data_9JD3 # _model_server_result.job_id NNpgMdcDBls-SBgUuYEviA _model_server_result.datetime_utc '2025-07-21 00:38:11' _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 9jd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":714}' # _entry.id 9JD3 # _exptl.entry_id 9JD3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 170.335 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DODECANE _entity.pdbx_number_of_molecules 3 _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 9JD3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JD3 _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,V _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 ? 2 B N N ? 2 M N N ? 2 O N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 162 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 162 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 171 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 171 _struct_conn.ptnr2_symmetry 1_555 _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 2.032 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H26' _chem_comp.formula_weight 170.335 _chem_comp.id D12 _chem_comp.mon_nstd_flag . _chem_comp.name DODECANE _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 C1 C2 D12 sing 191 n n C1 H11 D12 sing 192 n n C1 H12 D12 sing 193 n n C1 H13 D12 sing 194 n n C2 C3 D12 sing 195 n n C2 H21 D12 sing 196 n n C2 H22 D12 sing 197 n n C3 C4 D12 sing 198 n n C3 H31 D12 sing 199 n n C3 H32 D12 sing 200 n n C4 C5 D12 sing 201 n n C4 H41 D12 sing 202 n n C4 H42 D12 sing 203 n n C5 C6 D12 sing 204 n n C5 H51 D12 sing 205 n n C5 H52 D12 sing 206 n n C6 C7 D12 sing 207 n n C6 H61 D12 sing 208 n n C6 H62 D12 sing 209 n n C7 C8 D12 sing 210 n n C7 H71 D12 sing 211 n n C7 H72 D12 sing 212 n n C8 C9 D12 sing 213 n n C8 H81 D12 sing 214 n n C8 H82 D12 sing 215 n n C9 C10 D12 sing 216 n n C9 H91 D12 sing 217 n n C9 H92 D12 sing 218 n n C10 C11 D12 sing 219 n n C10 H101 D12 sing 220 n n C10 H102 D12 sing 221 n n C11 C12 D12 sing 222 n n C11 H111 D12 sing 223 n n C11 H112 D12 sing 224 n n C12 H121 D12 sing 225 n n C12 H122 D12 sing 226 n n C12 H123 D12 sing 227 n n # _atom_sites.entry_id 9JD3 _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 D12 A 1 701 601 D12 D12 . C 3 LNK A 1 702 602 LNK LNK . D 4 OCT A 1 703 603 OCT OCT . E 4 OCT A 1 704 604 OCT OCT . F 4 OCT A 1 705 605 OCT OCT . G 5 D10 A 1 706 606 D10 D10 . H 6 HEX A 1 707 607 HEX HEX . I 6 HEX A 1 708 608 HEX HEX . J 6 HEX A 1 709 609 HEX HEX . K 6 HEX A 1 710 610 HEX HEX . L 4 OCT A 1 711 611 OCT OCT . M 2 D12 A 1 712 612 D12 D12 . N 5 D10 A 1 713 613 D10 D10 . O 2 D12 A 1 714 614 D12 D12 . P 6 HEX A 1 715 615 HEX HEX . Q 6 HEX A 1 716 616 HEX HEX . R 6 HEX A 1 717 617 HEX HEX . S 7 CLR A 1 718 618 CLR CLR . T 8 CL A 1 719 701 CL CL . U 9 NAG A 1 720 702 NAG NAG . V 10 HOH A 1 801 623 HOH HOH . V 10 HOH A 2 802 622 HOH HOH . V 10 HOH A 3 803 621 HOH HOH . V 10 HOH A 4 804 627 HOH HOH . V 10 HOH A 5 805 625 HOH HOH . V 10 HOH A 6 806 624 HOH HOH . V 10 HOH A 7 807 626 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 D12 . . . O 2 117.971 137.984 165.835 1 114.27 ? C1 D12 714 A 1 HETATM 2 C C2 D12 . . . O 2 118.419 136.544 165.625 1 116.07 ? C2 D12 714 A 1 HETATM 3 C C3 D12 . . . O 2 118.585 135.779 166.932 1 116.53 ? C3 D12 714 A 1 HETATM 4 C C4 D12 . . . O 2 118.9 134.301 166.734 1 116.19 ? C4 D12 714 A 1 HETATM 5 C C5 D12 . . . O 2 120.264 134.055 166.1 1 116.52 ? C5 D12 714 A 1 HETATM 6 C C6 D12 . . . O 2 120.418 132.657 165.515 1 118.56 ? C6 D12 714 A 1 HETATM 7 C C7 D12 . . . O 2 120.206 131.538 166.528 1 119.05 ? C7 D12 714 A 1 HETATM 8 C C8 D12 . . . O 2 120.367 130.148 165.925 1 117.46 ? C8 D12 714 A 1 HETATM 9 C C9 D12 . . . O 2 120.3 129.027 166.955 1 117.89 ? C9 D12 714 A 1 HETATM 10 C C10 D12 . . . O 2 120.341 127.638 166.332 1 118.84 ? C10 D12 714 A 1 HETATM 11 C C11 D12 . . . O 2 120.178 126.512 167.346 1 116.53 ? C11 D12 714 A 1 HETATM 12 C C12 D12 . . . O 2 119.937 125.159 166.69 1 115 ? C12 D12 714 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 546 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #