data_410D # _model_server_result.job_id Pa9JihsdOfOOdNaywZyZzQ _model_server_result.datetime_utc '2025-07-06 11:44:05' _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 410d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":21}' # _entry.id 410D # _exptl.entry_id 410D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _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 90 _cell.angle_gamma 90 _cell.entry_id 410D _cell.length_a 24.62 _cell.length_b 44.08 _cell.length_c 46.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 410D _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 O3' DA 5 A DA 5 1_555 A P T38 6 A T38 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? covale ? covale2 A O3' T38 6 A T38 6 1_555 A P DA 7 A DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale3 B O3' DA 5 B DA 15 1_555 B P T38 6 B T38 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale4 B O3' T38 6 B T38 16 1_555 B P DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? hydrog WATSON-CRICK hydrog1 A N1 DG 1 A DG 1 1_555 B N3 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 A DG 1 1_555 B O2 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 A DG 1 1_555 B N4 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 3 A DG 3 1_555 B N3 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DT 4 A DT 4 1_555 B N1 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O4 DT 4 A DT 4 1_555 B N6 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 5 A DA 5 1_555 B N3 T38 6 B T38 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 5 A DA 5 1_555 B O4 T38 6 B T38 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 T38 6 A T38 6 1_555 B N1 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 T38 6 A T38 6 1_555 B N6 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DA 7 A DA 7 1_555 B N3 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N6 DA 7 A DA 7 1_555 B O4 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DC 8 A DC 8 1_555 B N1 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 DC 8 A DC 8 1_555 B O6 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 DC 8 A DC 8 1_555 B N2 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DG 9 A DG 9 1_555 B N3 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N2 DG 9 A DG 9 1_555 B O2 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O6 DG 9 A DG 9 1_555 B N4 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N3 DC 10 A DC 10 1_555 B N1 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N4 DC 10 A DC 10 1_555 B O6 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O2 DC 10 A DC 10 1_555 B N2 DG 1 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _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 N1 C2 SPM sing 152 n n N1 HN11 SPM sing 153 n n N1 HN12 SPM sing 154 n n C2 C3 SPM sing 155 n n C2 H21 SPM sing 156 n n C2 H22 SPM sing 157 n n C3 C4 SPM sing 158 n n C3 H31 SPM sing 159 n n C3 H32 SPM sing 160 n n C4 N5 SPM sing 161 n n C4 H41 SPM sing 162 n n C4 H42 SPM sing 163 n n N5 C6 SPM sing 164 n n N5 HN5 SPM sing 165 n n C6 C7 SPM sing 166 n n C6 H61 SPM sing 167 n n C6 H62 SPM sing 168 n n C7 C8 SPM sing 169 n n C7 H71 SPM sing 170 n n C7 H72 SPM sing 171 n n C8 C9 SPM sing 172 n n C8 H81 SPM sing 173 n n C8 H82 SPM sing 174 n n C9 N10 SPM sing 175 n n C9 H91 SPM sing 176 n n C9 H92 SPM sing 177 n n N10 C11 SPM sing 178 n n N10 HN0 SPM sing 179 n n C11 C12 SPM sing 180 n n C11 H111 SPM sing 181 n n C11 H112 SPM sing 182 n n C12 C13 SPM sing 183 n n C12 H121 SPM sing 184 n n C12 H122 SPM sing 185 n n C13 N14 SPM sing 186 n n C13 H131 SPM sing 187 n n C13 H132 SPM sing 188 n n N14 HN41 SPM sing 189 n n N14 HN42 SPM sing 190 n n # _atom_sites.entry_id 410D _atom_sites.fract_transf_matrix[1][1] 0.040617 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022686 _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] 0.021654 _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 SPM B 1 21 21 SPM SPM . D 3 HOH A 1 101 101 HOH HOH . D 3 HOH A 2 102 102 HOH HOH . D 3 HOH A 3 103 103 HOH HOH . D 3 HOH A 4 104 104 HOH HOH . D 3 HOH A 5 106 106 HOH HOH . D 3 HOH A 6 108 108 HOH HOH . D 3 HOH A 7 109 109 HOH HOH . D 3 HOH A 8 111 111 HOH HOH . D 3 HOH A 9 113 113 HOH HOH . D 3 HOH A 10 117 117 HOH HOH . D 3 HOH A 11 118 118 HOH HOH . D 3 HOH A 12 120 120 HOH HOH . D 3 HOH A 13 123 123 HOH HOH . D 3 HOH A 14 125 125 HOH HOH . D 3 HOH A 15 126 126 HOH HOH . D 3 HOH A 16 130 130 HOH HOH . D 3 HOH A 17 131 131 HOH HOH . D 3 HOH A 18 132 132 HOH HOH . D 3 HOH A 19 135 135 HOH HOH . D 3 HOH A 20 136 136 HOH HOH . D 3 HOH A 21 137 137 HOH HOH . D 3 HOH A 22 138 138 HOH HOH . D 3 HOH A 23 141 141 HOH HOH . D 3 HOH A 24 142 142 HOH HOH . D 3 HOH A 25 143 143 HOH HOH . D 3 HOH A 26 145 145 HOH HOH . D 3 HOH A 27 147 147 HOH HOH . D 3 HOH A 28 149 149 HOH HOH . D 3 HOH A 29 152 152 HOH HOH . D 3 HOH A 30 153 153 HOH HOH . D 3 HOH A 31 155 155 HOH HOH . D 3 HOH A 32 156 156 HOH HOH . D 3 HOH A 33 157 157 HOH HOH . D 3 HOH A 34 158 158 HOH HOH . D 3 HOH A 35 160 160 HOH HOH . D 3 HOH A 36 161 161 HOH HOH . D 3 HOH A 37 162 162 HOH HOH . D 3 HOH A 38 163 163 HOH HOH . D 3 HOH A 39 165 165 HOH HOH . D 3 HOH A 40 169 169 HOH HOH . D 3 HOH A 41 173 173 HOH HOH . D 3 HOH A 42 178 178 HOH HOH . D 3 HOH A 43 179 179 HOH HOH . D 3 HOH A 44 182 182 HOH HOH . D 3 HOH A 45 184 184 HOH HOH . D 3 HOH A 46 186 186 HOH HOH . D 3 HOH A 47 188 188 HOH HOH . D 3 HOH A 48 190 190 HOH HOH . D 3 HOH A 49 192 192 HOH HOH . D 3 HOH A 50 193 193 HOH HOH . D 3 HOH A 51 197 197 HOH HOH . D 3 HOH A 52 201 201 HOH HOH . D 3 HOH A 53 204 204 HOH HOH . D 3 HOH A 54 205 205 HOH HOH . D 3 HOH A 55 206 206 HOH HOH . D 3 HOH A 56 207 207 HOH HOH . D 3 HOH A 57 209 209 HOH HOH . D 3 HOH A 58 210 210 HOH HOH . D 3 HOH A 59 212 212 HOH HOH . D 3 HOH A 60 214 214 HOH HOH . D 3 HOH A 61 215 215 HOH HOH . D 3 HOH A 62 216 216 HOH HOH . D 3 HOH A 63 218 218 HOH HOH . D 3 HOH A 64 220 220 HOH HOH . D 3 HOH A 65 221 221 HOH HOH . D 3 HOH A 66 222 222 HOH HOH . D 3 HOH A 67 224 224 HOH HOH . D 3 HOH A 68 226 226 HOH HOH . D 3 HOH A 69 229 229 HOH HOH . D 3 HOH A 70 232 232 HOH HOH . D 3 HOH A 71 235 235 HOH HOH . D 3 HOH A 72 236 236 HOH HOH . E 3 HOH B 1 105 105 HOH HOH . E 3 HOH B 2 107 107 HOH HOH . E 3 HOH B 3 110 110 HOH HOH . E 3 HOH B 4 112 112 HOH HOH . E 3 HOH B 5 114 114 HOH HOH . E 3 HOH B 6 115 115 HOH HOH . E 3 HOH B 7 116 116 HOH HOH . E 3 HOH B 8 119 119 HOH HOH . E 3 HOH B 9 121 121 HOH HOH . E 3 HOH B 10 122 122 HOH HOH . E 3 HOH B 11 124 124 HOH HOH . E 3 HOH B 12 127 127 HOH HOH . E 3 HOH B 13 128 128 HOH HOH . E 3 HOH B 14 129 129 HOH HOH . E 3 HOH B 15 133 133 HOH HOH . E 3 HOH B 16 134 134 HOH HOH . E 3 HOH B 17 139 139 HOH HOH . E 3 HOH B 18 140 140 HOH HOH . E 3 HOH B 19 144 144 HOH HOH . E 3 HOH B 20 146 146 HOH HOH . E 3 HOH B 21 148 148 HOH HOH . E 3 HOH B 22 150 150 HOH HOH . E 3 HOH B 23 151 151 HOH HOH . E 3 HOH B 24 154 154 HOH HOH . E 3 HOH B 25 159 159 HOH HOH . E 3 HOH B 26 164 164 HOH HOH . E 3 HOH B 27 166 166 HOH HOH . E 3 HOH B 28 167 167 HOH HOH . E 3 HOH B 29 168 168 HOH HOH . E 3 HOH B 30 170 170 HOH HOH . E 3 HOH B 31 171 171 HOH HOH . E 3 HOH B 32 172 172 HOH HOH . E 3 HOH B 33 174 174 HOH HOH . E 3 HOH B 34 175 175 HOH HOH . E 3 HOH B 35 176 176 HOH HOH . E 3 HOH B 36 177 177 HOH HOH . E 3 HOH B 37 180 180 HOH HOH . E 3 HOH B 38 181 181 HOH HOH . E 3 HOH B 39 183 183 HOH HOH . E 3 HOH B 40 185 185 HOH HOH . E 3 HOH B 41 187 187 HOH HOH . E 3 HOH B 42 189 189 HOH HOH . E 3 HOH B 43 191 191 HOH HOH . E 3 HOH B 44 194 194 HOH HOH . E 3 HOH B 45 195 195 HOH HOH . E 3 HOH B 46 196 196 HOH HOH . E 3 HOH B 47 198 198 HOH HOH . E 3 HOH B 48 199 199 HOH HOH . E 3 HOH B 49 200 200 HOH HOH . E 3 HOH B 50 202 202 HOH HOH . E 3 HOH B 51 203 203 HOH HOH . E 3 HOH B 52 208 208 HOH HOH . E 3 HOH B 53 211 211 HOH HOH . E 3 HOH B 54 213 213 HOH HOH . E 3 HOH B 55 217 217 HOH HOH . E 3 HOH B 56 219 219 HOH HOH . E 3 HOH B 57 223 223 HOH HOH . E 3 HOH B 58 225 225 HOH HOH . E 3 HOH B 59 227 227 HOH HOH . E 3 HOH B 60 228 228 HOH HOH . E 3 HOH B 61 230 230 HOH HOH . E 3 HOH B 62 231 231 HOH HOH . E 3 HOH B 63 233 233 HOH HOH . E 3 HOH B 64 234 234 HOH HOH . E 3 HOH B 65 237 237 HOH HOH . E 3 HOH B 66 238 238 HOH HOH . E 3 HOH B 67 239 239 HOH HOH . E 3 HOH B 68 240 240 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 SPM . . . C 2 -1.711 5.704 24.782 1 10.08 ? N1 SPM 21 B 1 HETATM 2 C C2 SPM . . . C 2 -2.602 4.506 24.936 1 11.59 ? C2 SPM 21 B 1 HETATM 3 C C3 SPM . . . C 2 -2.177 3.295 24.11 1 11.66 ? C3 SPM 21 B 1 HETATM 4 C C4 SPM . . . C 2 -3.106 2.145 24.32 1 13.41 ? C4 SPM 21 B 1 HETATM 5 N N5 SPM . . . C 2 -2.595 0.912 23.734 1 13.74 ? N5 SPM 21 B 1 HETATM 6 C C6 SPM . . . C 2 -3.652 -0.094 23.646 1 18.16 ? C6 SPM 21 B 1 HETATM 7 C C7 SPM . . . C 2 -3.139 -1.514 23.843 1 23.14 ? C7 SPM 21 B 1 HETATM 8 C C8 SPM . . . C 2 -1.933 -1.768 22.936 1 26.55 ? C8 SPM 21 B 1 HETATM 9 C C9 SPM . . . C 2 -1.592 -3.26 22.83 1 30.41 ? C9 SPM 21 B 1 HETATM 10 N N10 SPM . . . C 2 -0.47 -3.554 21.937 1 33.48 ? N10 SPM 21 B 1 HETATM 11 C C11 SPM . . . C 2 -0.768 -4.834 21.283 1 35.11 ? C11 SPM 21 B 1 HETATM 12 C C12 SPM . . . C 2 0.504 -5.667 20.871 1 35.91 ? C12 SPM 21 B 1 HETATM 13 C C13 SPM . . . C 2 -0.103 -7.035 20.511 1 36.92 ? C13 SPM 21 B 1 HETATM 14 N N14 SPM . . . C 2 0.823 -8.095 19.979 1 35.91 ? N14 SPM 21 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #