data_9JD9 # _model_server_result.job_id PKfXdGHIJbwUxtW7iSLMeg _model_server_result.datetime_utc '2025-07-21 01:26:22' _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 9jd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 9JD9 # _exptl.entry_id 9JD9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 128.255 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description nonane _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 9JD9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JD9 _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,T,U _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 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 A SG CYS 162 A CYS 162 1_555 A SG CYS 171 A CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 190 A ASN 190 1_555 T C1 NAG . A NAG 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? metalc ? metalc1 A O GLY 56 A GLY 56 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc2 A O PHE 58 A PHE 58 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc3 A O VAL 59 A VAL 59 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc4 A O SER 301 A SER 301 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A OG SER 301 A SER 301 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc6 A O LEU 398 A LEU 398 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? metalc ? metalc7 B O2 TAU . A TAU 701 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _chem_comp.formula 'C9 H20' _chem_comp.formula_weight 128.255 _chem_comp.id DD9 _chem_comp.mon_nstd_flag . _chem_comp.name nonane _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 C2 C1 DD9 sing 194 n n C1 H1 DD9 sing 195 n n C1 H1A DD9 sing 196 n n C1 H1B DD9 sing 197 n n C3 C2 DD9 sing 198 n n C2 H2 DD9 sing 199 n n C2 H2A DD9 sing 200 n n C4 C3 DD9 sing 201 n n C3 H3 DD9 sing 202 n n C3 H3A DD9 sing 203 n n C5 C4 DD9 sing 204 n n C4 H4 DD9 sing 205 n n C4 H4A DD9 sing 206 n n C6 C5 DD9 sing 207 n n C5 H5 DD9 sing 208 n n C5 H5A DD9 sing 209 n n C7 C6 DD9 sing 210 n n C6 H6 DD9 sing 211 n n C6 H6A DD9 sing 212 n n C8 C7 DD9 sing 213 n n C7 H7 DD9 sing 214 n n C7 H7A DD9 sing 215 n n C9 C8 DD9 sing 216 n n C8 H8 DD9 sing 217 n n C8 H8A DD9 sing 218 n n C9 H9 DD9 sing 219 n n C9 H9A DD9 sing 220 n n C9 H9B DD9 sing 221 n n # _atom_sites.entry_id 9JD9 _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 TAU A 1 701 601 TAU TAU . C 3 D12 A 1 702 602 D12 D12 . D 4 OCT A 1 703 603 OCT OCT . E 5 C14 A 1 704 604 C14 C14 . F 6 DD9 A 1 705 605 DD9 DD9 . G 7 HP6 A 1 706 606 HP6 HP6 . H 8 D10 A 1 707 607 D10 D10 . I 4 OCT A 1 708 608 OCT OCT . J 7 HP6 A 1 709 609 HP6 HP6 . K 3 D12 A 1 710 610 D12 D12 . L 4 OCT A 1 711 611 OCT OCT . M 4 OCT A 1 712 612 OCT OCT . N 8 D10 A 1 713 613 D10 D10 . O 3 D12 A 1 714 614 D12 D12 . P 9 HEX A 1 715 615 HEX HEX . Q 10 CL A 1 716 701 CL CL . R 11 NA A 1 717 702 NA NA . S 11 NA A 1 718 703 NA NA . T 12 NAG A 1 719 704 NAG NAG . U 13 HOH A 1 801 621 HOH HOH . U 13 HOH A 2 802 622 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 C1 DD9 . . . F 6 127.347 114.417 100.371 1 89.26 ? C1 DD9 705 A 1 HETATM 2 C C2 DD9 . . . F 6 128.191 113.534 101.28 1 90.9 ? C2 DD9 705 A 1 HETATM 3 C C3 DD9 . . . F 6 129.685 113.763 101.09 1 91.37 ? C3 DD9 705 A 1 HETATM 4 C C4 DD9 . . . F 6 130.511 112.498 101.28 1 92.77 ? C4 DD9 705 A 1 HETATM 5 C C5 DD9 . . . F 6 131.88 112.582 100.621 1 90.9 ? C5 DD9 705 A 1 HETATM 6 C C6 DD9 . . . F 6 132.377 111.243 100.093 1 90.21 ? C6 DD9 705 A 1 HETATM 7 C C7 DD9 . . . F 6 133.583 111.39 99.175 1 94.74 ? C7 DD9 705 A 1 HETATM 8 C C8 DD9 . . . F 6 133.775 110.214 98.227 1 95.71 ? C8 DD9 705 A 1 HETATM 9 C C9 DD9 . . . F 6 134.791 110.516 97.133 1 94.52 ? C9 DD9 705 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #