data_3BNM # _model_server_result.job_id o2rKUpsw-EjL4XlN9811bw _model_server_result.datetime_utc '2025-01-25 15:28:54' _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 3bnm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":802}' # _entry.id 3BNM # _exptl.entry_id 3BNM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.393 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(3R,3'R)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine" _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 94.9 _cell.angle_gamma 90 _cell.entry_id 3BNM _cell.length_a 162.237 _cell.length_b 103.969 _cell.length_c 77.583 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BNM _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 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 disulf ? disulf1 A SG CYS 221 B CYS 221 1_555 A SG CYS 238 B CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 221 A CYS 221 1_555 B SG CYS 238 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _chem_comp.formula 'C12 H30 N4' _chem_comp.formula_weight 230.393 _chem_comp.id SPJ _chem_comp.mon_nstd_flag . _chem_comp.name "(3R,3'R)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "bis-(3R,3'R)-methyl spermine" # 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 N1B C1C SPJ sing 381 n n C1C C1A SPJ sing 382 n n C1C C1D SPJ sing 383 n n C1D C1E SPJ sing 384 n n C1E N1F SPJ sing 385 n n N1F C1G SPJ sing 386 n n C1G C1H SPJ sing 387 n n C1H C1I SPJ sing 388 n n C1I C1J SPJ sing 389 n n C1J N1K SPJ sing 390 n n N1K C1L SPJ sing 391 n n C1L C1M SPJ sing 392 n n C1M C1N SPJ sing 393 n n C1N C1P SPJ sing 394 n n C1N N1O SPJ sing 395 n n N1B HN1B SPJ sing 396 n n N1B HN1A SPJ sing 397 n n C1C H1C SPJ sing 398 n n C1A H1A SPJ sing 399 n n C1A H1AA SPJ sing 400 n n C1A H1AB SPJ sing 401 n n C1D H1D SPJ sing 402 n n C1D H1DA SPJ sing 403 n n C1E H1E SPJ sing 404 n n C1E H1EA SPJ sing 405 n n N1F HN1F SPJ sing 406 n n C1G H1G SPJ sing 407 n n C1G H1GA SPJ sing 408 n n C1H H1H SPJ sing 409 n n C1H H1HA SPJ sing 410 n n C1I H1I SPJ sing 411 n n C1I H1IA SPJ sing 412 n n C1J H1J SPJ sing 413 n n C1J H1JA SPJ sing 414 n n N1K HN1K SPJ sing 415 n n C1L H1L SPJ sing 416 n n C1L H1LA SPJ sing 417 n n C1M H1M SPJ sing 418 n n C1M H1MA SPJ sing 419 n n C1N H1N SPJ sing 420 n n C1P H1P SPJ sing 421 n n C1P H1PA SPJ sing 422 n n C1P H1PB SPJ sing 423 n n N1O HN1O SPJ sing 424 n n N1O HN1C SPJ sing 425 n n # _atom_sites.entry_id 3BNM _atom_sites.fract_transf_matrix[1][1] 0.006164 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000528 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009618 _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] 0.012937 _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 FAD B 1 802 802 FAD FAD . D 3 SPJ B 1 803 2 SPJ SPJ . E 2 FAD A 1 801 801 FAD FAD . F 3 SPJ A 1 802 1 SPJ SPJ . G 4 HOH B 1 804 6 HOH HOH . G 4 HOH B 2 805 10 HOH HOH . G 4 HOH B 3 806 11 HOH HOH . G 4 HOH B 4 807 13 HOH HOH . G 4 HOH B 5 808 15 HOH HOH . G 4 HOH B 6 809 16 HOH HOH . G 4 HOH B 7 810 17 HOH HOH . G 4 HOH B 8 811 20 HOH HOH . G 4 HOH B 9 812 22 HOH HOH . G 4 HOH B 10 813 24 HOH HOH . G 4 HOH B 11 814 27 HOH HOH . G 4 HOH B 12 815 29 HOH HOH . G 4 HOH B 13 816 32 HOH HOH . G 4 HOH B 14 817 33 HOH HOH . G 4 HOH B 15 818 34 HOH HOH . G 4 HOH B 16 819 36 HOH HOH . G 4 HOH B 17 820 38 HOH HOH . G 4 HOH B 18 821 39 HOH HOH . G 4 HOH B 19 822 40 HOH HOH . G 4 HOH B 20 823 41 HOH HOH . G 4 HOH B 21 824 42 HOH HOH . G 4 HOH B 22 825 44 HOH HOH . G 4 HOH B 23 826 46 HOH HOH . G 4 HOH B 24 827 47 HOH HOH . G 4 HOH B 25 828 54 HOH HOH . G 4 HOH B 26 829 57 HOH HOH . G 4 HOH B 27 830 58 HOH HOH . G 4 HOH B 28 831 59 HOH HOH . G 4 HOH B 29 832 60 HOH HOH . G 4 HOH B 30 833 61 HOH HOH . G 4 HOH B 31 834 62 HOH HOH . G 4 HOH B 32 835 63 HOH HOH . G 4 HOH B 33 836 64 HOH HOH . G 4 HOH B 34 837 65 HOH HOH . G 4 HOH B 35 838 66 HOH HOH . G 4 HOH B 36 839 68 HOH HOH . G 4 HOH B 37 840 70 HOH HOH . G 4 HOH B 38 841 71 HOH HOH . G 4 HOH B 39 842 75 HOH HOH . G 4 HOH B 40 843 78 HOH HOH . G 4 HOH B 41 844 81 HOH HOH . G 4 HOH B 42 845 83 HOH HOH . G 4 HOH B 43 846 86 HOH HOH . G 4 HOH B 44 847 87 HOH HOH . G 4 HOH B 45 848 88 HOH HOH . G 4 HOH B 46 849 92 HOH HOH . G 4 HOH B 47 850 93 HOH HOH . G 4 HOH B 48 851 95 HOH HOH . G 4 HOH B 49 852 98 HOH HOH . G 4 HOH B 50 853 99 HOH HOH . G 4 HOH B 51 854 100 HOH HOH . G 4 HOH B 52 855 101 HOH HOH . G 4 HOH B 53 856 103 HOH HOH . G 4 HOH B 54 857 106 HOH HOH . G 4 HOH B 55 858 109 HOH HOH . G 4 HOH B 56 859 112 HOH HOH . G 4 HOH B 57 860 116 HOH HOH . G 4 HOH B 58 861 118 HOH HOH . G 4 HOH B 59 862 119 HOH HOH . G 4 HOH B 60 863 122 HOH HOH . G 4 HOH B 61 864 125 HOH HOH . G 4 HOH B 62 865 127 HOH HOH . G 4 HOH B 63 866 128 HOH HOH . G 4 HOH B 64 867 129 HOH HOH . G 4 HOH B 65 868 132 HOH HOH . G 4 HOH B 66 869 136 HOH HOH . G 4 HOH B 67 870 138 HOH HOH . G 4 HOH B 68 871 143 HOH HOH . G 4 HOH B 69 872 146 HOH HOH . G 4 HOH B 70 873 148 HOH HOH . G 4 HOH B 71 874 149 HOH HOH . G 4 HOH B 72 875 150 HOH HOH . G 4 HOH B 73 876 152 HOH HOH . G 4 HOH B 74 877 153 HOH HOH . G 4 HOH B 75 878 154 HOH HOH . G 4 HOH B 76 879 156 HOH HOH . G 4 HOH B 77 880 158 HOH HOH . G 4 HOH B 78 881 161 HOH HOH . G 4 HOH B 79 882 162 HOH HOH . G 4 HOH B 80 883 164 HOH HOH . G 4 HOH B 81 884 165 HOH HOH . G 4 HOH B 82 885 175 HOH HOH . G 4 HOH B 83 886 179 HOH HOH . G 4 HOH B 84 887 180 HOH HOH . G 4 HOH B 85 888 181 HOH HOH . G 4 HOH B 86 889 182 HOH HOH . G 4 HOH B 87 890 183 HOH HOH . G 4 HOH B 88 891 185 HOH HOH . G 4 HOH B 89 892 186 HOH HOH . G 4 HOH B 90 893 188 HOH HOH . G 4 HOH B 91 894 191 HOH HOH . G 4 HOH B 92 895 193 HOH HOH . G 4 HOH B 93 896 194 HOH HOH . G 4 HOH B 94 897 198 HOH HOH . G 4 HOH B 95 898 199 HOH HOH . G 4 HOH B 96 899 200 HOH HOH . G 4 HOH B 97 900 203 HOH HOH . G 4 HOH B 98 901 204 HOH HOH . G 4 HOH B 99 902 205 HOH HOH . G 4 HOH B 100 903 206 HOH HOH . G 4 HOH B 101 904 209 HOH HOH . G 4 HOH B 102 905 210 HOH HOH . G 4 HOH B 103 906 219 HOH HOH . G 4 HOH B 104 907 220 HOH HOH . H 4 HOH A 1 803 1 HOH HOH . H 4 HOH A 2 804 2 HOH HOH . H 4 HOH A 3 805 3 HOH HOH . H 4 HOH A 4 806 4 HOH HOH . H 4 HOH A 5 807 5 HOH HOH . H 4 HOH A 6 808 7 HOH HOH . H 4 HOH A 7 809 8 HOH HOH . H 4 HOH A 8 810 9 HOH HOH . H 4 HOH A 9 811 12 HOH HOH . H 4 HOH A 10 812 14 HOH HOH . H 4 HOH A 11 813 18 HOH HOH . H 4 HOH A 12 814 19 HOH HOH . H 4 HOH A 13 815 21 HOH HOH . H 4 HOH A 14 816 23 HOH HOH . H 4 HOH A 15 817 25 HOH HOH . H 4 HOH A 16 818 26 HOH HOH . H 4 HOH A 17 819 28 HOH HOH . H 4 HOH A 18 820 30 HOH HOH . H 4 HOH A 19 821 31 HOH HOH . H 4 HOH A 20 822 35 HOH HOH . H 4 HOH A 21 823 37 HOH HOH . H 4 HOH A 22 824 43 HOH HOH . H 4 HOH A 23 825 45 HOH HOH . H 4 HOH A 24 826 48 HOH HOH . H 4 HOH A 25 827 49 HOH HOH . H 4 HOH A 26 828 50 HOH HOH . H 4 HOH A 27 829 51 HOH HOH . H 4 HOH A 28 830 52 HOH HOH . H 4 HOH A 29 831 53 HOH HOH . H 4 HOH A 30 832 55 HOH HOH . H 4 HOH A 31 833 56 HOH HOH . H 4 HOH A 32 834 67 HOH HOH . H 4 HOH A 33 835 69 HOH HOH . H 4 HOH A 34 836 72 HOH HOH . H 4 HOH A 35 837 73 HOH HOH . H 4 HOH A 36 838 74 HOH HOH . H 4 HOH A 37 839 76 HOH HOH . H 4 HOH A 38 840 77 HOH HOH . H 4 HOH A 39 841 79 HOH HOH . H 4 HOH A 40 842 80 HOH HOH . H 4 HOH A 41 843 82 HOH HOH . H 4 HOH A 42 844 84 HOH HOH . H 4 HOH A 43 845 85 HOH HOH . H 4 HOH A 44 846 89 HOH HOH . H 4 HOH A 45 847 90 HOH HOH . H 4 HOH A 46 848 91 HOH HOH . H 4 HOH A 47 849 94 HOH HOH . H 4 HOH A 48 850 96 HOH HOH . H 4 HOH A 49 851 97 HOH HOH . H 4 HOH A 50 852 102 HOH HOH . H 4 HOH A 51 853 104 HOH HOH . H 4 HOH A 52 854 105 HOH HOH . H 4 HOH A 53 855 107 HOH HOH . H 4 HOH A 54 856 108 HOH HOH . H 4 HOH A 55 857 110 HOH HOH . H 4 HOH A 56 858 111 HOH HOH . H 4 HOH A 57 859 113 HOH HOH . H 4 HOH A 58 860 114 HOH HOH . H 4 HOH A 59 861 115 HOH HOH . H 4 HOH A 60 862 117 HOH HOH . H 4 HOH A 61 863 120 HOH HOH . H 4 HOH A 62 864 121 HOH HOH . H 4 HOH A 63 865 123 HOH HOH . H 4 HOH A 64 866 124 HOH HOH . H 4 HOH A 65 867 126 HOH HOH . H 4 HOH A 66 868 130 HOH HOH . H 4 HOH A 67 869 131 HOH HOH . H 4 HOH A 68 870 133 HOH HOH . H 4 HOH A 69 871 134 HOH HOH . H 4 HOH A 70 872 135 HOH HOH . H 4 HOH A 71 873 137 HOH HOH . H 4 HOH A 72 874 139 HOH HOH . H 4 HOH A 73 875 140 HOH HOH . H 4 HOH A 74 876 141 HOH HOH . H 4 HOH A 75 877 142 HOH HOH . H 4 HOH A 76 878 144 HOH HOH . H 4 HOH A 77 879 145 HOH HOH . H 4 HOH A 78 880 147 HOH HOH . H 4 HOH A 79 881 151 HOH HOH . H 4 HOH A 80 882 155 HOH HOH . H 4 HOH A 81 883 157 HOH HOH . H 4 HOH A 82 884 159 HOH HOH . H 4 HOH A 83 885 160 HOH HOH . H 4 HOH A 84 886 163 HOH HOH . H 4 HOH A 85 887 166 HOH HOH . H 4 HOH A 86 888 167 HOH HOH . H 4 HOH A 87 889 168 HOH HOH . H 4 HOH A 88 890 169 HOH HOH . H 4 HOH A 89 891 170 HOH HOH . H 4 HOH A 90 892 171 HOH HOH . H 4 HOH A 91 893 172 HOH HOH . H 4 HOH A 92 894 173 HOH HOH . H 4 HOH A 93 895 174 HOH HOH . H 4 HOH A 94 896 176 HOH HOH . H 4 HOH A 95 897 177 HOH HOH . H 4 HOH A 96 898 178 HOH HOH . H 4 HOH A 97 899 184 HOH HOH . H 4 HOH A 98 900 187 HOH HOH . H 4 HOH A 99 901 189 HOH HOH . H 4 HOH A 100 902 190 HOH HOH . H 4 HOH A 101 903 192 HOH HOH . H 4 HOH A 102 904 195 HOH HOH . H 4 HOH A 103 905 196 HOH HOH . H 4 HOH A 104 906 197 HOH HOH . H 4 HOH A 105 907 201 HOH HOH . H 4 HOH A 106 908 202 HOH HOH . H 4 HOH A 107 909 207 HOH HOH . H 4 HOH A 108 910 208 HOH HOH . H 4 HOH A 109 911 211 HOH HOH . H 4 HOH A 110 912 212 HOH HOH . H 4 HOH A 111 913 213 HOH HOH . H 4 HOH A 112 914 214 HOH HOH . H 4 HOH A 113 915 215 HOH HOH . H 4 HOH A 114 916 216 HOH HOH . H 4 HOH A 115 917 217 HOH HOH . H 4 HOH A 116 918 218 HOH HOH . H 4 HOH A 117 919 221 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 N1B SPJ . . . F 3 97.534 38.02 55.619 1 59.96 ? N1B SPJ 802 A 1 HETATM 2 C C1C SPJ . . . F 3 96.398 37.118 55.854 1 61.12 ? C1C SPJ 802 A 1 HETATM 3 C C1A SPJ . . . F 3 96.699 36.244 57.073 1 60.52 ? C1A SPJ 802 A 1 HETATM 4 C C1D SPJ . . . F 3 96.17 36.255 54.61 1 61.69 ? C1D SPJ 802 A 1 HETATM 5 C C1E SPJ . . . F 3 94.923 35.38 54.756 1 62.11 ? C1E SPJ 802 A 1 HETATM 6 N N1F SPJ . . . F 3 94.801 34.49 53.592 1 61.43 ? N1F SPJ 802 A 1 HETATM 7 C C1G SPJ . . . F 3 95.945 33.567 53.574 1 59.75 ? C1G SPJ 802 A 1 HETATM 8 C C1H SPJ . . . F 3 95.921 32.705 52.31 1 57.91 ? C1H SPJ 802 A 1 HETATM 9 C C1I SPJ . . . F 3 97.198 31.866 52.233 1 59.29 ? C1I SPJ 802 A 1 HETATM 10 C C1J SPJ . . . F 3 97.255 31.028 50.954 1 59.82 ? C1J SPJ 802 A 1 HETATM 11 N N1K SPJ . . . F 3 98.563 30.36 50.873 1 60.27 ? N1K SPJ 802 A 1 HETATM 12 C C1L SPJ . . . F 3 98.414 28.906 51.027 1 59.68 ? C1L SPJ 802 A 1 HETATM 13 C C1M SPJ . . . F 3 98.045 28.556 52.47 1 57.39 ? C1M SPJ 802 A 1 HETATM 14 C C1N SPJ . . . F 3 97.79 27.054 52.615 1 56.87 ? C1N SPJ 802 A 1 HETATM 15 C C1P SPJ . . . F 3 99.029 26.242 52.232 1 56.67 ? C1P SPJ 802 A 1 HETATM 16 N N1O SPJ . . . F 3 97.417 26.749 54.004 1 55.26 ? N1O SPJ 802 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #