data_5DHK # _model_server_result.job_id ApvFPZhLEVybIuK5ZOteQA _model_server_result.datetime_utc '2025-03-06 09:40:11' _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 5dhk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 5DHK # _exptl.entry_id 5DHK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.367 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description FARNESYL _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 5DHK _cell.length_a 126.69 _cell.length_b 126.69 _cell.length_c 122 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DHK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _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 _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 3 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASP 289 A ASP 301 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc2 A OD2 ASP 289 A ASP 301 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc3 A OD2 ASP 293 A ASP 305 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc4 A OD2 ASP 293 A ASP 305 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc5 A OE2 GLU 367 A GLU 379 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? # _chem_comp.formula 'C15 H26' _chem_comp.formula_weight 206.367 _chem_comp.id FAR _chem_comp.mon_nstd_flag . _chem_comp.name FARNESYL _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 FAR sing 83 n n C1 H11 FAR sing 84 n n C1 H12A FAR sing 85 n n C1 H13 FAR sing 86 n n C2 C3 FAR doub 87 e n C2 H2 FAR sing 88 n n C3 C5 FAR sing 89 n n C3 C4 FAR sing 90 n n C5 C6 FAR sing 91 n n C5 H51 FAR sing 92 n n C5 H52 FAR sing 93 n n C6 C7 FAR sing 94 n n C6 H61 FAR sing 95 n n C6 H62 FAR sing 96 n n C7 C8 FAR doub 97 e n C7 H7 FAR sing 98 n n C8 C9 FAR sing 99 n n C8 C10 FAR sing 100 n n C9 C11 FAR sing 101 n n C9 H91 FAR sing 102 n n C9 H92 FAR sing 103 n n C11 C12 FAR sing 104 n n C11 H111 FAR sing 105 n n C11 H112 FAR sing 106 n n C12 C13 FAR doub 107 n n C12 H12 FAR sing 108 n n C13 C14 FAR sing 109 n n C13 C15 FAR sing 110 n n C14 H141 FAR sing 111 n n C14 H142 FAR sing 112 n n C14 H143 FAR sing 113 n n C15 H151 FAR sing 114 n n C15 H152 FAR sing 115 n n C15 H153 FAR sing 116 n n C4 H41 FAR sing 117 n n C4 H42 FAR sing 118 n n C4 H43 FAR sing 119 n n C10 H101 FAR sing 120 n n C10 H102 FAR sing 121 n n C10 H103 FAR sing 122 n n # _atom_sites.entry_id 5DHK _atom_sites.fract_transf_matrix[1][1] 0.007893 _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] 0.007893 _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] 0.008197 _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 MG A 1 601 1 MG MG . C 2 MG A 1 602 2 MG MG . D 3 FAR A 1 603 1 FAR FAR . E 4 HOH A 1 701 9 HOH HOH . E 4 HOH A 2 702 89 HOH HOH . E 4 HOH A 3 703 85 HOH HOH . E 4 HOH A 4 704 108 HOH HOH . E 4 HOH A 5 705 36 HOH HOH . E 4 HOH A 6 706 107 HOH HOH . E 4 HOH A 7 707 88 HOH HOH . E 4 HOH A 8 708 80 HOH HOH . E 4 HOH A 9 709 21 HOH HOH . E 4 HOH A 10 710 19 HOH HOH . E 4 HOH A 11 711 45 HOH HOH . E 4 HOH A 12 712 33 HOH HOH . E 4 HOH A 13 713 7 HOH HOH . E 4 HOH A 14 714 11 HOH HOH . E 4 HOH A 15 715 77 HOH HOH . E 4 HOH A 16 716 53 HOH HOH . E 4 HOH A 17 717 52 HOH HOH . E 4 HOH A 18 718 54 HOH HOH . E 4 HOH A 19 719 32 HOH HOH . E 4 HOH A 20 720 86 HOH HOH . E 4 HOH A 21 721 78 HOH HOH . E 4 HOH A 22 722 12 HOH HOH . E 4 HOH A 23 723 3 HOH HOH . E 4 HOH A 24 724 48 HOH HOH . E 4 HOH A 25 725 29 HOH HOH . E 4 HOH A 26 726 74 HOH HOH . E 4 HOH A 27 727 26 HOH HOH . E 4 HOH A 28 728 110 HOH HOH . E 4 HOH A 29 729 58 HOH HOH . E 4 HOH A 30 730 92 HOH HOH . E 4 HOH A 31 731 50 HOH HOH . E 4 HOH A 32 732 14 HOH HOH . E 4 HOH A 33 733 44 HOH HOH . E 4 HOH A 34 734 68 HOH HOH . E 4 HOH A 35 735 4 HOH HOH . E 4 HOH A 36 736 91 HOH HOH . E 4 HOH A 37 737 79 HOH HOH . E 4 HOH A 38 738 106 HOH HOH . E 4 HOH A 39 739 1 HOH HOH . E 4 HOH A 40 740 81 HOH HOH . E 4 HOH A 41 741 15 HOH HOH . E 4 HOH A 42 742 100 HOH HOH . E 4 HOH A 43 743 41 HOH HOH . E 4 HOH A 44 744 27 HOH HOH . E 4 HOH A 45 745 64 HOH HOH . E 4 HOH A 46 746 57 HOH HOH . E 4 HOH A 47 747 51 HOH HOH . E 4 HOH A 48 748 63 HOH HOH . E 4 HOH A 49 749 16 HOH HOH . E 4 HOH A 50 750 10 HOH HOH . E 4 HOH A 51 751 35 HOH HOH . E 4 HOH A 52 752 2 HOH HOH . E 4 HOH A 53 753 34 HOH HOH . E 4 HOH A 54 754 8 HOH HOH . E 4 HOH A 55 755 38 HOH HOH . E 4 HOH A 56 756 24 HOH HOH . E 4 HOH A 57 757 114 HOH HOH . E 4 HOH A 58 758 90 HOH HOH . E 4 HOH A 59 759 31 HOH HOH . E 4 HOH A 60 760 39 HOH HOH . E 4 HOH A 61 761 76 HOH HOH . E 4 HOH A 62 762 87 HOH HOH . E 4 HOH A 63 763 23 HOH HOH . E 4 HOH A 64 764 30 HOH HOH . E 4 HOH A 65 765 98 HOH HOH . E 4 HOH A 66 766 75 HOH HOH . E 4 HOH A 67 767 61 HOH HOH . E 4 HOH A 68 768 104 HOH HOH . E 4 HOH A 69 769 70 HOH HOH . E 4 HOH A 70 770 22 HOH HOH . E 4 HOH A 71 771 118 HOH HOH . E 4 HOH A 72 772 62 HOH HOH . E 4 HOH A 73 773 67 HOH HOH . E 4 HOH A 74 774 102 HOH HOH . E 4 HOH A 75 775 6 HOH HOH . E 4 HOH A 76 776 5 HOH HOH . E 4 HOH A 77 777 47 HOH HOH . E 4 HOH A 78 778 73 HOH HOH . E 4 HOH A 79 779 112 HOH HOH . E 4 HOH A 80 780 72 HOH HOH . E 4 HOH A 81 781 20 HOH HOH . E 4 HOH A 82 782 40 HOH HOH . E 4 HOH A 83 783 13 HOH HOH . E 4 HOH A 84 784 59 HOH HOH . E 4 HOH A 85 785 42 HOH HOH . E 4 HOH A 86 786 43 HOH HOH . E 4 HOH A 87 787 25 HOH HOH . E 4 HOH A 88 788 46 HOH HOH . E 4 HOH A 89 789 103 HOH HOH . E 4 HOH A 90 790 84 HOH HOH . E 4 HOH A 91 791 109 HOH HOH . E 4 HOH A 92 792 18 HOH HOH . E 4 HOH A 93 793 105 HOH HOH . E 4 HOH A 94 794 60 HOH HOH . E 4 HOH A 95 795 56 HOH HOH . E 4 HOH A 96 796 115 HOH HOH . E 4 HOH A 97 797 95 HOH HOH . E 4 HOH A 98 798 17 HOH HOH . E 4 HOH A 99 799 99 HOH HOH . E 4 HOH A 100 800 111 HOH HOH . E 4 HOH A 101 801 69 HOH HOH . E 4 HOH A 102 802 71 HOH HOH . E 4 HOH A 103 803 82 HOH HOH . E 4 HOH A 104 804 97 HOH HOH . E 4 HOH A 105 805 28 HOH HOH . E 4 HOH A 106 806 49 HOH HOH . E 4 HOH A 107 807 83 HOH HOH . E 4 HOH A 108 808 101 HOH HOH . E 4 HOH A 109 809 113 HOH HOH . E 4 HOH A 110 810 117 HOH HOH . E 4 HOH A 111 811 93 HOH HOH . E 4 HOH A 112 812 116 HOH HOH . E 4 HOH A 113 813 65 HOH HOH . E 4 HOH A 114 814 37 HOH HOH . E 4 HOH A 115 815 66 HOH HOH . E 4 HOH A 116 816 55 HOH HOH . E 4 HOH A 117 817 96 HOH HOH . E 4 HOH A 118 818 94 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 FAR . . . D 3 78.375 27.664 49.417 0.83 60.26 ? C1 FAR 603 A 1 HETATM 2 C C2 FAR . . . D 3 79.17 26.353 49.28 0.83 57.62 ? C2 FAR 603 A 1 HETATM 3 C C3 FAR . . . D 3 78.885 25.524 48.305 0.83 59.68 ? C3 FAR 603 A 1 HETATM 4 C C5 FAR . . . D 3 79.672 24.204 48.157 0.83 64.23 ? C5 FAR 603 A 1 HETATM 5 C C6 FAR . . . D 3 79.926 23.825 46.665 0.83 60.84 ? C6 FAR 603 A 1 HETATM 6 C C7 FAR . . . D 3 78.593 23.407 46.024 0.83 63.47 ? C7 FAR 603 A 1 HETATM 7 C C8 FAR . . . D 3 78.056 22.196 46.112 0.83 60.34 ? C8 FAR 603 A 1 HETATM 8 C C9 FAR . . . D 3 76.713 22.008 45.409 0.83 58.83 ? C9 FAR 603 A 1 HETATM 9 C C11 FAR . . . D 3 75.495 22.201 46.359 0.83 58.39 ? C11 FAR 603 A 1 HETATM 10 C C12 FAR . . . D 3 75.182 23.637 46.861 0.83 58.5 ? C12 FAR 603 A 1 HETATM 11 C C13 FAR . . . D 3 74.763 24.65 46.078 0.83 54.43 ? C13 FAR 603 A 1 HETATM 12 C C14 FAR . . . D 3 74.437 26.032 46.665 0.83 51.21 ? C14 FAR 603 A 1 HETATM 13 C C15 FAR . . . D 3 74.546 24.486 44.576 0.83 55.25 ? C15 FAR 603 A 1 HETATM 14 C C4 FAR . . . D 3 77.744 25.904 47.364 0.83 60.51 ? C4 FAR 603 A 1 HETATM 15 C C10 FAR . . . D 3 78.742 21.022 46.82 0.83 70.67 ? C10 FAR 603 A 1 HETATM 16 H H11 FAR . . . D 3 77.316 27.438 49.503 0.83 72.32 ? H11 FAR 603 A 1 HETATM 17 H H12A FAR . . . D 3 78.705 28.196 50.304 0.83 72.32 ? H12A FAR 603 A 1 HETATM 18 H H2 FAR . . . D 3 79.97 26.125 49.973 0.83 69.14 ? H2 FAR 603 A 1 HETATM 19 H H51 FAR . . . D 3 80.63 24.308 48.661 0.83 77.08 ? H51 FAR 603 A 1 HETATM 20 H H52 FAR . . . D 3 79.11 23.406 48.631 0.83 77.08 ? H52 FAR 603 A 1 HETATM 21 H H61 FAR . . . D 3 80.33 24.679 46.138 0.83 73.01 ? H61 FAR 603 A 1 HETATM 22 H H62 FAR . . . D 3 80.63 22.999 46.614 0.83 73.01 ? H62 FAR 603 A 1 HETATM 23 H H7 FAR . . . D 3 78.029 24.168 45.501 0.83 76.17 ? H7 FAR 603 A 1 HETATM 24 H H91 FAR . . . D 3 76.675 21.007 44.993 0.83 70.6 ? H91 FAR 603 A 1 HETATM 25 H H92 FAR . . . D 3 76.64 22.728 44.597 0.83 70.6 ? H92 FAR 603 A 1 HETATM 26 H H111 FAR . . . D 3 75.655 21.577 47.228 0.83 70.07 ? H111 FAR 603 A 1 HETATM 27 H H112 FAR . . . D 3 74.617 21.835 45.845 0.83 70.07 ? H112 FAR 603 A 1 HETATM 28 H H12 FAR . . . D 3 75.293 23.835 47.927 0.83 70.2 ? H12 FAR 603 A 1 HETATM 29 H H141 FAR . . . D 3 75.306 26.417 47.189 0.83 61.45 ? H141 FAR 603 A 1 HETATM 30 H H142 FAR . . . D 3 73.606 25.944 47.357 0.83 61.45 ? H142 FAR 603 A 1 HETATM 31 H H143 FAR . . . D 3 74.165 26.717 45.856 0.83 61.45 ? H143 FAR 603 A 1 HETATM 32 H H151 FAR . . . D 3 73.794 23.72 44.399 0.83 66.3 ? H151 FAR 603 A 1 HETATM 33 H H152 FAR . . . D 3 75.475 24.194 44.107 0.83 66.3 ? H152 FAR 603 A 1 HETATM 34 H H153 FAR . . . D 3 74.208 25.428 44.154 0.83 66.3 ? H153 FAR 603 A 1 HETATM 35 H H41 FAR . . . D 3 77.257 25.001 47 0.83 72.61 ? H41 FAR 603 A 1 HETATM 36 H H42 FAR . . . D 3 78.138 26.463 46.527 0.83 72.61 ? H42 FAR 603 A 1 HETATM 37 H H43 FAR . . . D 3 77.025 26.511 47.897 0.83 72.61 ? H43 FAR 603 A 1 HETATM 38 H H101 FAR . . . D 3 79.576 21.39 47.404 0.83 84.81 ? H101 FAR 603 A 1 HETATM 39 H H102 FAR . . . D 3 78.033 20.529 47.473 0.83 84.81 ? H102 FAR 603 A 1 HETATM 40 H H103 FAR . . . D 3 79.103 20.315 46.079 0.83 84.81 ? H103 FAR 603 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #