data_8XOM
#
_model_server_result.job_id            6V18hjB7XHm4Z6mn54NgRg 
_model_server_result.datetime_utc      '2025-01-03 04:43:43' 
_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          8xom 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1416}' 
#
_entry.id    8XOM 
#
_exptl.entry_id    8XOM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              516.752 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" 
_entity.pdbx_number_of_molecules    14 
_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            8XOM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XOM 
_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I N N 
? 4 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P N N 
? 4 Q N 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 B O2B ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc2 B O1A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc3 B O2A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 B O3A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
#
_chem_comp.formula           'C32 H52 O5' 
_chem_comp.formula_weight    516.752 
_chem_comp.id                DU0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" 
_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
C13 C12 DU0 sing 133 n n 
C12 C11 DU0 sing 134 n n 
C12 C14 DU0 sing 135 n n 
C11 O10 DU0 sing 136 n n 
C14 C15 DU0 sing 137 n n 
O10 C09 DU0 sing 138 n n 
C15 C09 DU0 sing 139 n n 
C09 O16 DU0 sing 140 n n 
C09 C07 DU0 sing 141 n n 
C08 C07 DU0 sing 142 n n 
O16 C05 DU0 sing 143 n n 
C07 C06 DU0 sing 144 n n 
C05 C06 DU0 sing 145 n n 
C05 C04 DU0 sing 146 n n 
C06 C02 DU0 sing 147 n n 
C04 C03 DU0 sing 148 n n 
C02 C01 DU0 sing 149 n n 
C02 C03 DU0 sing 150 n n 
C02 C81 DU0 sing 151 n n 
C03 C17 DU0 sing 152 n n 
C81 C80 DU0 sing 153 n n 
C17 C18 DU0 sing 154 n n 
C17 C79 DU0 sing 155 n n 
C80 C79 DU0 sing 156 n n 
C18 C19 DU0 sing 157 n n 
C79 C77 DU0 sing 158 n n 
C19 C20 DU0 doub 159 n n 
C77 C20 DU0 sing 160 n n 
C77 C78 DU0 sing 161 n n 
C77 C76 DU0 sing 162 n n 
C20 C21 DU0 sing 163 n n 
C76 C75 DU0 sing 164 n n 
C21 C22 DU0 sing 165 n n 
C75 C22 DU0 sing 166 n n 
C22 O23 DU0 sing 167 n n 
O23 C24 DU0 sing 168 n n 
C24 C25 DU0 sing 169 n n 
C25 C26 DU0 sing 170 n n 
C26 C27 DU0 sing 171 n n 
C26 C51 DU0 sing 172 n n 
C27 O28 DU0 sing 173 n n 
C51 O52 DU0 sing 174 n n 
C13 H1 DU0 sing 175 n n 
C13 H2 DU0 sing 176 n n 
C13 H3 DU0 sing 177 n n 
C15 H4 DU0 sing 178 n n 
C15 H5 DU0 sing 179 n n 
C17 H6 DU0 sing 180 n n 
C21 H7 DU0 sing 181 n n 
C21 H8 DU0 sing 182 n n 
C22 H9 DU0 sing 183 n n 
C24 H10 DU0 sing 184 n n 
C24 H11 DU0 sing 185 n n 
C26 H12 DU0 sing 186 n n 
C01 H13 DU0 sing 187 n n 
C01 H14 DU0 sing 188 n n 
C01 H15 DU0 sing 189 n n 
C03 H16 DU0 sing 190 n n 
C04 H17 DU0 sing 191 n n 
C04 H18 DU0 sing 192 n n 
C05 H19 DU0 sing 193 n n 
C06 H20 DU0 sing 194 n n 
C07 H21 DU0 sing 195 n n 
C08 H22 DU0 sing 196 n n 
C08 H23 DU0 sing 197 n n 
C08 H24 DU0 sing 198 n n 
C11 H25 DU0 sing 199 n n 
C11 H26 DU0 sing 200 n n 
C12 H27 DU0 sing 201 n n 
C14 H28 DU0 sing 202 n n 
C14 H29 DU0 sing 203 n n 
C18 H30 DU0 sing 204 n n 
C18 H31 DU0 sing 205 n n 
C19 H32 DU0 sing 206 n n 
C25 H33 DU0 sing 207 n n 
C25 H34 DU0 sing 208 n n 
C27 H35 DU0 sing 209 n n 
C27 H36 DU0 sing 210 n n 
C51 H37 DU0 sing 211 n n 
C51 H38 DU0 sing 212 n n 
C75 H39 DU0 sing 213 n n 
C75 H40 DU0 sing 214 n n 
C76 H41 DU0 sing 215 n n 
C76 H42 DU0 sing 216 n n 
C78 H43 DU0 sing 217 n n 
C78 H44 DU0 sing 218 n n 
C78 H45 DU0 sing 219 n n 
C79 H46 DU0 sing 220 n n 
C80 H47 DU0 sing 221 n n 
C80 H48 DU0 sing 222 n n 
C81 H49 DU0 sing 223 n n 
C81 H50 DU0 sing 224 n n 
O28 H51 DU0 sing 225 n n 
O52 H52 DU0 sing 226 n n 
#
_atom_sites.entry_id                     8XOM 
_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 ANP A 1 1401 1401 ANP ANP . 
C 3 MTX A 1 1402 1501 MTX MTX . 
D 4 DU0 A 1 1403 1 DU0 DU0 . 
E 4 DU0 A 1 1404 2 DU0 DU0 . 
F 4 DU0 A 1 1405 3 DU0 DU0 . 
G 4 DU0 A 1 1406 4 DU0 DU0 . 
H 4 DU0 A 1 1407 5 DU0 DU0 . 
I 4 DU0 A 1 1408 6 DU0 DU0 . 
J 4 DU0 A 1 1409 7 DU0 DU0 . 
K 4 DU0 A 1 1410 8 DU0 DU0 . 
L 4 DU0 A 1 1411 9 DU0 DU0 . 
M 4 DU0 A 1 1412 10 DU0 DU0 . 
N 4 DU0 A 1 1413 11 DU0 DU0 . 
O 4 DU0 A 1 1414 12 DU0 DU0 . 
P 4 DU0 A 1 1415 13 DU0 DU0 . 
Q 4 DU0 A 1 1416 14 DU0 DU0 . 
R 5 PLM A 1 1417 16 PLM PLM . 
S 6 MG A 1 1418 1 MG MG . 
#
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 C C13 DU0 . . . Q 4 129.387 99.81 115.818 1 145.81 ? C13 DU0 1416 A 1 
HETATM 2 C C15 DU0 . . . Q 4 132.678 99.25 113.87 1 185.88 ? C15 DU0 1416 A 1 
HETATM 3 C C17 DU0 . . . Q 4 136.005 102.907 109.666 1 222.42 ? C17 DU0 1416 A 1 
HETATM 4 C C20 DU0 . . . Q 4 138.23 104.267 108.447 1 235.09 ? C20 DU0 1416 A 1 
HETATM 5 C C21 DU0 . . . Q 4 139.228 104.935 107.527 1 233.06 ? C21 DU0 1416 A 1 
HETATM 6 C C22 DU0 . . . Q 4 140.54 104.177 107.294 1 233.82 ? C22 DU0 1416 A 1 
HETATM 7 C C24 DU0 . . . Q 4 141.886 105.381 108.883 1 228.71 ? C24 DU0 1416 A 1 
HETATM 8 C C26 DU0 . . . Q 4 143.333 106.298 110.824 1 221.31 ? C26 DU0 1416 A 1 
HETATM 9 C C01 DU0 . . . Q 4 135.617 100.46 111.395 1 212.36 ? C01 DU0 1416 A 1 
HETATM 10 C C02 DU0 . . . Q 4 134.751 100.746 110.163 1 212.34 ? C02 DU0 1416 A 1 
HETATM 11 C C03 DU0 . . . Q 4 134.651 102.248 109.869 1 209.08 ? C03 DU0 1416 A 1 
HETATM 12 C C04 DU0 . . . Q 4 133.706 102.787 110.943 1 200.9 ? C04 DU0 1416 A 1 
HETATM 13 C C05 DU0 . . . Q 4 132.716 101.636 111.164 1 193.05 ? C05 DU0 1416 A 1 
HETATM 14 C C06 DU0 . . . Q 4 133.268 100.405 110.415 1 201.35 ? C06 DU0 1416 A 1 
HETATM 15 C C07 DU0 . . . Q 4 132.933 99.227 111.336 1 199.43 ? C07 DU0 1416 A 1 
HETATM 16 C C08 DU0 . . . Q 4 132.152 98.106 110.672 1 180.57 ? C08 DU0 1416 A 1 
HETATM 17 C C09 DU0 . . . Q 4 132.243 99.878 112.552 1 193.82 ? C09 DU0 1416 A 1 
HETATM 18 C C11 DU0 . . . Q 4 130.032 100.177 113.428 1 163.28 ? C11 DU0 1416 A 1 
HETATM 19 C C12 DU0 . . . Q 4 130.328 99.4 114.696 1 165.8 ? C12 DU0 1416 A 1 
HETATM 20 C C14 DU0 . . . Q 4 131.79 99.637 115.045 1 176.37 ? C14 DU0 1416 A 1 
HETATM 21 C C18 DU0 . . . Q 4 135.861 104.379 109.305 1 218.64 ? C18 DU0 1416 A 1 
HETATM 22 C C19 DU0 . . . Q 4 137.122 104.951 108.743 1 228.73 ? C19 DU0 1416 A 1 
HETATM 23 C C25 DU0 . . . Q 4 142.916 105.095 109.965 1 223.72 ? C25 DU0 1416 A 1 
HETATM 24 C C27 DU0 . . . Q 4 144.242 105.842 111.96 1 222.41 ? C27 DU0 1416 A 1 
HETATM 25 C C51 DU0 . . . Q 4 142.064 106.985 111.319 1 215.59 ? C51 DU0 1416 A 1 
HETATM 26 C C75 DU0 . . . Q 4 140.289 102.739 106.869 1 230.79 ? C75 DU0 1416 A 1 
HETATM 27 C C76 DU0 . . . Q 4 138.858 102.281 107.125 1 230.93 ? C76 DU0 1416 A 1 
HETATM 28 C C77 DU0 . . . Q 4 138.241 102.747 108.459 1 234.69 ? C77 DU0 1416 A 1 
HETATM 29 C C78 DU0 . . . Q 4 139.07 102.243 109.654 1 232.16 ? C78 DU0 1416 A 1 
HETATM 30 C C79 DU0 . . . Q 4 136.795 102.198 108.552 1 224.35 ? C79 DU0 1416 A 1 
HETATM 31 C C80 DU0 . . . Q 4 136.759 100.667 108.663 1 217.65 ? C80 DU0 1416 A 1 
HETATM 32 C C81 DU0 . . . Q 4 135.367 100.091 108.933 1 205.73 ? C81 DU0 1416 A 1 
HETATM 33 O O10 DU0 . . . Q 4 130.855 99.758 112.354 1 182.21 ? O10 DU0 1416 A 1 
HETATM 34 O O16 DU0 . . . Q 4 132.624 101.229 112.523 1 193.52 ? O16 DU0 1416 A 1 
HETATM 35 O O23 DU0 . . . Q 4 141.388 104.143 108.428 1 236.57 ? O23 DU0 1416 A 1 
HETATM 36 O O28 DU0 . . . Q 4 143.614 104.873 112.765 1 221.54 ? O28 DU0 1416 A 1 
HETATM 37 O O52 DU0 . . . Q 4 142.297 107.69 112.516 1 208.08 ? O52 DU0 1416 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           355 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           37 
#