data_4RDN # _model_server_result.job_id 4D81WGGxGodRc-6JyQanhA _model_server_result.datetime_utc '2024-11-27 18:24:53' _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 4rdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 4RDN # _exptl.entry_id 4RDN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.268 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-methyladenosine _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 4RDN _cell.length_a 80.73 _cell.length_b 80.73 _cell.length_c 113.48 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RDN _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 F N N # _chem_comp.formula 'C11 H15 N5 O4' _chem_comp.formula_weight 281.268 _chem_comp.id 6MD _chem_comp.mon_nstd_flag . _chem_comp.name N-methyladenosine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C2 N1 6MD doub 1 n y C2 N3 6MD sing 2 n y N1 C6 6MD sing 3 n y N3 C4 6MD doub 4 n y CZ N6 6MD sing 5 n n C6 N6 6MD sing 6 n n C6 C5 6MD doub 7 n y C4 C5 6MD sing 8 n y C4 N9 6MD sing 9 n y C4' O4' 6MD sing 10 n n C4' C5' 6MD sing 11 n n C4' C3' 6MD sing 12 n n O4' C1' 6MD sing 13 n n C5 N7 6MD sing 14 n y C5' O5' 6MD sing 15 n n O3' C3' 6MD sing 16 n n C1' N9 6MD sing 17 n n C1' C2' 6MD sing 18 n n N9 C8 6MD sing 19 n y C3' C2' 6MD sing 20 n n C2' O2' 6MD sing 21 n n N7 C8 6MD doub 22 n y O5' H1 6MD sing 23 n n C5' H2 6MD sing 24 n n C5' H3 6MD sing 25 n n C4' H4 6MD sing 26 n n C3' H5 6MD sing 27 n n O3' H6 6MD sing 28 n n C2' H7 6MD sing 29 n n O2' H8 6MD sing 30 n n C1' H9 6MD sing 31 n n C8 H10 6MD sing 32 n n N6 H11 6MD sing 33 n n C2 H12 6MD sing 34 n n CZ H13 6MD sing 35 n n CZ H14 6MD sing 36 n n CZ H15 6MD sing 37 n n # _atom_sites.entry_id 4RDN _atom_sites.fract_transf_matrix[1][1] 0.012387 _atom_sites.fract_transf_matrix[1][2] 0.007152 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014303 _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] 0.008812 _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 6MD A 1 601 1 6MD 6MZ . D 3 SO4 A 1 602 1 SO4 SO4 . E 3 SO4 A 1 603 3 SO4 SO4 . F 2 6MD B 1 601 2 6MD 6MZ . G 3 SO4 B 1 602 2 SO4 SO4 . H 3 SO4 B 1 603 4 SO4 SO4 . I 4 HOH A 1 701 1 HOH HOH . I 4 HOH A 2 702 2 HOH HOH . I 4 HOH A 3 703 3 HOH HOH . I 4 HOH A 4 704 4 HOH HOH . I 4 HOH A 5 705 5 HOH HOH . I 4 HOH A 6 706 6 HOH HOH . I 4 HOH A 7 707 7 HOH HOH . I 4 HOH A 8 708 8 HOH HOH . I 4 HOH A 9 709 10 HOH HOH . I 4 HOH A 10 710 11 HOH HOH . I 4 HOH A 11 711 14 HOH HOH . I 4 HOH A 12 712 15 HOH HOH . I 4 HOH A 13 713 16 HOH HOH . I 4 HOH A 14 714 17 HOH HOH . I 4 HOH A 15 715 19 HOH HOH . I 4 HOH A 16 716 20 HOH HOH . I 4 HOH A 17 717 21 HOH HOH . I 4 HOH A 18 718 23 HOH HOH . I 4 HOH A 19 719 25 HOH HOH . I 4 HOH A 20 720 28 HOH HOH . I 4 HOH A 21 721 29 HOH HOH . I 4 HOH A 22 722 30 HOH HOH . I 4 HOH A 23 723 31 HOH HOH . I 4 HOH A 24 724 32 HOH HOH . I 4 HOH A 25 725 34 HOH HOH . I 4 HOH A 26 726 35 HOH HOH . I 4 HOH A 27 727 38 HOH HOH . I 4 HOH A 28 728 40 HOH HOH . I 4 HOH A 29 729 41 HOH HOH . I 4 HOH A 30 730 43 HOH HOH . I 4 HOH A 31 731 44 HOH HOH . I 4 HOH A 32 732 46 HOH HOH . I 4 HOH A 33 733 48 HOH HOH . I 4 HOH A 34 734 50 HOH HOH . I 4 HOH A 35 735 51 HOH HOH . I 4 HOH A 36 736 52 HOH HOH . I 4 HOH A 37 737 53 HOH HOH . I 4 HOH A 38 738 54 HOH HOH . I 4 HOH A 39 739 55 HOH HOH . I 4 HOH A 40 740 56 HOH HOH . I 4 HOH A 41 741 57 HOH HOH . I 4 HOH A 42 742 58 HOH HOH . I 4 HOH A 43 743 60 HOH HOH . I 4 HOH A 44 744 61 HOH HOH . I 4 HOH A 45 745 62 HOH HOH . I 4 HOH A 46 746 63 HOH HOH . I 4 HOH A 47 747 64 HOH HOH . I 4 HOH A 48 748 66 HOH HOH . I 4 HOH A 49 749 68 HOH HOH . I 4 HOH A 50 750 70 HOH HOH . I 4 HOH A 51 751 72 HOH HOH . I 4 HOH A 52 752 73 HOH HOH . I 4 HOH A 53 753 74 HOH HOH . I 4 HOH A 54 754 75 HOH HOH . I 4 HOH A 55 755 76 HOH HOH . I 4 HOH A 56 756 78 HOH HOH . I 4 HOH A 57 757 79 HOH HOH . I 4 HOH A 58 758 82 HOH HOH . I 4 HOH A 59 759 84 HOH HOH . I 4 HOH A 60 760 85 HOH HOH . I 4 HOH A 61 761 86 HOH HOH . I 4 HOH A 62 762 87 HOH HOH . I 4 HOH A 63 763 89 HOH HOH . I 4 HOH A 64 764 90 HOH HOH . I 4 HOH A 65 765 91 HOH HOH . I 4 HOH A 66 766 93 HOH HOH . I 4 HOH A 67 767 94 HOH HOH . I 4 HOH A 68 768 96 HOH HOH . I 4 HOH A 69 769 98 HOH HOH . I 4 HOH A 70 770 100 HOH HOH . I 4 HOH A 71 771 101 HOH HOH . I 4 HOH A 72 772 103 HOH HOH . I 4 HOH A 73 773 106 HOH HOH . I 4 HOH A 74 774 107 HOH HOH . I 4 HOH A 75 775 109 HOH HOH . I 4 HOH A 76 776 110 HOH HOH . I 4 HOH A 77 777 112 HOH HOH . I 4 HOH A 78 778 115 HOH HOH . I 4 HOH A 79 779 124 HOH HOH . I 4 HOH A 80 780 127 HOH HOH . I 4 HOH A 81 781 128 HOH HOH . I 4 HOH A 82 782 130 HOH HOH . I 4 HOH A 83 783 131 HOH HOH . I 4 HOH A 84 784 133 HOH HOH . I 4 HOH A 85 785 135 HOH HOH . I 4 HOH A 86 786 139 HOH HOH . I 4 HOH A 87 787 140 HOH HOH . I 4 HOH A 88 788 141 HOH HOH . I 4 HOH A 89 789 143 HOH HOH . I 4 HOH A 90 790 144 HOH HOH . I 4 HOH A 91 791 146 HOH HOH . I 4 HOH A 92 792 147 HOH HOH . I 4 HOH A 93 793 148 HOH HOH . I 4 HOH A 94 794 149 HOH HOH . I 4 HOH A 95 795 153 HOH HOH . I 4 HOH A 96 796 155 HOH HOH . I 4 HOH A 97 797 158 HOH HOH . I 4 HOH A 98 798 160 HOH HOH . I 4 HOH A 99 799 161 HOH HOH . I 4 HOH A 100 800 164 HOH HOH . I 4 HOH A 101 801 168 HOH HOH . I 4 HOH A 102 802 173 HOH HOH . I 4 HOH A 103 803 180 HOH HOH . I 4 HOH A 104 804 181 HOH HOH . I 4 HOH A 105 805 183 HOH HOH . I 4 HOH A 106 806 184 HOH HOH . I 4 HOH A 107 807 186 HOH HOH . I 4 HOH A 108 808 187 HOH HOH . I 4 HOH A 109 809 188 HOH HOH . I 4 HOH A 110 810 190 HOH HOH . I 4 HOH A 111 811 191 HOH HOH . I 4 HOH A 112 812 192 HOH HOH . I 4 HOH A 113 813 194 HOH HOH . I 4 HOH A 114 814 196 HOH HOH . I 4 HOH A 115 815 199 HOH HOH . I 4 HOH A 116 816 201 HOH HOH . I 4 HOH A 117 817 202 HOH HOH . I 4 HOH A 118 818 203 HOH HOH . I 4 HOH A 119 819 205 HOH HOH . I 4 HOH A 120 820 207 HOH HOH . I 4 HOH A 121 821 208 HOH HOH . I 4 HOH A 122 822 211 HOH HOH . I 4 HOH A 123 823 212 HOH HOH . I 4 HOH A 124 824 214 HOH HOH . I 4 HOH A 125 825 215 HOH HOH . I 4 HOH A 126 826 216 HOH HOH . I 4 HOH A 127 827 217 HOH HOH . I 4 HOH A 128 828 218 HOH HOH . I 4 HOH A 129 829 220 HOH HOH . I 4 HOH A 130 830 226 HOH HOH . I 4 HOH A 131 831 228 HOH HOH . I 4 HOH A 132 832 231 HOH HOH . I 4 HOH A 133 833 236 HOH HOH . I 4 HOH A 134 834 239 HOH HOH . I 4 HOH A 135 835 240 HOH HOH . I 4 HOH A 136 836 242 HOH HOH . I 4 HOH A 137 837 247 HOH HOH . J 4 HOH B 1 701 9 HOH HOH . J 4 HOH B 2 702 12 HOH HOH . J 4 HOH B 3 703 13 HOH HOH . J 4 HOH B 4 704 18 HOH HOH . J 4 HOH B 5 705 22 HOH HOH . J 4 HOH B 6 706 24 HOH HOH . J 4 HOH B 7 707 26 HOH HOH . J 4 HOH B 8 708 27 HOH HOH . J 4 HOH B 9 709 33 HOH HOH . J 4 HOH B 10 710 37 HOH HOH . J 4 HOH B 11 711 39 HOH HOH . J 4 HOH B 12 712 42 HOH HOH . J 4 HOH B 13 713 45 HOH HOH . J 4 HOH B 14 714 47 HOH HOH . J 4 HOH B 15 715 49 HOH HOH . J 4 HOH B 16 716 59 HOH HOH . J 4 HOH B 17 717 65 HOH HOH . J 4 HOH B 18 718 67 HOH HOH . J 4 HOH B 19 719 69 HOH HOH . J 4 HOH B 20 720 71 HOH HOH . J 4 HOH B 21 721 77 HOH HOH . J 4 HOH B 22 722 80 HOH HOH . J 4 HOH B 23 723 88 HOH HOH . J 4 HOH B 24 724 92 HOH HOH . J 4 HOH B 25 725 95 HOH HOH . J 4 HOH B 26 726 102 HOH HOH . J 4 HOH B 27 727 105 HOH HOH . J 4 HOH B 28 728 108 HOH HOH . J 4 HOH B 29 729 113 HOH HOH . J 4 HOH B 30 730 116 HOH HOH . J 4 HOH B 31 731 117 HOH HOH . J 4 HOH B 32 732 118 HOH HOH . J 4 HOH B 33 733 120 HOH HOH . J 4 HOH B 34 734 121 HOH HOH . J 4 HOH B 35 735 123 HOH HOH . J 4 HOH B 36 736 126 HOH HOH . J 4 HOH B 37 737 129 HOH HOH . J 4 HOH B 38 738 134 HOH HOH . J 4 HOH B 39 739 136 HOH HOH . J 4 HOH B 40 740 137 HOH HOH . J 4 HOH B 41 741 138 HOH HOH . J 4 HOH B 42 742 142 HOH HOH . J 4 HOH B 43 743 145 HOH HOH . J 4 HOH B 44 744 150 HOH HOH . J 4 HOH B 45 745 151 HOH HOH . J 4 HOH B 46 746 152 HOH HOH . J 4 HOH B 47 747 154 HOH HOH . J 4 HOH B 48 748 156 HOH HOH . J 4 HOH B 49 749 157 HOH HOH . J 4 HOH B 50 750 159 HOH HOH . J 4 HOH B 51 751 162 HOH HOH . J 4 HOH B 52 752 163 HOH HOH . J 4 HOH B 53 753 165 HOH HOH . J 4 HOH B 54 754 166 HOH HOH . J 4 HOH B 55 755 167 HOH HOH . J 4 HOH B 56 756 169 HOH HOH . J 4 HOH B 57 757 170 HOH HOH . J 4 HOH B 58 758 171 HOH HOH . J 4 HOH B 59 759 172 HOH HOH . J 4 HOH B 60 760 174 HOH HOH . J 4 HOH B 61 761 175 HOH HOH . J 4 HOH B 62 762 176 HOH HOH . J 4 HOH B 63 763 177 HOH HOH . J 4 HOH B 64 764 178 HOH HOH . J 4 HOH B 65 765 179 HOH HOH . J 4 HOH B 66 766 185 HOH HOH . J 4 HOH B 67 767 189 HOH HOH . J 4 HOH B 68 768 193 HOH HOH . J 4 HOH B 69 769 195 HOH HOH . J 4 HOH B 70 770 197 HOH HOH . J 4 HOH B 71 771 198 HOH HOH . J 4 HOH B 72 772 200 HOH HOH . J 4 HOH B 73 773 204 HOH HOH . J 4 HOH B 74 774 206 HOH HOH . J 4 HOH B 75 775 209 HOH HOH . J 4 HOH B 76 776 210 HOH HOH . J 4 HOH B 77 777 213 HOH HOH . J 4 HOH B 78 778 219 HOH HOH . J 4 HOH B 79 779 221 HOH HOH . J 4 HOH B 80 780 222 HOH HOH . J 4 HOH B 81 781 223 HOH HOH . J 4 HOH B 82 782 224 HOH HOH . J 4 HOH B 83 783 225 HOH HOH . J 4 HOH B 84 784 227 HOH HOH . J 4 HOH B 85 785 229 HOH HOH . J 4 HOH B 86 786 230 HOH HOH . J 4 HOH B 87 787 232 HOH HOH . J 4 HOH B 88 788 233 HOH HOH . J 4 HOH B 89 789 234 HOH HOH . J 4 HOH B 90 790 235 HOH HOH . J 4 HOH B 91 791 238 HOH HOH . J 4 HOH B 92 792 241 HOH HOH . J 4 HOH B 93 793 243 HOH HOH . J 4 HOH B 94 794 244 HOH HOH . J 4 HOH B 95 795 245 HOH HOH . J 4 HOH B 96 796 246 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 O O5' 6MD . . . C 2 -9.175 -29.262 14.542 1 20.14 ? O5' 6MD 601 A 1 HETATM 2 C C5' 6MD . . . C 2 -8.659 -29.055 13.245 1 19.64 ? C5' 6MD 601 A 1 HETATM 3 C C4' 6MD . . . C 2 -9.111 -30.2 12.353 1 19.06 ? C4' 6MD 601 A 1 HETATM 4 O O4' 6MD . . . C 2 -10.54 -30.186 12.18 1 18.32 ? O4' 6MD 601 A 1 HETATM 5 C C3' 6MD . . . C 2 -8.509 -30.082 10.964 1 18.6 ? C3' 6MD 601 A 1 HETATM 6 O O3' 6MD . . . C 2 -7.227 -30.694 10.842 1 18.92 ? O3' 6MD 601 A 1 HETATM 7 C C2' 6MD . . . C 2 -9.557 -30.749 10.096 1 18.52 ? C2' 6MD 601 A 1 HETATM 8 O O2' 6MD . . . C 2 -9.331 -32.151 9.987 1 17.34 ? O2' 6MD 601 A 1 HETATM 9 C C1' 6MD . . . C 2 -10.868 -30.461 10.821 1 18.38 ? C1' 6MD 601 A 1 HETATM 10 N N9 6MD . . . C 2 -11.542 -29.234 10.337 1 18.59 ? N9 6MD 601 A 1 HETATM 11 C C8 6MD . . . C 2 -10.967 -28.147 9.773 1 18.64 ? C8 6MD 601 A 1 HETATM 12 N N7 6MD . . . C 2 -11.896 -27.202 9.49 1 18.62 ? N7 6MD 601 A 1 HETATM 13 C C5 6MD . . . C 2 -13.084 -27.682 9.885 1 18.49 ? C5 6MD 601 A 1 HETATM 14 C C6 6MD . . . C 2 -14.481 -27.193 9.868 1 18.52 ? C6 6MD 601 A 1 HETATM 15 N N6 6MD . . . C 2 -14.75 -25.959 9.393 1 18.31 ? N6 6MD 601 A 1 HETATM 16 N N1 6MD . . . C 2 -15.43 -28.015 10.386 1 17.79 ? N1 6MD 601 A 1 HETATM 17 C C2 6MD . . . C 2 -15.139 -29.223 10.894 1 17.66 ? C2 6MD 601 A 1 HETATM 18 N N3 6MD . . . C 2 -13.896 -29.726 10.934 1 17.75 ? N3 6MD 601 A 1 HETATM 19 C C4 6MD . . . C 2 -12.847 -29.016 10.45 1 18.34 ? C4 6MD 601 A 1 HETATM 20 C CZ 6MD . . . C 2 -16.062 -25.351 9.534 1 18.56 ? CZ 6MD 601 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 20 #