data_5DEL # _model_server_result.job_id reWJ3be48rdYEYQBIC2C5Q _model_server_result.datetime_utc '2024-11-29 07:05:24' _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 5del # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":606}' # _entry.id 5DEL # _exptl.entry_id 5DEL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5DEL _cell.length_a 85.046 _cell.length_b 85.046 _cell.length_c 137.704 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DEL _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64' # _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,F,G,H _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 ? 5 E N N ? 5 G N N # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 215 n n C1 C2 GOL sing 216 n n C1 H11 GOL sing 217 n n C1 H12 GOL sing 218 n n O1 HO1 GOL sing 219 n n C2 O2 GOL sing 220 n n C2 C3 GOL sing 221 n n C2 H2 GOL sing 222 n n O2 HO2 GOL sing 223 n n C3 O3 GOL sing 224 n n C3 H31 GOL sing 225 n n C3 H32 GOL sing 226 n n O3 HO3 GOL sing 227 n n # _atom_sites.entry_id 5DEL _atom_sites.fract_transf_matrix[1][1] 0.011758 _atom_sites.fract_transf_matrix[1][2] 0.006789 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013577 _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] 0.007262 _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 FMN A 1 601 1002 FMN FMN . C 3 ORO A 1 602 1003 ORO ORO . D 4 D59 A 1 603 1004 D59 D59 . E 5 GOL A 1 604 1005 GOL GOL . F 6 LDA A 1 605 1006 LDA LDA . G 5 GOL A 1 606 1007 GOL GOL . H 7 HOH A 1 701 154 HOH HOH . H 7 HOH A 2 702 164 HOH HOH . H 7 HOH A 3 703 90 HOH HOH . H 7 HOH A 4 704 74 HOH HOH . H 7 HOH A 5 705 48 HOH HOH . H 7 HOH A 6 706 19 HOH HOH . H 7 HOH A 7 707 60 HOH HOH . H 7 HOH A 8 708 61 HOH HOH . H 7 HOH A 9 709 85 HOH HOH . H 7 HOH A 10 710 9 HOH HOH . H 7 HOH A 11 711 54 HOH HOH . H 7 HOH A 12 712 141 HOH HOH . H 7 HOH A 13 713 137 HOH HOH . H 7 HOH A 14 714 15 HOH HOH . H 7 HOH A 15 715 37 HOH HOH . H 7 HOH A 16 716 94 HOH HOH . H 7 HOH A 17 717 130 HOH HOH . H 7 HOH A 18 718 73 HOH HOH . H 7 HOH A 19 719 72 HOH HOH . H 7 HOH A 20 720 11 HOH HOH . H 7 HOH A 21 721 62 HOH HOH . H 7 HOH A 22 722 31 HOH HOH . H 7 HOH A 23 723 12 HOH HOH . H 7 HOH A 24 724 126 HOH HOH . H 7 HOH A 25 725 41 HOH HOH . H 7 HOH A 26 726 69 HOH HOH . H 7 HOH A 27 727 63 HOH HOH . H 7 HOH A 28 728 17 HOH HOH . H 7 HOH A 29 729 171 HOH HOH . H 7 HOH A 30 730 151 HOH HOH . H 7 HOH A 31 731 14 HOH HOH . H 7 HOH A 32 732 25 HOH HOH . H 7 HOH A 33 733 10 HOH HOH . H 7 HOH A 34 734 47 HOH HOH . H 7 HOH A 35 735 93 HOH HOH . H 7 HOH A 36 736 39 HOH HOH . H 7 HOH A 37 737 5 HOH HOH . H 7 HOH A 38 738 89 HOH HOH . H 7 HOH A 39 739 78 HOH HOH . H 7 HOH A 40 740 179 HOH HOH . H 7 HOH A 41 741 33 HOH HOH . H 7 HOH A 42 742 6 HOH HOH . H 7 HOH A 43 743 142 HOH HOH . H 7 HOH A 44 744 20 HOH HOH . H 7 HOH A 45 745 108 HOH HOH . H 7 HOH A 46 746 36 HOH HOH . H 7 HOH A 47 747 40 HOH HOH . H 7 HOH A 48 748 30 HOH HOH . H 7 HOH A 49 749 32 HOH HOH . H 7 HOH A 50 750 8 HOH HOH . H 7 HOH A 51 751 49 HOH HOH . H 7 HOH A 52 752 42 HOH HOH . H 7 HOH A 53 753 105 HOH HOH . H 7 HOH A 54 754 116 HOH HOH . H 7 HOH A 55 755 57 HOH HOH . H 7 HOH A 56 756 2 HOH HOH . H 7 HOH A 57 757 1 HOH HOH . H 7 HOH A 58 758 16 HOH HOH . H 7 HOH A 59 759 86 HOH HOH . H 7 HOH A 60 760 26 HOH HOH . H 7 HOH A 61 761 27 HOH HOH . H 7 HOH A 62 762 3 HOH HOH . H 7 HOH A 63 763 82 HOH HOH . H 7 HOH A 64 764 76 HOH HOH . H 7 HOH A 65 765 75 HOH HOH . H 7 HOH A 66 766 101 HOH HOH . H 7 HOH A 67 767 103 HOH HOH . H 7 HOH A 68 768 77 HOH HOH . H 7 HOH A 69 769 95 HOH HOH . H 7 HOH A 70 770 112 HOH HOH . H 7 HOH A 71 771 160 HOH HOH . H 7 HOH A 72 772 34 HOH HOH . H 7 HOH A 73 773 13 HOH HOH . H 7 HOH A 74 774 188 HOH HOH . H 7 HOH A 75 775 87 HOH HOH . H 7 HOH A 76 776 139 HOH HOH . H 7 HOH A 77 777 51 HOH HOH . H 7 HOH A 78 778 56 HOH HOH . H 7 HOH A 79 779 43 HOH HOH . H 7 HOH A 80 780 187 HOH HOH . H 7 HOH A 81 781 177 HOH HOH . H 7 HOH A 82 782 46 HOH HOH . H 7 HOH A 83 783 55 HOH HOH . H 7 HOH A 84 784 91 HOH HOH . H 7 HOH A 85 785 38 HOH HOH . H 7 HOH A 86 786 110 HOH HOH . H 7 HOH A 87 787 80 HOH HOH . H 7 HOH A 88 788 166 HOH HOH . H 7 HOH A 89 789 44 HOH HOH . H 7 HOH A 90 790 64 HOH HOH . H 7 HOH A 91 791 152 HOH HOH . H 7 HOH A 92 792 109 HOH HOH . H 7 HOH A 93 793 132 HOH HOH . H 7 HOH A 94 794 92 HOH HOH . H 7 HOH A 95 795 67 HOH HOH . H 7 HOH A 96 796 190 HOH HOH . H 7 HOH A 97 797 22 HOH HOH . H 7 HOH A 98 798 99 HOH HOH . H 7 HOH A 99 799 88 HOH HOH . H 7 HOH A 100 800 131 HOH HOH . H 7 HOH A 101 801 24 HOH HOH . H 7 HOH A 102 802 45 HOH HOH . H 7 HOH A 103 803 96 HOH HOH . H 7 HOH A 104 804 150 HOH HOH . H 7 HOH A 105 805 136 HOH HOH . H 7 HOH A 106 806 168 HOH HOH . H 7 HOH A 107 807 58 HOH HOH . H 7 HOH A 108 808 65 HOH HOH . H 7 HOH A 109 809 79 HOH HOH . H 7 HOH A 110 810 70 HOH HOH . H 7 HOH A 111 811 123 HOH HOH . H 7 HOH A 112 812 107 HOH HOH . H 7 HOH A 113 813 176 HOH HOH . H 7 HOH A 114 814 135 HOH HOH . H 7 HOH A 115 815 106 HOH HOH . H 7 HOH A 116 816 165 HOH HOH . H 7 HOH A 117 817 113 HOH HOH . H 7 HOH A 118 818 125 HOH HOH . H 7 HOH A 119 819 52 HOH HOH . H 7 HOH A 120 820 50 HOH HOH . H 7 HOH A 121 821 155 HOH HOH . H 7 HOH A 122 822 163 HOH HOH . H 7 HOH A 123 823 145 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 GOL . . . G 5 -2.176 -1.823 2.601 1 49.93 ? C1 GOL 606 A 1 HETATM 2 O O1 GOL . . . G 5 -1.605 -1.183 3.717 1 42.06 ? O1 GOL 606 A 1 HETATM 3 C C2 GOL . . . G 5 -3.43 -1.089 2.147 1 51.79 ? C2 GOL 606 A 1 HETATM 4 O O2 GOL . . . G 5 -3.411 0.241 2.615 1 52.14 ? O2 GOL 606 A 1 HETATM 5 C C3 GOL . . . G 5 -3.492 -1.1 0.624 1 55.22 ? C3 GOL 606 A 1 HETATM 6 O O3 GOL . . . G 5 -4.775 -0.707 0.196 1 53.77 ? O3 GOL 606 A 1 HETATM 7 H H11 GOL . . . G 5 -2.428 -2.851 2.859 1 59.92 ? H11 GOL 606 A 1 HETATM 8 H H12 GOL . . . G 5 -1.453 -1.848 1.786 1 59.92 ? H12 GOL 606 A 1 HETATM 9 H HO1 GOL . . . G 5 -0.839 -1.703 4.036 1 50.48 ? HO1 GOL 606 A 1 HETATM 10 H H2 GOL . . . G 5 -4.304 -1.609 2.539 1 62.15 ? H2 GOL 606 A 1 HETATM 11 H HO2 GOL . . . G 5 -2.631 0.706 2.246 1 62.57 ? HO2 GOL 606 A 1 HETATM 12 H H31 GOL . . . G 5 -3.272 -2.101 0.254 1 66.27 ? H31 GOL 606 A 1 HETATM 13 H H32 GOL . . . G 5 -2.745 -0.416 0.221 1 66.27 ? H32 GOL 606 A 1 HETATM 14 H HO3 GOL . . . G 5 -4.825 -0.766 -0.781 1 64.53 ? HO3 GOL 606 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #