data_8PY4 # _model_server_result.job_id uJmM2kLR63hT1FxItIclrw _model_server_result.datetime_utc '2024-12-03 21:28:35' _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 8py4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":707}' # _entry.id 8PY4 # _exptl.entry_id 8PY4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 469.573 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'tert-butyl 3-[(2S,5S,8S)-14-methoxy-2-(2-methylpropyl)-4,7-bis(oxidanylidene)-3,6,17-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1(10),11,13,15-tetraen-5-yl]propanoate' _entity.pdbx_number_of_molecules 2 _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 8PY4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PY4 _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,T,U,V,W,X _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 S N N ? 6 T N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n G NAG 1 G 1 NAG G 1 NAG 4 n G NAG 2 G 2 NAG G 2 NAG 4 n H NAG 1 H 1 NAG H 1 NAG 4 n H NAG 2 H 2 NAG H 2 NAG # 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 A SG CYS 22 D CYS 22 1_555 A SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 23 E CYS 23 1_555 B SG CYS 88 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 C SG CYS 22 F CYS 22 1_555 C SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 D SG CYS 602 B CYS 592 1_555 D SG CYS 618 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 D SG CYS 613 B CYS 603 1_555 E SG CYS 613 A CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 E SG CYS 602 A CYS 592 1_555 E SG CYS 618 A CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 F SG CYS 23 C CYS 23 1_555 F SG CYS 88 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 D ND2 ASN 606 B ASN 596 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? covale ? covale2 E ND2 ASN 606 A ASN 596 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? covale ? covale3 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _chem_comp.formula 'C26 H35 N3 O5' _chem_comp.formula_weight 469.573 _chem_comp.id I3O _chem_comp.mon_nstd_flag . _chem_comp.name 'tert-butyl 3-[(2S,5S,8S)-14-methoxy-2-(2-methylpropyl)-4,7-bis(oxidanylidene)-3,6,17-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1(10),11,13,15-tetraen-5-yl]propanoate' _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 C12 O01 I3O sing 229 n n O01 C02 I3O sing 230 n n C02 C03 I3O doub 231 n y C02 C01 I3O sing 232 n y C03 C04 I3O sing 233 n y C01 C06 I3O doub 234 n y C04 N01 I3O sing 235 n y C04 C05 I3O doub 236 n y N01 C07 I3O sing 237 n y C06 C05 I3O sing 238 n y C05 C08 I3O sing 239 n y C15 C14 I3O sing 240 n n C14 C16 I3O sing 241 n n C14 C13 I3O sing 242 n n C07 C08 I3O doub 243 n y C07 C09 I3O sing 244 n n C08 C11 I3O sing 245 n n C09 C13 I3O sing 246 n n C09 N02 I3O sing 247 n n C11 C10 I3O sing 248 n n N02 C10 I3O sing 249 n n N02 C17 I3O sing 250 n n C10 C18 I3O sing 251 n n O03 C17 I3O doub 252 n n C17 C19 I3O sing 253 n n C18 O02 I3O doub 254 n n C18 N03 I3O sing 255 n n C19 N03 I3O sing 256 n n C19 C20 I3O sing 257 n n C21 C20 I3O sing 258 n n C21 C22 I3O sing 259 n n C22 O04 I3O sing 260 n n C22 O05 I3O doub 261 n n O04 C23 I3O sing 262 n n C25 C23 I3O sing 263 n n C26 C23 I3O sing 264 n n C23 C24 I3O sing 265 n n C10 H1 I3O sing 266 n n C13 H2 I3O sing 267 n n C13 H3 I3O sing 268 n n C15 H4 I3O sing 269 n n C15 H5 I3O sing 270 n n C15 H6 I3O sing 271 n n C20 H7 I3O sing 272 n n C20 H8 I3O sing 273 n n C21 H9 I3O sing 274 n n C21 H10 I3O sing 275 n n C24 H11 I3O sing 276 n n C24 H12 I3O sing 277 n n C24 H13 I3O sing 278 n n C26 H14 I3O sing 279 n n C26 H15 I3O sing 280 n n C26 H16 I3O sing 281 n n C01 H17 I3O sing 282 n n C03 H18 I3O sing 283 n n C06 H19 I3O sing 284 n n C09 H20 I3O sing 285 n n C11 H21 I3O sing 286 n n C11 H22 I3O sing 287 n n C12 H23 I3O sing 288 n n C12 H24 I3O sing 289 n n C12 H25 I3O sing 290 n n C14 H26 I3O sing 291 n n C16 H27 I3O sing 292 n n C16 H28 I3O sing 293 n n C16 H29 I3O sing 294 n n C19 H30 I3O sing 295 n n C25 H31 I3O sing 296 n n C25 H32 I3O sing 297 n n C25 H33 I3O sing 298 n n N01 H34 I3O sing 299 n n N03 H35 I3O sing 300 n n # _atom_sites.entry_id 8PY4 _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 I 5 CLR B 1 701 702 CLR CLR . J 5 CLR B 1 702 703 CLR CLR . K 5 CLR B 1 703 704 CLR CLR . L 5 CLR B 1 704 706 CLR CLR . M 5 CLR B 1 705 1201 CLR CLR . N 5 CLR A 1 701 702 CLR CLR . O 5 CLR A 1 702 703 CLR CLR . P 5 CLR A 1 703 704 CLR CLR . Q 5 CLR A 1 704 706 CLR CLR . R 5 CLR A 1 705 1201 CLR CLR . S 6 I3O A 1 706 1104 I3O LIG . T 6 I3O A 1 707 1104 I3O LIG . U 7 HOH E 1 301 45 HOH HOH . V 7 HOH B 1 801 39 HOH HOH . V 7 HOH B 2 802 2 HOH HOH . V 7 HOH B 3 803 9 HOH HOH . V 7 HOH B 4 804 21 HOH HOH . V 7 HOH B 5 805 35 HOH HOH . V 7 HOH B 6 806 41 HOH HOH . V 7 HOH B 7 807 12 HOH HOH . V 7 HOH B 8 808 7 HOH HOH . V 7 HOH B 9 809 48 HOH HOH . V 7 HOH B 10 810 37 HOH HOH . V 7 HOH B 11 811 22 HOH HOH . V 7 HOH B 12 812 24 HOH HOH . V 7 HOH B 13 813 20 HOH HOH . V 7 HOH B 14 814 31 HOH HOH . V 7 HOH B 15 815 50 HOH HOH . V 7 HOH B 16 816 5 HOH HOH . V 7 HOH B 17 817 51 HOH HOH . W 7 HOH A 1 801 26 HOH HOH . W 7 HOH A 2 802 10 HOH HOH . W 7 HOH A 3 803 1 HOH HOH . W 7 HOH A 4 804 30 HOH HOH . W 7 HOH A 5 805 40 HOH HOH . W 7 HOH A 6 806 11 HOH HOH . W 7 HOH A 7 807 8 HOH HOH . W 7 HOH A 8 808 29 HOH HOH . W 7 HOH A 9 809 28 HOH HOH . W 7 HOH A 10 810 27 HOH HOH . W 7 HOH A 11 811 25 HOH HOH . W 7 HOH A 12 812 32 HOH HOH . W 7 HOH A 13 813 49 HOH HOH . W 7 HOH A 14 814 6 HOH HOH . X 7 HOH C 1 301 47 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 C C10 I3O . . . T 6 121.81 128.472 131.86 1 34.63 ? C10 I3O 707 A 1 HETATM 2 C C13 I3O . . . T 6 120.753 131.667 130.389 1 34.63 ? C13 I3O 707 A 1 HETATM 3 C C15 I3O . . . T 6 118.995 132.849 128.969 1 34.63 ? C15 I3O 707 A 1 HETATM 4 C C17 I3O . . . T 6 119.437 129.565 132.376 1 34.63 ? C17 I3O 707 A 1 HETATM 5 C C20 I3O . . . T 6 118.69 129.762 134.914 1 34.63 ? C20 I3O 707 A 1 HETATM 6 C C21 I3O . . . T 6 118.361 131.237 134.519 1 34.63 ? C21 I3O 707 A 1 HETATM 7 C C22 I3O . . . T 6 118.199 132.218 135.737 1 34.63 ? C22 I3O 707 A 1 HETATM 8 C C24 I3O . . . T 6 118.23 134.439 137.926 1 34.63 ? C24 I3O 707 A 1 HETATM 9 C C26 I3O . . . T 6 116.578 134.479 135.96 1 34.63 ? C26 I3O 707 A 1 HETATM 10 C C01 I3O . . . T 6 125.093 127.488 126.836 1 34.63 ? C01 I3O 707 A 1 HETATM 11 C C02 I3O . . . T 6 124.273 127.822 125.694 1 34.63 ? C02 I3O 707 A 1 HETATM 12 C C03 I3O . . . T 6 123.052 128.481 125.927 1 34.63 ? C03 I3O 707 A 1 HETATM 13 C C04 I3O . . . T 6 122.635 128.809 127.266 1 34.63 ? C04 I3O 707 A 1 HETATM 14 C C05 I3O . . . T 6 123.457 128.473 128.397 1 34.63 ? C05 I3O 707 A 1 HETATM 15 C C06 I3O . . . T 6 124.699 127.803 128.144 1 34.63 ? C06 I3O 707 A 1 HETATM 16 C C07 I3O . . . T 6 121.572 129.524 129.192 1 34.63 ? C07 I3O 707 A 1 HETATM 17 C C08 I3O . . . T 6 122.749 128.946 129.583 1 34.63 ? C08 I3O 707 A 1 HETATM 18 C C09 I3O . . . T 6 120.576 130.133 130.179 1 34.63 ? C09 I3O 707 A 1 HETATM 19 C C11 I3O . . . T 6 123.136 128.849 131.022 1 34.63 ? C11 I3O 707 A 1 HETATM 20 C C12 I3O . . . T 6 123.82 127.84 123.293 1 34.63 ? C12 I3O 707 A 1 HETATM 21 C C14 I3O . . . T 6 120.501 132.549 129.147 1 34.63 ? C14 I3O 707 A 1 HETATM 22 C C16 I3O . . . T 6 121.3 133.868 129.251 1 34.63 ? C16 I3O 707 A 1 HETATM 23 C C18 I3O . . . T 6 122.14 128.39 133.464 1 34.63 ? C18 I3O 707 A 1 HETATM 24 C C19 I3O . . . T 6 119.591 128.942 133.878 1 34.63 ? C19 I3O 707 A 1 HETATM 25 C C23 I3O . . . T 6 118.073 134.576 136.386 1 34.63 ? C23 I3O 707 A 1 HETATM 26 C C25 I3O . . . T 6 118.648 135.971 135.927 1 34.63 ? C25 I3O 707 A 1 HETATM 27 N N01 I3O . . . T 6 121.464 129.464 127.776 1 34.63 ? N01 I3O 707 A 1 HETATM 28 N N02 I3O . . . T 6 120.615 129.446 131.57 1 34.63 ? N02 I3O 707 A 1 HETATM 29 N N03 I3O . . . T 6 121.069 128.881 134.25 1 34.63 ? N03 I3O 707 A 1 HETATM 30 O O01 I3O . . . T 6 124.675 127.505 124.39 1 34.63 ? O01 I3O 707 A 1 HETATM 31 O O02 I3O . . . T 6 123.176 127.948 133.865 1 34.63 ? O02 I3O 707 A 1 HETATM 32 O O03 I3O . . . T 6 118.403 130.065 132.029 1 34.63 ? O03 I3O 707 A 1 HETATM 33 O O04 I3O . . . T 6 118.759 133.471 135.745 1 34.63 ? O04 I3O 707 A 1 HETATM 34 O O05 I3O . . . T 6 117.557 131.839 136.684 1 34.63 ? O05 I3O 707 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 34 #