data_9JD4 # _model_server_result.job_id QP1rSO8kQsZ2JENBO3096A _model_server_result.datetime_utc '2025-07-20 21:01:22' _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 9jd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 9JD4 # _exptl.entry_id 9JD4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 170.335 _entity.id 4 _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 9JD4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JD4 _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 _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 F N N ? 4 H 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 disulf ? disulf1 A SG CYS 162 A CYS 162 1_555 A SG CYS 171 A CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 190 A ASN 190 1_555 M C1 NAG . A NAG 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.528 ? metalc ? metalc1 A O GLY 56 A GLY 56 1_555 K NA NA . A NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc2 A O PHE 58 A PHE 58 1_555 L NA NA . A NA 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc3 A O VAL 59 A VAL 59 1_555 K NA NA . A NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc4 A O SER 301 A SER 301 1_555 L NA NA . A NA 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc5 B O ABU . A ABU 701 1_555 L NA NA . A NA 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.064 ? # _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 98 n n C1 H11 D12 sing 99 n n C1 H12 D12 sing 100 n n C1 H13 D12 sing 101 n n C2 C3 D12 sing 102 n n C2 H21 D12 sing 103 n n C2 H22 D12 sing 104 n n C3 C4 D12 sing 105 n n C3 H31 D12 sing 106 n n C3 H32 D12 sing 107 n n C4 C5 D12 sing 108 n n C4 H41 D12 sing 109 n n C4 H42 D12 sing 110 n n C5 C6 D12 sing 111 n n C5 H51 D12 sing 112 n n C5 H52 D12 sing 113 n n C6 C7 D12 sing 114 n n C6 H61 D12 sing 115 n n C6 H62 D12 sing 116 n n C7 C8 D12 sing 117 n n C7 H71 D12 sing 118 n n C7 H72 D12 sing 119 n n C8 C9 D12 sing 120 n n C8 H81 D12 sing 121 n n C8 H82 D12 sing 122 n n C9 C10 D12 sing 123 n n C9 H91 D12 sing 124 n n C9 H92 D12 sing 125 n n C10 C11 D12 sing 126 n n C10 H101 D12 sing 127 n n C10 H102 D12 sing 128 n n C11 C12 D12 sing 129 n n C11 H111 D12 sing 130 n n C11 H112 D12 sing 131 n n C12 H121 D12 sing 132 n n C12 H122 D12 sing 133 n n C12 H123 D12 sing 134 n n # _atom_sites.entry_id 9JD4 _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 ABU A 1 701 601 ABU ABU . C 3 OCT A 1 702 602 OCT OCT . D 4 D12 A 1 703 603 D12 D12 . E 3 OCT A 1 704 604 OCT OCT . F 4 D12 A 1 705 605 D12 D12 . G 5 HEX A 1 706 606 HEX HEX . H 4 D12 A 1 707 607 D12 D12 . I 3 OCT A 1 708 608 OCT OCT . J 6 CL A 1 709 701 CL CL . K 7 NA A 1 710 702 NA NA . L 7 NA A 1 711 703 NA NA . M 8 NAG A 1 712 704 NAG NAG . # 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 . . . F 4 108.975 120.078 157.046 1 76.03 ? C1 D12 705 A 1 HETATM 2 C C2 D12 . . . F 4 110.078 120.665 156.177 1 76.72 ? C2 D12 705 A 1 HETATM 3 C C3 D12 . . . F 4 111.471 120.445 156.756 1 75.41 ? C3 D12 705 A 1 HETATM 4 C C4 D12 . . . F 4 112.524 121.359 156.14 1 75.2 ? C4 D12 705 A 1 HETATM 5 C C5 D12 . . . F 4 113.923 121.176 156.717 1 75.11 ? C5 D12 705 A 1 HETATM 6 C C6 D12 . . . F 4 114.594 119.879 156.284 1 72.97 ? C6 D12 705 A 1 HETATM 7 C C7 D12 . . . F 4 116.094 119.863 156.548 1 73.16 ? C7 D12 705 A 1 HETATM 8 C C8 D12 . . . F 4 116.652 118.453 156.693 1 74.41 ? C8 D12 705 A 1 HETATM 9 C C9 D12 . . . F 4 118.174 118.397 156.755 1 75.99 ? C9 D12 705 A 1 HETATM 10 C C10 D12 . . . F 4 118.845 118.803 155.45 1 75.28 ? C10 D12 705 A 1 HETATM 11 C C11 D12 . . . F 4 120.27 118.282 155.308 1 75.06 ? C11 D12 705 A 1 HETATM 12 C C12 D12 . . . F 4 120.327 116.777 155.086 1 72.51 ? C12 D12 705 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 12 #