data_8IEM
#
_model_server_result.job_id            U0PYja1vzE4-LhyoIEpDTg 
_model_server_result.datetime_utc      '2025-03-01 11:41:19' 
_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          8iem 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1201}' 
#
_entry.id    8IEM 
#
_exptl.entry_id    8IEM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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            8IEM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8IEM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                             B 
_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
metalc ? metalc1 A OG1 THR 475 P THR 515 1_555 C MG MG . P MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc2 A OD2 ASP 838 P ASP 878 1_555 C MG MG . P MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? 
#
_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 291 n n 
N1 HN11 SPM sing 292 n n 
N1 HN12 SPM sing 293 n n 
C2 C3 SPM sing 294 n n 
C2 H21 SPM sing 295 n n 
C2 H22 SPM sing 296 n n 
C3 C4 SPM sing 297 n n 
C3 H31 SPM sing 298 n n 
C3 H32 SPM sing 299 n n 
C4 N5 SPM sing 300 n n 
C4 H41 SPM sing 301 n n 
C4 H42 SPM sing 302 n n 
N5 C6 SPM sing 303 n n 
N5 HN5 SPM sing 304 n n 
C6 C7 SPM sing 305 n n 
C6 H61 SPM sing 306 n n 
C6 H62 SPM sing 307 n n 
C7 C8 SPM sing 308 n n 
C7 H71 SPM sing 309 n n 
C7 H72 SPM sing 310 n n 
C8 C9 SPM sing 311 n n 
C8 H81 SPM sing 312 n n 
C8 H82 SPM sing 313 n n 
C9 N10 SPM sing 314 n n 
C9 H91 SPM sing 315 n n 
C9 H92 SPM sing 316 n n 
N10 C11 SPM sing 317 n n 
N10 HN0 SPM sing 318 n n 
C11 C12 SPM sing 319 n n 
C11 H111 SPM sing 320 n n 
C11 H112 SPM sing 321 n n 
C12 C13 SPM sing 322 n n 
C12 H121 SPM sing 323 n n 
C12 H122 SPM sing 324 n n 
C13 N14 SPM sing 325 n n 
C13 H131 SPM sing 326 n n 
C13 H132 SPM sing 327 n n 
N14 HN41 SPM sing 328 n n 
N14 HN42 SPM sing 329 n n 
#
_atom_sites.entry_id                     8IEM 
_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 
#
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
B 2 SPM P 1 1201 1201 SPM SPM . 
C 3 MG P 1 1202 1202 MG MG . 
D 4 BEF P 1 1203 1205 BEF BEF . 
#
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 . . . B 2 132.908 166.834 152.21 1 20 ? N1 SPM 1201 P 1 
HETATM 2 C C2 SPM . . . B 2 134.139 167.585 151.951 1 20 ? C2 SPM 1201 P 1 
HETATM 3 C C3 SPM . . . B 2 135.1 167.382 153.112 1 20 ? C3 SPM 1201 P 1 
HETATM 4 C C4 SPM . . . B 2 136.35 168.231 152.892 1 20 ? C4 SPM 1201 P 1 
HETATM 5 N N5 SPM . . . B 2 137.48 167.345 152.614 1 20 ? N5 SPM 1201 P 1 
HETATM 6 C C6 SPM . . . B 2 138.608 167.868 153.38 1 20 ? C6 SPM 1201 P 1 
HETATM 7 C C7 SPM . . . B 2 139.905 167.373 152.759 1 20 ? C7 SPM 1201 P 1 
HETATM 8 C C8 SPM . . . B 2 141.069 167.977 153.532 1 20 ? C8 SPM 1201 P 1 
HETATM 9 C C9 SPM . . . B 2 142.365 167.789 152.737 1 20 ? C9 SPM 1201 P 1 
HETATM 10 N N10 SPM . . . B 2 143.454 167.403 153.652 1 20 ? N10 SPM 1201 P 1 
HETATM 11 C C11 SPM . . . B 2 144.51 166.708 152.915 1 20 ? C11 SPM 1201 P 1 
HETATM 12 C C12 SPM . . . B 2 145.018 165.555 153.768 1 20 ? C12 SPM 1201 P 1 
HETATM 13 C C13 SPM . . . B 2 146.261 164.999 153.109 1 20 ? C13 SPM 1201 P 1 
HETATM 14 N N14 SPM . . . B 2 146.146 163.543 153.11 1 20 ? N14 SPM 1201 P 1 
HETATM 15 H HN11 SPM . . . B 2 132.298 167.011 151.427 1 20 ? HN11 SPM 1201 P 1 
HETATM 16 H HN12 SPM . . . B 2 133.16 165.859 152.167 1 20 ? HN12 SPM 1201 P 1 
HETATM 17 H H21 SPM . . . B 2 134.603 167.225 151.035 1 20 ? H21 SPM 1201 P 1 
HETATM 18 H H22 SPM . . . B 2 133.909 168.645 151.855 1 20 ? H22 SPM 1201 P 1 
HETATM 19 H H31 SPM . . . B 2 134.61 167.679 154.036 1 20 ? H31 SPM 1201 P 1 
HETATM 20 H H32 SPM . . . B 2 135.38 166.33 153.165 1 20 ? H32 SPM 1201 P 1 
HETATM 21 H H41 SPM . . . B 2 136.19 168.904 152.052 1 20 ? H41 SPM 1201 P 1 
HETATM 22 H H42 SPM . . . B 2 136.55 168.805 153.795 1 20 ? H42 SPM 1201 P 1 
HETATM 23 H HN5 SPM . . . B 2 137.711 167.456 151.64 1 20 ? HN5 SPM 1201 P 1 
HETATM 24 H H61 SPM . . . B 2 138.599 168.956 153.353 1 20 ? H61 SPM 1201 P 1 
HETATM 25 H H62 SPM . . . B 2 138.544 167.524 154.411 1 20 ? H62 SPM 1201 P 1 
HETATM 26 H H71 SPM . . . B 2 139.935 166.289 152.801 1 20 ? H71 SPM 1201 P 1 
HETATM 27 H H72 SPM . . . B 2 139.957 167.7 151.722 1 20 ? H72 SPM 1201 P 1 
HETATM 28 H H81 SPM . . . B 2 140.888 169.041 153.668 1 20 ? H81 SPM 1201 P 1 
HETATM 29 H H82 SPM . . . B 2 141.143 167.504 154.509 1 20 ? H82 SPM 1201 P 1 
HETATM 30 H H91 SPM . . . B 2 142.204 167.025 151.979 1 20 ? H91 SPM 1201 P 1 
HETATM 31 H H92 SPM . . . B 2 142.627 168.727 152.251 1 20 ? H92 SPM 1201 P 1 
HETATM 32 H HN0 SPM . . . B 2 143.082 166.737 154.307 1 20 ? HN0 SPM 1201 P 1 
HETATM 33 H H111 SPM . . . B 2 144.129 166.326 151.973 1 20 ? H111 SPM 1201 P 1 
HETATM 34 H H112 SPM . . . B 2 145.332 167.397 152.725 1 20 ? H112 SPM 1201 P 1 
HETATM 35 H H121 SPM . . . B 2 145.251 165.91 154.772 1 20 ? H121 SPM 1201 P 1 
HETATM 36 H H122 SPM . . . B 2 144.277 164.763 153.824 1 20 ? H122 SPM 1201 P 1 
HETATM 37 H H131 SPM . . . B 2 147.144 165.305 153.668 1 20 ? H131 SPM 1201 P 1 
HETATM 38 H H132 SPM . . . B 2 146.324 165.365 152.085 1 20 ? H132 SPM 1201 P 1 
HETATM 39 H HN41 SPM . . . B 2 145.896 163.277 154.05 1 20 ? HN41 SPM 1201 P 1 
HETATM 40 H HN42 SPM . . . B 2 147.069 163.18 152.94 1 20 ? HN42 SPM 1201 P 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           40 
#