data_8XJM # _model_server_result.job_id IBl4JzSpY3pYqZozevbtBg _model_server_result.datetime_utc '2024-12-26 15:21:02' _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 8xjm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 8XJM # _exptl.entry_id 8XJM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 390.513 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Z-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(3R)-3-oxidanyl-5-phenyl-pentyl]cyclopentyl]hept-5-enoic acid' _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 8XJM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XJM _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 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 21 E CYS 21 1_555 D SG CYS 95 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 D SG CYS 158 E CYS 159 1_555 D SG CYS 228 E CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 E SG CYS 193 R CYS 108 1_555 E SG CYS 271 R CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C23 H34 O5' _chem_comp.formula_weight 390.513 _chem_comp.id 7WT _chem_comp.mon_nstd_flag . _chem_comp.name 'Z-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(3R)-3-oxidanyl-5-phenyl-pentyl]cyclopentyl]hept-5-enoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '7-[3,5-Dihydroxy-2-(3-hydroxy-5-phenylpentyl)cyclopentyl]hept-5-enoic acid' # 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 O28 C26 7WT doub 1 n n C26 O27 7WT sing 2 n n C26 C25 7WT sing 3 n n C25 C24 7WT sing 4 n n C24 C23 7WT sing 5 n n C23 C22 7WT sing 6 n n C22 C21 7WT doub 7 z n C21 C20 7WT sing 8 n n C17 C16 7WT doub 9 n y C17 C18 7WT sing 10 n y C16 C15 7WT sing 11 n y C20 C03 7WT sing 12 n n C18 C13 7WT doub 13 n y C15 C14 7WT doub 14 n y O01 C02 7WT sing 15 n n C13 C14 7WT sing 16 n y C13 C12 7WT sing 17 n n C03 C02 7WT sing 18 n n C03 C04 7WT sing 19 n n C02 C06 7WT sing 20 n n C12 C11 7WT sing 21 n n C11 C10 7WT sing 22 n n C04 C08 7WT sing 23 n n C04 C05 7WT sing 24 n n C08 C09 7WT sing 25 n n C06 C05 7WT sing 26 n n C05 O07 7WT sing 27 n n C10 C09 7WT sing 28 n n C10 O19 7WT sing 29 n n C10 H1 7WT sing 30 n n C15 H2 7WT sing 31 n n C17 H3 7WT sing 32 n n C20 H4 7WT sing 33 n n C20 H5 7WT sing 34 n n C21 H6 7WT sing 35 n n C22 H8 7WT sing 36 n n C24 H10 7WT sing 37 n n C24 H11 7WT sing 38 n n C02 H12 7WT sing 39 n n C03 H13 7WT sing 40 n n C04 H14 7WT sing 41 n n C05 H15 7WT sing 42 n n C06 H16 7WT sing 43 n n C06 H17 7WT sing 44 n n C08 H18 7WT sing 45 n n C08 H19 7WT sing 46 n n C09 H20 7WT sing 47 n n C09 H21 7WT sing 48 n n C11 H22 7WT sing 49 n n C11 H23 7WT sing 50 n n C12 H24 7WT sing 51 n n C12 H25 7WT sing 52 n n C14 H26 7WT sing 53 n n C16 H27 7WT sing 54 n n C18 H28 7WT sing 55 n n C23 H29 7WT sing 56 n n C23 H30 7WT sing 57 n n C25 H31 7WT sing 58 n n C25 H32 7WT sing 59 n n O01 H33 7WT sing 60 n n O07 H34 7WT sing 61 n n O19 H35 7WT sing 62 n n O27 H36 7WT sing 63 n n # _atom_sites.entry_id 8XJM _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 7WT _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 7WT _pdbx_nonpoly_scheme.auth_mon_id LIG _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 C C10 7WT . . . F 6 101.127 122.639 115.953 1 62.8 ? C10 7WT 601 R 1 HETATM 2 C C13 7WT . . . F 6 103.231 125.88 114.509 1 62.59 ? C13 7WT 601 R 1 HETATM 3 C C15 7WT . . . F 6 105.676 126.253 114.395 1 63.67 ? C15 7WT 601 R 1 HETATM 4 C C17 7WT . . . F 6 104.173 128.052 113.778 1 59.55 ? C17 7WT 601 R 1 HETATM 5 C C20 7WT . . . F 6 99.316 126.571 119.728 1 60.95 ? C20 7WT 601 R 1 HETATM 6 C C21 7WT . . . F 6 100.146 126.87 120.875 1 64.83 ? C21 7WT 601 R 1 HETATM 7 C C22 7WT . . . F 6 99.967 127.966 121.634 1 65.39 ? C22 7WT 601 R 1 HETATM 8 C C24 7WT . . . F 6 99.357 130.326 120.743 1 62.82 ? C24 7WT 601 R 1 HETATM 9 C C26 7WT . . . F 6 97.241 131.772 121.413 1 70.56 ? C26 7WT 601 R 1 HETATM 10 C C02 7WT . . . F 6 97.167 125.104 120.348 1 66.31 ? C02 7WT 601 R 1 HETATM 11 C C03 7WT . . . F 6 98.636 125.164 119.775 1 62.16 ? C03 7WT 601 R 1 HETATM 12 C C04 7WT . . . F 6 98.49 124.585 118.382 1 63.65 ? C04 7WT 601 R 1 HETATM 13 C C05 7WT . . . F 6 97.425 123.444 118.576 1 64.35 ? C05 7WT 601 R 1 HETATM 14 C C06 7WT . . . F 6 96.59 123.773 119.858 1 66.15 ? C06 7WT 601 R 1 HETATM 15 C C08 7WT . . . F 6 99.884 124.119 117.796 1 60.91 ? C08 7WT 601 R 1 HETATM 16 C C09 7WT . . . F 6 99.791 123.05 116.699 1 61.01 ? C09 7WT 601 R 1 HETATM 17 C C11 7WT . . . F 6 102.212 123.791 115.872 1 59.28 ? C11 7WT 601 R 1 HETATM 18 C C12 7WT . . . F 6 101.998 124.941 114.815 1 59.58 ? C12 7WT 601 R 1 HETATM 19 C C14 7WT . . . F 6 104.56 125.426 114.668 1 64.24 ? C14 7WT 601 R 1 HETATM 20 C C16 7WT . . . F 6 105.485 127.572 113.949 1 62.45 ? C16 7WT 601 R 1 HETATM 21 C C18 7WT . . . F 6 103.066 127.214 114.056 1 62.61 ? C18 7WT 601 R 1 HETATM 22 C C23 7WT . . . F 6 98.899 128.962 121.372 1 63.02 ? C23 7WT 601 R 1 HETATM 23 C C25 7WT . . . F 6 98.24 131.294 120.277 1 67.53 ? C25 7WT 601 R 1 HETATM 24 O O01 7WT . . . F 6 96.354 126.138 119.841 1 64.97 ? O01 7WT 601 R 1 HETATM 25 O O07 7WT . . . F 6 96.55 123.38 117.512 1 64.55 ? O07 7WT 601 R 1 HETATM 26 O O19 7WT . . . F 6 100.805 122.196 114.666 1 64.38 ? O19 7WT 601 R 1 HETATM 27 O O27 7WT . . . F 6 95.992 131.726 121.203 1 68.27 ? O27 7WT 601 R 1 HETATM 28 O O28 7WT . . . F 6 97.709 132.191 122.512 1 71.25 ? O28 7WT 601 R 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 376 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #