46.637 37.675 25.13 1 51.34 ? O4 CB3 602 B 1 HETATM 7 C C4A CB3 . . . F 3 46.813 36.371 23.083 1 56.52 ? C4A CB3 602 B 1 HETATM 8 C C5 CB3 . . . F 3 45.903 37.171 22.391 1 54.7 ? C5 CB3 602 B 1 HETATM 9 C C6 CB3 . . . F 3 45.54 36.868 21.067 1 56.35 ? C6 CB3 602 B 1 HETATM 10 C C7 CB3 . . . F 3 46.07 35.722 20.455 1 57.7 ? C7 CB3 602 B 1 HETATM 11 C C8 CB3 . . . F 3 46.994 34.917 21.141 1 59.6 ? C8 CB3 602 B 1 HETATM 12 C C8A CB3 . . . F 3 47.383 35.245 22.449 1 58.6 ? C8A CB3 602 B 1 HETATM 13 C C9 CB3 . . . F 3 44.821 37.845 20.216 1 56.43 ? C9 CB3 602 B 1 HETATM 14 N N10 CB3 . . . F 3 44.516 39.178 20.813 1 55.87 ? N10 CB3 602 B 1 HETATM 15 C C11 CB3 . . . F 3 47.458 41.906 22.125 1 58.36 ? C11 CB3 602 B 1 HETATM 16 C C12 CB3 . . . F 3 46.218 41.823 22.78 1 55.23 ? C12 CB3 602 B 1 HETATM 17 C C13 CB3 . . . F 3 45.244 40.917 22.332 1 52.96 ? C13 CB3 602 B 1 HETATM 18 C C14 CB3 . . . F 3 45.478 40.068 21.227 1 56.12 ? C14 CB3 602 B 1 HETATM 19 C C15 CB3 . . . F 3 46.738 40.156 20.59 1 58.74 ? C15 CB3 602 B 1 HETATM 20 C C16 CB3 . . . F 3 47.717 41.062 21.034 1 57.42 ? C16 CB3 602 B 1 HETATM 21 C C CB3 . . . F 3 48.462 42.873 22.528 1 62.07 ? C CB3 602 B 1 HETATM 22 O O CB3 . . . F 3 49.664 42.691 22.335 1 58.79 ? O CB3 602 B 1 HETATM 23 N N CB3 . . . F 3 48.035 43.999 23.11 1 70.76 ? N CB3 602 B 1 HETATM 24 C CA CB3 . . . F 3 48.787 45.273 23.161 1 79.85 ? CA CB3 602 B 1 HETATM 25 C CB CB3 . . . F 3 48.392 46.295 22.089 1 84.58 ? CB CB3 602 B 1 HETATM 26 C CG CB3 . . . F 3 48.835 45.93 20.678 1 91.42 ? CG CB3 602 B 1 HETATM 27 C CD CB3 . . . F 3 48.304 46.889 19.626 1 94.15 ? CD CB3 602 B 1 HETATM 28 O OE1 CB3 . . . F 3 47.194 47.431 19.811 1 95.27 ? OE1 CB3 602 B 1 HETATM 29 O OE2 CB3 . . . F 3 48.99 47.093 18.603 1 96.58 ? OE2 CB3 602 B 1 HETATM 30 C CT CB3 . . . F 3 48.646 45.886 24.551 1 80.07 ? CT CB3 602 B 1 HETATM 31 O O1 CB3 . . . F 3 49.672 45.955 25.252 1 79.54 ? O1 CB3 602 B 1 HETATM 32 O O2 CB3 . . . F 3 47.516 46.263 24.932 1 80.02 ? O2 CB3 602 B 1 HETATM 33 C CP1 CB3 . . . F 3 43.092 39.544 20.901 1 53.42 ? CP1 CB3 602 B 1 HETATM 34 C CP2 CB3 . . . F 3 42.614 39.226 22.234 1 50.66 ? CP2 CB3 602 B 1 HETATM 35 C CP3 CB3 . . . F 3 42.296 38.945 23.352 1 44.78 ? CP3 CB3 602 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 35 #