data_1YB9 # _model_server_result.job_id wwUC0lnAzUjq8YPCIeZyKA _model_server_result.datetime_utc '2025-03-06 06:32:16' _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 1yb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":100}' # _entry.id 1YB9 # _exptl.entry_id 1YB9 _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 1YB9 _cell.length_a 24.84 _cell.length_b 44.64 _cell.length_c 45.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YB9 _symmetry.cell_setting ? _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 2OT 6 A 2OT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale2 A O3' 2OT 6 A 2OT 6 1_555 A P DA 7 A DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale3 B O3' DA 5 B DA 15 1_555 B P 2OT 6 B 2OT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale4 B O3' 2OT 6 B 2OT 16 1_555 B P DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? 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 2OT 6 B 2OT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 5 A DA 5 1_555 B O4 2OT 6 B 2OT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 2OT 6 A 2OT 6 1_555 B N1 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 2OT 6 A 2OT 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 205 n n N1 HN11 SPM sing 206 n n N1 HN12 SPM sing 207 n n C2 C3 SPM sing 208 n n C2 H21 SPM sing 209 n n C2 H22 SPM sing 210 n n C3 C4 SPM sing 211 n n C3 H31 SPM sing 212 n n C3 H32 SPM sing 213 n n C4 N5 SPM sing 214 n n C4 H41 SPM sing 215 n n C4 H42 SPM sing 216 n n N5 C6 SPM sing 217 n n N5 HN5 SPM sing 218 n n C6 C7 SPM sing 219 n n C6 H61 SPM sing 220 n n C6 H62 SPM sing 221 n n C7 C8 SPM sing 222 n n C7 H71 SPM sing 223 n n C7 H72 SPM sing 224 n n C8 C9 SPM sing 225 n n C8 H81 SPM sing 226 n n C8 H82 SPM sing 227 n n C9 N10 SPM sing 228 n n C9 H91 SPM sing 229 n n C9 H92 SPM sing 230 n n N10 C11 SPM sing 231 n n N10 HN0 SPM sing 232 n n C11 C12 SPM sing 233 n n C11 H111 SPM sing 234 n n C11 H112 SPM sing 235 n n C12 C13 SPM sing 236 n n C12 H121 SPM sing 237 n n C12 H122 SPM sing 238 n n C13 N14 SPM sing 239 n n C13 H131 SPM sing 240 n n C13 H132 SPM sing 241 n n N14 HN41 SPM sing 242 n n N14 HN42 SPM sing 243 n n # _atom_sites.entry_id 1YB9 _atom_sites.fract_transf_matrix[1][1] 0.040258 _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] 0.022401 _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] 0.022134 _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 1 100 100 SPM SPM . D 3 HOH A 1 101 101 HOH HOH . D 3 HOH A 2 102 102 HOH HOH . D 3 HOH A 3 104 104 HOH HOH . D 3 HOH A 4 107 107 HOH HOH . D 3 HOH A 5 109 109 HOH HOH . D 3 HOH A 6 110 110 HOH HOH . D 3 HOH A 7 111 111 HOH HOH . D 3 HOH A 8 116 116 HOH HOH . D 3 HOH A 9 117 117 HOH HOH . D 3 HOH A 10 118 118 HOH HOH . D 3 HOH A 11 119 119 HOH HOH . D 3 HOH A 12 121 121 HOH HOH . D 3 HOH A 13 123 123 HOH HOH . D 3 HOH A 14 125 125 HOH HOH . D 3 HOH A 15 128 128 HOH HOH . D 3 HOH A 16 132 132 HOH HOH . D 3 HOH A 17 133 133 HOH HOH . D 3 HOH A 18 134 134 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 22 139 139 HOH HOH . D 3 HOH A 23 141 141 HOH HOH . D 3 HOH A 24 142 142 HOH HOH . D 3 HOH A 25 145 145 HOH HOH . D 3 HOH A 26 146 146 HOH HOH . D 3 HOH A 27 147 147 HOH HOH . D 3 HOH A 28 149 149 HOH HOH . D 3 HOH A 29 151 151 HOH HOH . D 3 HOH A 30 152 152 HOH HOH . D 3 HOH A 31 157 157 HOH HOH . D 3 HOH A 32 158 158 HOH HOH . D 3 HOH A 33 160 160 HOH HOH . D 3 HOH A 34 164 164 HOH HOH . D 3 HOH A 35 167 167 HOH HOH . D 3 HOH A 36 168 168 HOH HOH . D 3 HOH A 37 172 172 HOH HOH . D 3 HOH A 38 173 173 HOH HOH . D 3 HOH A 39 174 174 HOH HOH . D 3 HOH A 40 176 176 HOH HOH . D 3 HOH A 41 177 177 HOH HOH . D 3 HOH A 42 178 178 HOH HOH . D 3 HOH A 43 180 180 HOH HOH . D 3 HOH A 44 183 183 HOH HOH . D 3 HOH A 45 185 185 HOH HOH . D 3 HOH A 46 186 186 HOH HOH . D 3 HOH A 47 189 189 HOH HOH . D 3 HOH A 48 190 190 HOH HOH . D 3 HOH A 49 194 194 HOH HOH . D 3 HOH A 50 196 196 HOH HOH . D 3 HOH A 51 197 197 HOH HOH . D 3 HOH A 52 198 198 HOH HOH . D 3 HOH A 53 201 201 HOH HOH . D 3 HOH A 54 204 204 HOH HOH . D 3 HOH A 55 205 205 HOH HOH . D 3 HOH A 56 207 207 HOH HOH . D 3 HOH A 57 208 208 HOH HOH . D 3 HOH A 58 209 209 HOH HOH . D 3 HOH A 59 211 211 HOH HOH . D 3 HOH A 60 212 212 HOH HOH . D 3 HOH A 61 215 215 HOH HOH . D 3 HOH A 62 216 216 HOH HOH . D 3 HOH A 63 217 217 HOH HOH . D 3 HOH A 64 218 218 HOH HOH . D 3 HOH A 65 221 221 HOH HOH . D 3 HOH A 66 223 223 HOH HOH . D 3 HOH A 67 224 224 HOH HOH . E 3 HOH B 1 103 103 HOH HOH . E 3 HOH B 2 105 105 HOH HOH . E 3 HOH B 3 106 106 HOH HOH . E 3 HOH B 4 108 108 HOH HOH . E 3 HOH B 5 112 112 HOH HOH . E 3 HOH B 6 113 113 HOH HOH . E 3 HOH B 7 114 114 HOH HOH . E 3 HOH B 8 115 115 HOH HOH . E 3 HOH B 9 120 120 HOH HOH . E 3 HOH B 10 122 122 HOH HOH . E 3 HOH B 11 124 124 HOH HOH . E 3 HOH B 12 126 126 HOH HOH . E 3 HOH B 13 127 127 HOH HOH . E 3 HOH B 14 129 129 HOH HOH . E 3 HOH B 15 130 130 HOH HOH . E 3 HOH B 16 131 131 HOH HOH . E 3 HOH B 17 138 138 HOH HOH . E 3 HOH B 18 140 140 HOH HOH . E 3 HOH B 19 143 143 HOH HOH . E 3 HOH B 20 144 144 HOH HOH . E 3 HOH B 21 148 148 HOH HOH . E 3 HOH B 22 150 150 HOH HOH . E 3 HOH B 23 153 153 HOH HOH . E 3 HOH B 24 154 154 HOH HOH . E 3 HOH B 25 155 155 HOH HOH . E 3 HOH B 26 156 156 HOH HOH . E 3 HOH B 27 159 159 HOH HOH . E 3 HOH B 28 161 161 HOH HOH . E 3 HOH B 29 162 162 HOH HOH . E 3 HOH B 30 163 163 HOH HOH . E 3 HOH B 31 165 165 HOH HOH . E 3 HOH B 32 166 166 HOH HOH . E 3 HOH B 33 169 169 HOH HOH . E 3 HOH B 34 170 170 HOH HOH . E 3 HOH B 35 171 171 HOH HOH . E 3 HOH B 36 175 175 HOH HOH . E 3 HOH B 37 179 179 HOH HOH . E 3 HOH B 38 181 181 HOH HOH . E 3 HOH B 39 182 182 HOH HOH . E 3 HOH B 40 184 184 HOH HOH . E 3 HOH B 41 187 187 HOH HOH . E 3 HOH B 42 188 188 HOH HOH . E 3 HOH B 43 191 191 HOH HOH . E 3 HOH B 44 192 192 HOH HOH . E 3 HOH B 45 193 193 HOH HOH . E 3 HOH B 46 195 195 HOH HOH . E 3 HOH B 47 199 199 HOH HOH . E 3 HOH B 48 200 200 HOH HOH . E 3 HOH B 49 202 202 HOH HOH . E 3 HOH B 50 203 203 HOH HOH . E 3 HOH B 51 206 206 HOH HOH . E 3 HOH B 52 210 210 HOH HOH . E 3 HOH B 53 213 213 HOH HOH . E 3 HOH B 54 214 214 HOH HOH . E 3 HOH B 55 219 219 HOH HOH . E 3 HOH B 56 220 220 HOH HOH . E 3 HOH B 57 222 222 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 14.509 10.491 11.463 1 26.83 ? N1 SPM 100 B 1 HETATM 2 C C2 SPM . . . C 2 15.776 10.548 12.29 1 30.21 ? C2 SPM 100 B 1 HETATM 3 C C3 SPM . . . C 2 15.727 9.579 13.468 1 30.22 ? C3 SPM 100 B 1 HETATM 4 C C4 SPM . . . C 2 16.346 10.182 14.727 1 30.51 ? C4 SPM 100 B 1 HETATM 5 N N5 SPM . . . C 2 16.108 9.344 15.901 1 30.97 ? N5 SPM 100 B 1 HETATM 6 C C6 SPM . . . C 2 17.174 9.527 16.888 1 30.97 ? C6 SPM 100 B 1 HETATM 7 C C7 SPM . . . C 2 16.666 10.049 18.236 1 32.61 ? C7 SPM 100 B 1 HETATM 8 C C8 SPM . . . C 2 16.125 11.477 18.177 1 28.17 ? C8 SPM 100 B 1 HETATM 9 C C9 SPM . . . C 2 14.72 11.551 17.562 1 29.57 ? C9 SPM 100 B 1 HETATM 10 N N10 SPM . . . C 2 14.056 12.838 17.819 1 25.85 ? N10 SPM 100 B 1 HETATM 11 C C11 SPM . A . C 2 13.444 13.315 16.578 0.5 27.2 ? C11 SPM 100 B 1 HETATM 12 C C11 SPM . B . C 2 13.81 12.983 19.25 0.5 23.9 ? C11 SPM 100 B 1 HETATM 13 C C12 SPM . A . C 2 14.417 13.294 15.403 0.5 27.33 ? C12 SPM 100 B 1 HETATM 14 C C12 SPM . B . C 2 14.023 14.4 19.77 0.5 24.27 ? C12 SPM 100 B 1 HETATM 15 C C13 SPM . A . C 2 14.111 14.417 14.418 0.5 28.56 ? C13 SPM 100 B 1 HETATM 16 C C13 SPM . B . C 2 12.857 15.301 19.416 0.5 23.71 ? C13 SPM 100 B 1 HETATM 17 N N14 SPM . A . C 2 14.246 14.036 12.976 0.5 28.5 ? N14 SPM 100 B 1 HETATM 18 N N14 SPM . B . C 2 12.646 16.319 20.482 0.5 24.76 ? N14 SPM 100 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #