data_8IW4 # _model_server_result.job_id vH21GsZ2V0QorbgHWGs3KQ _model_server_result.datetime_utc '2025-08-31 14:23:13' _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 8iw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 8IW4 # _exptl.entry_id 8IW4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 145.246 _entity.id 6 _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 ? _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 6 _struct_asym.id F _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 disulf ? disulf1 D SG CYS 22 R CYS 22 1_555 D SG CYS 186 R CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 D SG CYS 105 R CYS 105 1_555 D SG CYS 190 R CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 E SG CYS 59 S CYS 22 1_555 E SG CYS 133 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 288 n n N1 HN11 SPD sing 289 n n N1 HN12 SPD sing 290 n n C2 C3 SPD sing 291 n n C2 H21 SPD sing 292 n n C2 H22 SPD sing 293 n n C3 C4 SPD sing 294 n n C3 H31 SPD sing 295 n n C3 H32 SPD sing 296 n n C4 C5 SPD sing 297 n n C4 H41 SPD sing 298 n n C4 H42 SPD sing 299 n n C5 N6 SPD sing 300 n n C5 H51 SPD sing 301 n n C5 H52 SPD sing 302 n n N6 C7 SPD sing 303 n n N6 HN6 SPD sing 304 n n C7 C8 SPD sing 305 n n C7 H71 SPD sing 306 n n C7 H72 SPD sing 307 n n C8 C9 SPD sing 308 n n C8 H81 SPD sing 309 n n C8 H82 SPD sing 310 n n C9 N10 SPD sing 311 n n C9 H91 SPD sing 312 n n C9 H92 SPD sing 313 n n N10 H101 SPD sing 314 n n N10 H102 SPD sing 315 n n # _atom_sites.entry_id 8IW4 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id SPD _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id SPD _pdbx_nonpoly_scheme.auth_mon_id SPD _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . F 6 86.796 93.347 88.649 1 10.81 ? N1 SPD 401 R 1 HETATM 2 C C2 SPD . . . F 6 86.947 92.58 87.428 1 10.81 ? C2 SPD 401 R 1 HETATM 3 C C3 SPD . . . F 6 88.01 91.507 87.63 1 10.81 ? C3 SPD 401 R 1 HETATM 4 C C4 SPD . . . F 6 88.889 91.368 86.392 1 10.81 ? C4 SPD 401 R 1 HETATM 5 C C5 SPD . . . F 6 88.47 90.163 85.559 1 10.81 ? C5 SPD 401 R 1 HETATM 6 N N6 SPD . . . F 6 88.23 90.518 84.174 1 10.81 ? N6 SPD 401 R 1 HETATM 7 C C7 SPD . . . F 6 86.874 90.574 83.664 1 10.81 ? C7 SPD 401 R 1 HETATM 8 C C8 SPD . . . F 6 86.519 91.96 83.138 1 10.81 ? C8 SPD 401 R 1 HETATM 9 C C9 SPD . . . F 6 86.654 93.011 84.232 1 10.81 ? C9 SPD 401 R 1 HETATM 10 N N10 SPD . . . F 6 85.51 92.935 85.12 1 10.81 ? N10 SPD 401 R 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #