data_1VPT # _model_server_result.job_id L_iUP1RcxXInCD8d8RZ2PQ _model_server_result.datetime_utc '2024-11-24 13:35:00' _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 1vpt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1VPT # _exptl.entry_id 1VPT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 118.4 _cell.angle_gamma 90 _cell.entry_id 1VPT _cell.length_a 85.3 _cell.length_b 67.8 _cell.length_c 80.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VPT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 N CA SAM sing 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 1VPT _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006339 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014749 _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] 0.01414 _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 B 2 SAM A 1 400 400 SAM SAM . C 3 HOH A 1 700 700 HOH HOH . C 3 HOH A 2 701 701 HOH HOH . C 3 HOH A 3 702 702 HOH HOH . C 3 HOH A 4 703 703 HOH HOH . C 3 HOH A 5 704 704 HOH HOH . C 3 HOH A 6 705 705 HOH HOH . C 3 HOH A 7 706 706 HOH HOH . C 3 HOH A 8 707 707 HOH HOH . C 3 HOH A 9 708 708 HOH HOH . C 3 HOH A 10 709 709 HOH HOH . C 3 HOH A 11 710 710 HOH HOH . C 3 HOH A 12 711 711 HOH HOH . C 3 HOH A 13 712 712 HOH HOH . C 3 HOH A 14 713 713 HOH HOH . C 3 HOH A 15 714 714 HOH HOH . C 3 HOH A 16 715 715 HOH HOH . C 3 HOH A 17 716 716 HOH HOH . C 3 HOH A 18 717 717 HOH HOH . C 3 HOH A 19 718 718 HOH HOH . C 3 HOH A 20 719 719 HOH HOH . C 3 HOH A 21 720 720 HOH HOH . C 3 HOH A 22 721 721 HOH HOH . C 3 HOH A 23 722 722 HOH HOH . C 3 HOH A 24 723 723 HOH HOH . C 3 HOH A 25 724 724 HOH HOH . C 3 HOH A 26 725 725 HOH HOH . C 3 HOH A 27 726 726 HOH HOH . C 3 HOH A 28 727 727 HOH HOH . C 3 HOH A 29 728 728 HOH HOH . C 3 HOH A 30 729 729 HOH HOH . C 3 HOH A 31 730 730 HOH HOH . C 3 HOH A 32 731 731 HOH HOH . C 3 HOH A 33 732 732 HOH HOH . C 3 HOH A 34 733 733 HOH HOH . C 3 HOH A 35 734 734 HOH HOH . C 3 HOH A 36 735 735 HOH HOH . C 3 HOH A 37 736 736 HOH HOH . C 3 HOH A 38 737 737 HOH HOH . C 3 HOH A 39 738 738 HOH HOH . C 3 HOH A 40 739 739 HOH HOH . C 3 HOH A 41 740 740 HOH HOH . C 3 HOH A 42 741 741 HOH HOH . C 3 HOH A 43 742 742 HOH HOH . C 3 HOH A 44 743 743 HOH HOH . C 3 HOH A 45 744 744 HOH HOH . C 3 HOH A 46 745 745 HOH HOH . C 3 HOH A 47 746 746 HOH HOH . C 3 HOH A 48 747 747 HOH HOH . C 3 HOH A 49 748 748 HOH HOH . C 3 HOH A 50 749 749 HOH HOH . C 3 HOH A 51 750 750 HOH HOH . C 3 HOH A 52 751 751 HOH HOH . C 3 HOH A 53 752 752 HOH HOH . C 3 HOH A 54 753 753 HOH HOH . C 3 HOH A 55 754 754 HOH HOH . C 3 HOH A 56 755 755 HOH HOH . C 3 HOH A 57 756 756 HOH HOH . C 3 HOH A 58 757 757 HOH HOH . C 3 HOH A 59 758 758 HOH HOH . C 3 HOH A 60 759 759 HOH HOH . C 3 HOH A 61 760 760 HOH HOH . C 3 HOH A 62 761 761 HOH HOH . C 3 HOH A 63 762 762 HOH HOH . C 3 HOH A 64 763 763 HOH HOH . C 3 HOH A 65 764 764 HOH HOH . C 3 HOH A 66 765 765 HOH HOH . C 3 HOH A 67 766 766 HOH HOH . C 3 HOH A 68 767 767 HOH HOH . C 3 HOH A 69 768 768 HOH HOH . C 3 HOH A 70 769 769 HOH HOH . C 3 HOH A 71 770 770 HOH HOH . C 3 HOH A 72 771 771 HOH HOH . C 3 HOH A 73 772 772 HOH HOH . C 3 HOH A 74 773 773 HOH HOH . C 3 HOH A 75 774 774 HOH HOH . C 3 HOH A 76 775 775 HOH HOH . C 3 HOH A 77 776 776 HOH HOH . C 3 HOH A 78 777 777 HOH HOH . C 3 HOH A 79 778 778 HOH HOH . C 3 HOH A 80 779 779 HOH HOH . C 3 HOH A 81 780 780 HOH HOH . C 3 HOH A 82 781 781 HOH HOH . C 3 HOH A 83 782 782 HOH HOH . C 3 HOH A 84 783 783 HOH HOH . C 3 HOH A 85 784 784 HOH HOH . C 3 HOH A 86 785 785 HOH HOH . C 3 HOH A 87 786 786 HOH HOH . C 3 HOH A 88 787 787 HOH HOH . C 3 HOH A 89 788 788 HOH HOH . C 3 HOH A 90 789 789 HOH HOH . C 3 HOH A 91 790 790 HOH HOH . C 3 HOH A 92 791 791 HOH HOH . C 3 HOH A 93 792 792 HOH HOH . C 3 HOH A 94 793 793 HOH HOH . C 3 HOH A 95 794 794 HOH HOH . C 3 HOH A 96 795 795 HOH HOH . C 3 HOH A 97 796 796 HOH HOH . C 3 HOH A 98 797 797 HOH HOH . C 3 HOH A 99 798 798 HOH HOH . C 3 HOH A 100 799 799 HOH HOH . C 3 HOH A 101 800 800 HOH HOH . C 3 HOH A 102 802 802 HOH HOH . C 3 HOH A 103 803 803 HOH HOH . C 3 HOH A 104 804 804 HOH HOH . C 3 HOH A 105 805 805 HOH HOH . C 3 HOH A 106 806 806 HOH HOH . C 3 HOH A 107 807 807 HOH HOH . C 3 HOH A 108 808 808 HOH HOH . C 3 HOH A 109 809 809 HOH HOH . C 3 HOH A 110 810 810 HOH HOH . C 3 HOH A 111 811 811 HOH HOH . C 3 HOH A 112 812 812 HOH HOH . C 3 HOH A 113 813 813 HOH HOH . C 3 HOH A 114 814 814 HOH HOH . C 3 HOH A 115 815 815 HOH HOH . C 3 HOH A 116 816 816 HOH HOH . C 3 HOH A 117 817 817 HOH HOH . C 3 HOH A 118 818 818 HOH HOH . C 3 HOH A 119 819 819 HOH HOH . C 3 HOH A 120 820 820 HOH HOH . C 3 HOH A 121 821 821 HOH HOH . C 3 HOH A 122 822 822 HOH HOH . C 3 HOH A 123 823 823 HOH HOH . C 3 HOH A 124 824 824 HOH HOH . C 3 HOH A 125 825 825 HOH HOH . C 3 HOH A 126 826 826 HOH HOH . C 3 HOH A 127 827 827 HOH HOH . C 3 HOH A 128 828 828 HOH HOH . C 3 HOH A 129 829 829 HOH HOH . C 3 HOH A 130 830 830 HOH HOH . C 3 HOH A 131 831 831 HOH HOH . C 3 HOH A 132 832 832 HOH HOH . C 3 HOH A 133 833 833 HOH HOH . C 3 HOH A 134 834 834 HOH HOH . C 3 HOH A 135 835 835 HOH HOH . C 3 HOH A 136 836 836 HOH HOH . C 3 HOH A 137 837 837 HOH HOH . C 3 HOH A 138 838 838 HOH HOH . C 3 HOH A 139 839 839 HOH HOH . C 3 HOH A 140 840 840 HOH HOH . C 3 HOH A 141 841 841 HOH HOH . C 3 HOH A 142 842 842 HOH HOH . C 3 HOH A 143 843 843 HOH HOH . C 3 HOH A 144 844 844 HOH HOH . C 3 HOH A 145 845 845 HOH HOH . C 3 HOH A 146 846 846 HOH HOH . C 3 HOH A 147 847 847 HOH HOH . C 3 HOH A 148 848 848 HOH HOH . C 3 HOH A 149 849 849 HOH HOH . C 3 HOH A 150 850 850 HOH HOH . C 3 HOH A 151 851 851 HOH HOH . C 3 HOH A 152 852 852 HOH HOH . C 3 HOH A 153 853 853 HOH HOH . C 3 HOH A 154 854 854 HOH HOH . C 3 HOH A 155 855 855 HOH HOH . C 3 HOH A 156 856 856 HOH HOH . C 3 HOH A 157 857 857 HOH HOH . C 3 HOH A 158 858 858 HOH HOH . C 3 HOH A 159 859 859 HOH HOH . C 3 HOH A 160 860 860 HOH HOH . C 3 HOH A 161 861 861 HOH HOH . C 3 HOH A 162 862 862 HOH HOH . C 3 HOH A 163 863 863 HOH HOH . C 3 HOH A 164 864 864 HOH HOH . C 3 HOH A 165 865 865 HOH HOH . C 3 HOH A 166 866 866 HOH HOH . C 3 HOH A 167 867 867 HOH HOH . C 3 HOH A 168 868 868 HOH HOH . C 3 HOH A 169 869 869 HOH HOH . C 3 HOH A 170 870 870 HOH HOH . C 3 HOH A 171 871 871 HOH HOH . C 3 HOH A 172 872 872 HOH HOH . C 3 HOH A 173 873 873 HOH HOH . C 3 HOH A 174 874 874 HOH HOH . C 3 HOH A 175 875 875 HOH HOH . C 3 HOH A 176 876 876 HOH HOH . C 3 HOH A 177 877 877 HOH HOH . C 3 HOH A 178 878 878 HOH HOH . C 3 HOH A 179 879 879 HOH HOH . C 3 HOH A 180 880 880 HOH HOH . C 3 HOH A 181 881 881 HOH HOH . C 3 HOH A 182 882 882 HOH HOH . C 3 HOH A 183 883 883 HOH HOH . C 3 HOH A 184 884 884 HOH HOH . C 3 HOH A 185 885 885 HOH HOH . C 3 HOH A 186 886 886 HOH HOH . C 3 HOH A 187 887 887 HOH HOH . C 3 HOH A 188 888 888 HOH HOH . C 3 HOH A 189 889 889 HOH HOH . C 3 HOH A 190 890 890 HOH HOH . C 3 HOH A 191 891 891 HOH HOH . C 3 HOH A 192 892 892 HOH HOH . C 3 HOH A 193 893 893 HOH HOH . C 3 HOH A 194 894 894 HOH HOH . C 3 HOH A 195 895 895 HOH HOH . C 3 HOH A 196 896 896 HOH HOH . C 3 HOH A 197 897 897 HOH HOH . C 3 HOH A 198 898 898 HOH HOH . C 3 HOH A 199 899 899 HOH HOH . C 3 HOH A 200 900 900 HOH HOH . C 3 HOH A 201 901 901 HOH HOH . C 3 HOH A 202 902 902 HOH HOH . C 3 HOH A 203 903 903 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 N SAM . . . B 2 -4.645 12.855 23.965 1 13.48 ? N SAM 400 A 1 HETATM 2 C CA SAM . . . B 2 -4.748 11.817 24.989 1 14.22 ? CA SAM 400 A 1 HETATM 3 C C SAM . . . B 2 -5.105 12.418 26.348 1 16.31 ? C SAM 400 A 1 HETATM 4 O O SAM . . . B 2 -5.759 13.488 26.334 1 15.15 ? O SAM 400 A 1 HETATM 5 O OXT SAM . . . B 2 -5.044 11.666 27.358 1 14.61 ? OXT SAM 400 A 1 HETATM 6 C CB SAM . . . B 2 -3.448 10.999 25.076 1 10.97 ? CB SAM 400 A 1 HETATM 7 C CG SAM . . . B 2 -3.098 10.295 23.765 1 13.84 ? CG SAM 400 A 1 HETATM 8 S SD SAM . . . B 2 -1.735 9.087 23.786 1 17.42 ? SD SAM 400 A 1 HETATM 9 C CE SAM . . . B 2 -0.349 10.135 23.775 1 17.47 ? CE SAM 400 A 1 HETATM 10 C C5' SAM . . . B 2 -1.778 8.584 22.079 1 13.74 ? C5' SAM 400 A 1 HETATM 11 C C4' SAM . . . B 2 -2.997 7.832 21.791 1 15.88 ? C4' SAM 400 A 1 HETATM 12 O O4' SAM . . . B 2 -3.178 7.761 20.384 1 15.93 ? O4' SAM 400 A 1 HETATM 13 C C3' SAM . . . B 2 -3.223 6.454 22.486 1 20.46 ? C3' SAM 400 A 1 HETATM 14 O O3' SAM . . . B 2 -4.428 6.421 23.33 1 20.19 ? O3' SAM 400 A 1 HETATM 15 C C2' SAM . . . B 2 -3.468 5.574 21.243 1 19.57 ? C2' SAM 400 A 1 HETATM 16 O O2' SAM . . . B 2 -4.398 4.482 21.429 1 19.58 ? O2' SAM 400 A 1 HETATM 17 C C1' SAM . . . B 2 -3.969 6.589 20.231 1 17.88 ? C1' SAM 400 A 1 HETATM 18 N N9 SAM . . . B 2 -3.892 6.115 18.877 1 20.29 ? N9 SAM 400 A 1 HETATM 19 C C8 SAM . . . B 2 -2.806 5.519 18.201 1 20.57 ? C8 SAM 400 A 1 HETATM 20 N N7 SAM . . . B 2 -3.045 5.328 16.95 1 19.88 ? N7 SAM 400 A 1 HETATM 21 C C5 SAM . . . B 2 -4.415 5.68 16.816 1 23.9 ? C5 SAM 400 A 1 HETATM 22 C C6 SAM . . . B 2 -5.336 5.66 15.734 1 25.61 ? C6 SAM 400 A 1 HETATM 23 N N6 SAM . . . B 2 -5.029 5.267 14.492 1 23.26 ? N6 SAM 400 A 1 HETATM 24 N N1 SAM . . . B 2 -6.633 6.006 16.002 1 26.87 ? N1 SAM 400 A 1 HETATM 25 C C2 SAM . . . B 2 -6.95 6.532 17.175 1 21.91 ? C2 SAM 400 A 1 HETATM 26 N N3 SAM . . . B 2 -6.161 6.628 18.229 1 22.47 ? N3 SAM 400 A 1 HETATM 27 C C4 SAM . . . B 2 -4.933 6.112 18.01 1 20.5 ? C4 SAM 400 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #