data_1I2X # _model_server_result.job_id SRKzauCal3Mc4fvfr_O8EQ _model_server_result.datetime_utc '2025-09-14 05:02:50' _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 1i2x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":200}' # _entry.id 1I2X # _exptl.entry_id 1I2X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _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 1I2X _cell.length_a 27.69 _cell.length_b 47.71 _cell.length_c 113.62 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1I2X _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G 1 1 C,D,E,H,I 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id E _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 hydrog TYPE_28_PAIR hydrog1 A N1 G 1 A G 1 1_555 B O2 U 11 B U 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog2 A O6 G 1 A G 1 1_555 B N3 U 11 B U 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 C 2 A C 2 1_555 B N1 G 10 B G 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N4 C 2 A C 2 1_555 B O6 G 10 B G 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O2 C 2 A C 2 1_555 B N2 G 10 B G 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 3 1_555 B N3 C 9 B C 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 3 1_555 B O2 C 9 B C 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 3 1_555 B N4 C 9 B C 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 4 A DA 4 1_555 B N3 DT 7 B DT 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 4 A DA 4 1_555 B O4 DT 7 B DT 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DT 5 A DT 5 1_555 B N1 DA 6 B DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 DT 5 A DT 5 1_555 B N6 DA 6 B DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 6 A DA 6 1_555 B N3 DT 5 B DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 6 A DA 6 1_555 B O4 DT 5 B DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog15 A N3 DT 7 A DT 7 1_555 B N1 DA 4 B DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 C 9 A C 9 1_555 B N1 G 3 B G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 C 9 A C 9 1_555 B O6 G 3 B G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 C 9 A C 9 1_555 B N2 G 3 B G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 G 10 A G 10 1_555 B N3 C 2 B C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 G 10 A G 10 1_555 B O2 C 2 B C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 G 10 A G 10 1_555 B N4 C 2 B C 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog22 A N3 U 11 A U 11 1_555 B O6 G 1 B G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog23 A O2 U 11 A U 11 1_555 B N1 G 1 B G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog24 C N1 G 1 D G 101 1_555 D O2 U 11 C U 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog25 C O6 G 1 D G 101 1_555 D N3 U 11 C U 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N3 C 2 D C 102 1_555 D N1 G 10 C G 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N4 C 2 D C 102 1_555 D O6 G 10 C G 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C O2 C 2 D C 102 1_555 D N2 G 10 C G 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N1 G 3 D G 103 1_555 D N3 C 9 C C 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N2 G 3 D G 103 1_555 D O2 C 9 C C 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C O6 G 3 D G 103 1_555 D N4 C 9 C C 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N1 DA 4 D DA 104 1_555 D N3 DT 7 C DT 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N6 DA 4 D DA 104 1_555 D O4 DT 7 C DT 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N3 DT 5 D DT 105 1_555 D N1 DA 6 C DA 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O4 DT 5 D DT 105 1_555 D N6 DA 6 C DA 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N1 DA 6 D DA 106 1_555 D N3 DT 5 C DT 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N6 DA 6 D DA 106 1_555 D O4 DT 5 C DT 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N3 DT 7 D DT 107 1_555 D N1 DA 4 C DA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O4 DT 7 D DT 107 1_555 D N6 DA 4 C DA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N3 C 9 D C 109 1_555 D N1 G 3 C G 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N4 C 9 D C 109 1_555 D O6 G 3 C G 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C O2 C 9 D C 109 1_555 D N2 G 3 C G 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N1 G 10 D G 110 1_555 D N3 C 2 C C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C N2 G 10 D G 110 1_555 D O2 C 2 C C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C O6 G 10 D G 110 1_555 D N4 C 2 C C 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog46 C N3 U 11 D U 111 1_555 D O6 G 1 C G 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog47 C O2 U 11 D U 111 1_555 D N1 G 1 C G 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 SPD sing 193 n n N1 HN11 SPD sing 194 n n N1 HN12 SPD sing 195 n n C2 C3 SPD sing 196 n n C2 H21 SPD sing 197 n n C2 H22 SPD sing 198 n n C3 C4 SPD sing 199 n n C3 H31 SPD sing 200 n n C3 H32 SPD sing 201 n n C4 C5 SPD sing 202 n n C4 H41 SPD sing 203 n n C4 H42 SPD sing 204 n n C5 N6 SPD sing 205 n n C5 H51 SPD sing 206 n n C5 H52 SPD sing 207 n n N6 C7 SPD sing 208 n n N6 HN6 SPD sing 209 n n C7 C8 SPD sing 210 n n C7 H71 SPD sing 211 n n C7 H72 SPD sing 212 n n C8 C9 SPD sing 213 n n C8 H81 SPD sing 214 n n C8 H82 SPD sing 215 n n C9 N10 SPD sing 216 n n C9 H91 SPD sing 217 n n C9 H92 SPD sing 218 n n N10 H101 SPD sing 219 n n N10 H102 SPD sing 220 n n # _atom_sites.entry_id 1I2X _atom_sites.fract_transf_matrix[1][1] 0.036114 _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] 0.02096 _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] 0.008801 _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 E 2 SPD D 1 200 200 SPD SPD . F 3 HOH A 1 205 205 HOH HOH . F 3 HOH A 2 208 208 HOH HOH . F 3 HOH A 3 214 214 HOH HOH . F 3 HOH A 4 215 215 HOH HOH . F 3 HOH A 5 219 219 HOH HOH . F 3 HOH A 6 221 221 HOH HOH . F 3 HOH A 7 222 222 HOH HOH . F 3 HOH A 8 224 224 HOH HOH . F 3 HOH A 9 227 227 HOH HOH . F 3 HOH A 10 231 231 HOH HOH . F 3 HOH A 11 239 239 HOH HOH . F 3 HOH A 12 241 241 HOH HOH . F 3 HOH A 13 242 242 HOH HOH . F 3 HOH A 14 246 246 HOH HOH . F 3 HOH A 15 252 252 HOH HOH . F 3 HOH A 16 253 253 HOH HOH . F 3 HOH A 17 257 257 HOH HOH . F 3 HOH A 18 258 258 HOH HOH . F 3 HOH A 19 260 260 HOH HOH . F 3 HOH A 20 281 281 HOH HOH . G 3 HOH B 1 201 201 HOH HOH . G 3 HOH B 2 207 207 HOH HOH . G 3 HOH B 3 209 209 HOH HOH . G 3 HOH B 4 211 211 HOH HOH . G 3 HOH B 5 216 216 HOH HOH . G 3 HOH B 6 218 218 HOH HOH . G 3 HOH B 7 229 229 HOH HOH . G 3 HOH B 8 237 237 HOH HOH . G 3 HOH B 9 240 240 HOH HOH . G 3 HOH B 10 243 243 HOH HOH . G 3 HOH B 11 248 248 HOH HOH . G 3 HOH B 12 249 249 HOH HOH . G 3 HOH B 13 259 259 HOH HOH . G 3 HOH B 14 265 265 HOH HOH . G 3 HOH B 15 279 279 HOH HOH . H 3 HOH D 1 202 202 HOH HOH . H 3 HOH D 2 203 203 HOH HOH . H 3 HOH D 3 204 204 HOH HOH . H 3 HOH D 4 206 206 HOH HOH . H 3 HOH D 5 217 217 HOH HOH . H 3 HOH D 6 228 228 HOH HOH . H 3 HOH D 7 234 234 HOH HOH . H 3 HOH D 8 235 235 HOH HOH . H 3 HOH D 9 238 238 HOH HOH . H 3 HOH D 10 244 244 HOH HOH . H 3 HOH D 11 245 245 HOH HOH . H 3 HOH D 12 247 247 HOH HOH . H 3 HOH D 13 263 263 HOH HOH . H 3 HOH D 14 264 264 HOH HOH . H 3 HOH D 15 266 266 HOH HOH . H 3 HOH D 16 268 268 HOH HOH . H 3 HOH D 17 272 272 HOH HOH . H 3 HOH D 18 273 273 HOH HOH . H 3 HOH D 19 276 276 HOH HOH . H 3 HOH D 20 278 278 HOH HOH . I 3 HOH C 1 210 210 HOH HOH . I 3 HOH C 2 212 212 HOH HOH . I 3 HOH C 3 213 213 HOH HOH . I 3 HOH C 4 223 223 HOH HOH . I 3 HOH C 5 225 225 HOH HOH . I 3 HOH C 6 226 226 HOH HOH . I 3 HOH C 7 232 232 HOH HOH . I 3 HOH C 8 233 233 HOH HOH . I 3 HOH C 9 236 236 HOH HOH . I 3 HOH C 10 250 250 HOH HOH . I 3 HOH C 11 251 251 HOH HOH . I 3 HOH C 12 254 254 HOH HOH . I 3 HOH C 13 255 255 HOH HOH . I 3 HOH C 14 256 256 HOH HOH . I 3 HOH C 15 261 261 HOH HOH . I 3 HOH C 16 262 262 HOH HOH . I 3 HOH C 17 267 267 HOH HOH . I 3 HOH C 18 269 269 HOH HOH . I 3 HOH C 19 270 270 HOH HOH . I 3 HOH C 20 271 271 HOH HOH . I 3 HOH C 21 274 274 HOH HOH . I 3 HOH C 22 275 275 HOH HOH . I 3 HOH C 23 277 277 HOH HOH . I 3 HOH C 24 280 280 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 SPD . . . E 2 0.393 -12.328 45.285 1 49.79 ? N1 SPD 200 D 1 HETATM 2 C C2 SPD . . . E 2 1.212 -13.256 46.101 1 49.9 ? C2 SPD 200 D 1 HETATM 3 C C3 SPD . . . E 2 2.654 -13.257 45.634 1 49.79 ? C3 SPD 200 D 1 HETATM 4 C C4 SPD . . . E 2 3.512 -14.215 46.449 1 50 ? C4 SPD 200 D 1 HETATM 5 C C5 SPD . . . E 2 4.986 -13.984 46.143 1 50 ? C5 SPD 200 D 1 HETATM 6 N N6 SPD . . . E 2 5.431 -12.687 46.658 1 50 ? N6 SPD 200 D 1 HETATM 7 C C7 SPD . . . E 2 6.724 -12.288 46.105 1 50 ? C7 SPD 200 D 1 HETATM 8 C C8 SPD . . . E 2 7.301 -11.162 46.953 1 49.81 ? C8 SPD 200 D 1 HETATM 9 C C9 SPD . . . E 2 8.745 -10.804 46.636 1 49.34 ? C9 SPD 200 D 1 HETATM 10 N N10 SPD . . . E 2 9.26 -9.801 47.624 1 47.34 ? N10 SPD 200 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #