data_5LRT # _model_server_result.job_id iccvNcDLDIFK3nvr-SX-3w _model_server_result.datetime_utc '2025-09-11 22:52:11' _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 5lrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":611}' # _entry.id 5LRT # _exptl.entry_id 5LRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 120 _cell.entry_id 5LRT _cell.length_a 72.398 _cell.length_b 72.398 _cell.length_c 215.25 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id L _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 OE1 GLU 8 A GLU 8 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc2 A OE1 GLU 8 A GLU 8 1_555 E MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 A OE2 GLU 8 A GLU 8 1_555 E MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 A OE2 GLU 10 A GLU 10 1_555 F MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc5 A OH TYR 92 A TYR 92 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 A OD2 ASP 94 A ASP 94 1_555 F MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc7 A OE1 GLU 99 A GLU 99 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc8 A OE2 GLU 99 A GLU 99 1_555 F MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc9 A OG1 THR 217 A THR 217 1_555 L NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc10 A OE2 GLU 229 A GLU 229 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc11 B O3B ADP . A ADP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc12 B O2B ADP . A ADP 601 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc13 B O2A ADP . A ADP 601 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc14 B O1B ADP . A ADP 601 1_555 E MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc15 C MG MG . A MG 602 1_555 M O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc16 C MG MG . A MG 602 1_555 M O HOH . A HOH 738 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc17 C MG MG . A MG 602 1_555 M O HOH . A HOH 796 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc18 C MG MG . A MG 602 1_555 M O HOH . A HOH 864 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc19 D MG MG . A MG 603 1_555 G O4 PO4 . A PO4 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc20 E MG MG . A MG 604 1_555 G O1 PO4 . A PO4 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc21 F MG MG . A MG 605 1_555 G O3 PO4 . A PO4 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc22 F MG MG . A MG 605 1_555 G O4 PO4 . A PO4 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc23 F MG MG . A MG 605 1_555 M O HOH . A HOH 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc24 G O3 PO4 . A PO4 606 1_555 L NA NA . A NA 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc25 L NA NA . A NA 611 1_555 M O HOH . A HOH 779 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc26 L NA NA . A NA 611 1_555 M O HOH . A HOH 856 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc27 L NA NA . A NA 611 1_555 M O HOH . A HOH 869 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5LRT _atom_sites.fract_transf_matrix[1][1] 0.013813 _atom_sites.fract_transf_matrix[1][2] 0.007975 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015949 _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] 0.004646 _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 ADP A 1 601 1 ADP ADP . C 3 MG A 1 602 1 MG MG . D 3 MG A 1 603 2 MG MG . E 3 MG A 1 604 3 MG MG . F 3 MG A 1 605 4 MG MG . G 4 PO4 A 1 606 1 PO4 PO4 . H 5 P6G A 1 607 1 P6G P6G . I 6 PGE A 1 608 1 PGE PGE . J 6 PGE A 1 609 2 PGE PGE . K 7 PEG A 1 610 1 PEG PEG . L 8 NA A 1 611 1 NA NA . M 9 HOH A 1 701 121 HOH HOH . M 9 HOH A 2 702 144 HOH HOH . M 9 HOH A 3 703 45 HOH HOH . M 9 HOH A 4 704 163 HOH HOH . M 9 HOH A 5 705 147 HOH HOH . M 9 HOH A 6 706 214 HOH HOH . M 9 HOH A 7 707 207 HOH HOH . M 9 HOH A 8 708 101 HOH HOH . M 9 HOH A 9 709 211 HOH HOH . M 9 HOH A 10 710 76 HOH HOH . M 9 HOH A 11 711 172 HOH HOH . M 9 HOH A 12 712 122 HOH HOH . M 9 HOH A 13 713 24 HOH HOH . M 9 HOH A 14 714 191 HOH HOH . M 9 HOH A 15 715 180 HOH HOH . M 9 HOH A 16 716 213 HOH HOH . M 9 HOH A 17 717 137 HOH HOH . M 9 HOH A 18 718 110 HOH HOH . M 9 HOH A 19 719 176 HOH HOH . M 9 HOH A 20 720 2 HOH HOH . M 9 HOH A 21 721 31 HOH HOH . M 9 HOH A 22 722 43 HOH HOH . M 9 HOH A 23 723 199 HOH HOH . M 9 HOH A 24 724 94 HOH HOH . M 9 HOH A 25 725 100 HOH HOH . M 9 HOH A 26 726 38 HOH HOH . M 9 HOH A 27 727 149 HOH HOH . M 9 HOH A 28 728 57 HOH HOH . M 9 HOH A 29 729 46 HOH HOH . M 9 HOH A 30 730 36 HOH HOH . M 9 HOH A 31 731 169 HOH HOH . M 9 HOH A 32 732 224 HOH HOH . M 9 HOH A 33 733 44 HOH HOH . M 9 HOH A 34 734 86 HOH HOH . M 9 HOH A 35 735 194 HOH HOH . M 9 HOH A 36 736 21 HOH HOH . M 9 HOH A 37 737 25 HOH HOH . M 9 HOH A 38 738 17 HOH HOH . M 9 HOH A 39 739 80 HOH HOH . M 9 HOH A 40 740 77 HOH HOH . M 9 HOH A 41 741 8 HOH HOH . M 9 HOH A 42 742 66 HOH HOH . M 9 HOH A 43 743 33 HOH HOH . M 9 HOH A 44 744 42 HOH HOH . M 9 HOH A 45 745 22 HOH HOH . M 9 HOH A 46 746 41 HOH HOH . M 9 HOH A 47 747 70 HOH HOH . M 9 HOH A 48 748 79 HOH HOH . M 9 HOH A 49 749 67 HOH HOH . M 9 HOH A 50 750 18 HOH HOH . M 9 HOH A 51 751 4 HOH HOH . M 9 HOH A 52 752 11 HOH HOH . M 9 HOH A 53 753 133 HOH HOH . M 9 HOH A 54 754 28 HOH HOH . M 9 HOH A 55 755 56 HOH HOH . M 9 HOH A 56 756 54 HOH HOH . M 9 HOH A 57 757 98 HOH HOH . M 9 HOH A 58 758 142 HOH HOH . M 9 HOH A 59 759 111 HOH HOH . M 9 HOH A 60 760 27 HOH HOH . M 9 HOH A 61 761 202 HOH HOH . M 9 HOH A 62 762 114 HOH HOH . M 9 HOH A 63 763 198 HOH HOH . M 9 HOH A 64 764 74 HOH HOH . M 9 HOH A 65 765 220 HOH HOH . M 9 HOH A 66 766 89 HOH HOH . M 9 HOH A 67 767 19 HOH HOH . M 9 HOH A 68 768 222 HOH HOH . M 9 HOH A 69 769 93 HOH HOH . M 9 HOH A 70 770 61 HOH HOH . M 9 HOH A 71 771 197 HOH HOH . M 9 HOH A 72 772 5 HOH HOH . M 9 HOH A 73 773 34 HOH HOH . M 9 HOH A 74 774 59 HOH HOH . M 9 HOH A 75 775 72 HOH HOH . M 9 HOH A 76 776 87 HOH HOH . M 9 HOH A 77 777 82 HOH HOH . M 9 HOH A 78 778 10 HOH HOH . M 9 HOH A 79 779 219 HOH HOH . M 9 HOH A 80 780 60 HOH HOH . M 9 HOH A 81 781 13 HOH HOH . M 9 HOH A 82 782 16 HOH HOH . M 9 HOH A 83 783 104 HOH HOH . M 9 HOH A 84 784 20 HOH HOH . M 9 HOH A 85 785 32 HOH HOH . M 9 HOH A 86 786 52 HOH HOH . M 9 HOH A 87 787 64 HOH HOH . M 9 HOH A 88 788 6 HOH HOH . M 9 HOH A 89 789 26 HOH HOH . M 9 HOH A 90 790 37 HOH HOH . M 9 HOH A 91 791 14 HOH HOH . M 9 HOH A 92 792 51 HOH HOH . M 9 HOH A 93 793 106 HOH HOH . M 9 HOH A 94 794 128 HOH HOH . M 9 HOH A 95 795 65 HOH HOH . M 9 HOH A 96 796 15 HOH HOH . M 9 HOH A 97 797 49 HOH HOH . M 9 HOH A 98 798 30 HOH HOH . M 9 HOH A 99 799 53 HOH HOH . M 9 HOH A 100 800 127 HOH HOH . M 9 HOH A 101 801 139 HOH HOH . M 9 HOH A 102 802 112 HOH HOH . M 9 HOH A 103 803 84 HOH HOH . M 9 HOH A 104 804 103 HOH HOH . M 9 HOH A 105 805 97 HOH HOH . M 9 HOH A 106 806 83 HOH HOH . M 9 HOH A 107 807 170 HOH HOH . M 9 HOH A 108 808 63 HOH HOH . M 9 HOH A 109 809 113 HOH HOH . M 9 HOH A 110 810 9 HOH HOH . M 9 HOH A 111 811 184 HOH HOH . M 9 HOH A 112 812 118 HOH HOH . M 9 HOH A 113 813 123 HOH HOH . M 9 HOH A 114 814 107 HOH HOH . M 9 HOH A 115 815 155 HOH HOH . M 9 HOH A 116 816 29 HOH HOH . M 9 HOH A 117 817 165 HOH HOH . M 9 HOH A 118 818 153 HOH HOH . M 9 HOH A 119 819 92 HOH HOH . M 9 HOH A 120 820 1 HOH HOH . M 9 HOH A 121 821 206 HOH HOH . M 9 HOH A 122 822 134 HOH HOH . M 9 HOH A 123 823 40 HOH HOH . M 9 HOH A 124 824 151 HOH HOH . M 9 HOH A 125 825 3 HOH HOH . M 9 HOH A 126 826 12 HOH HOH . M 9 HOH A 127 827 130 HOH HOH . M 9 HOH A 128 828 178 HOH HOH . M 9 HOH A 129 829 48 HOH HOH . M 9 HOH A 130 830 35 HOH HOH . M 9 HOH A 131 831 203 HOH HOH . M 9 HOH A 132 832 71 HOH HOH . M 9 HOH A 133 833 201 HOH HOH . M 9 HOH A 134 834 23 HOH HOH . M 9 HOH A 135 835 150 HOH HOH . M 9 HOH A 136 836 138 HOH HOH . M 9 HOH A 137 837 99 HOH HOH . M 9 HOH A 138 838 116 HOH HOH . M 9 HOH A 139 839 158 HOH HOH . M 9 HOH A 140 840 7 HOH HOH . M 9 HOH A 141 841 148 HOH HOH . M 9 HOH A 142 842 166 HOH HOH . M 9 HOH A 143 843 85 HOH HOH . M 9 HOH A 144 844 131 HOH HOH . M 9 HOH A 145 845 216 HOH HOH . M 9 HOH A 146 846 115 HOH HOH . M 9 HOH A 147 847 108 HOH HOH . M 9 HOH A 148 848 69 HOH HOH . M 9 HOH A 149 849 90 HOH HOH . M 9 HOH A 150 850 124 HOH HOH . M 9 HOH A 151 851 162 HOH HOH . M 9 HOH A 152 852 55 HOH HOH . M 9 HOH A 153 853 135 HOH HOH . M 9 HOH A 154 854 47 HOH HOH . M 9 HOH A 155 855 208 HOH HOH . M 9 HOH A 156 856 157 HOH HOH . M 9 HOH A 157 857 91 HOH HOH . M 9 HOH A 158 858 145 HOH HOH . M 9 HOH A 159 859 132 HOH HOH . M 9 HOH A 160 860 73 HOH HOH . M 9 HOH A 161 861 152 HOH HOH . M 9 HOH A 162 862 39 HOH HOH . M 9 HOH A 163 863 136 HOH HOH . M 9 HOH A 164 864 50 HOH HOH . M 9 HOH A 165 865 161 HOH HOH . M 9 HOH A 166 866 217 HOH HOH . M 9 HOH A 167 867 140 HOH HOH . M 9 HOH A 168 868 102 HOH HOH . M 9 HOH A 169 869 125 HOH HOH . M 9 HOH A 170 870 120 HOH HOH . M 9 HOH A 171 871 109 HOH HOH . M 9 HOH A 172 872 119 HOH HOH . M 9 HOH A 173 873 218 HOH HOH . M 9 HOH A 174 874 141 HOH HOH . M 9 HOH A 175 875 88 HOH HOH . M 9 HOH A 176 876 168 HOH HOH . M 9 HOH A 177 877 177 HOH HOH . M 9 HOH A 178 878 105 HOH HOH . M 9 HOH A 179 879 209 HOH HOH . M 9 HOH A 180 880 205 HOH HOH . M 9 HOH A 181 881 159 HOH HOH . M 9 HOH A 182 882 62 HOH HOH . M 9 HOH A 183 883 189 HOH HOH . M 9 HOH A 184 884 129 HOH HOH . M 9 HOH A 185 885 164 HOH HOH . M 9 HOH A 186 886 183 HOH HOH . M 9 HOH A 187 887 179 HOH HOH . M 9 HOH A 188 888 117 HOH HOH . M 9 HOH A 189 889 160 HOH HOH . M 9 HOH A 190 890 126 HOH HOH . M 9 HOH A 191 891 221 HOH HOH . M 9 HOH A 192 892 195 HOH HOH . M 9 HOH A 193 893 154 HOH HOH . M 9 HOH A 194 894 143 HOH HOH . M 9 HOH A 195 895 186 HOH HOH . M 9 HOH A 196 896 156 HOH HOH . M 9 HOH A 197 897 167 HOH HOH . M 9 HOH A 198 898 78 HOH HOH . M 9 HOH A 199 899 181 HOH HOH . M 9 HOH A 200 900 215 HOH HOH . M 9 HOH A 201 901 204 HOH HOH . M 9 HOH A 202 902 182 HOH HOH . M 9 HOH A 203 903 58 HOH HOH . M 9 HOH A 204 904 223 HOH HOH . M 9 HOH A 205 905 200 HOH HOH . M 9 HOH A 206 906 196 HOH HOH . M 9 HOH A 207 907 212 HOH HOH . M 9 HOH A 208 908 96 HOH HOH . M 9 HOH A 209 909 146 HOH HOH . M 9 HOH A 210 910 188 HOH HOH . M 9 HOH A 211 911 210 HOH HOH . M 9 HOH A 212 912 68 HOH HOH . M 9 HOH A 213 913 75 HOH HOH . M 9 HOH A 214 914 185 HOH HOH . M 9 HOH A 215 915 192 HOH HOH . M 9 HOH A 216 916 174 HOH HOH . M 9 HOH A 217 917 81 HOH HOH . M 9 HOH A 218 918 187 HOH HOH . M 9 HOH A 219 919 171 HOH HOH . M 9 HOH A 220 920 173 HOH HOH . M 9 HOH A 221 921 175 HOH HOH . M 9 HOH A 222 922 190 HOH HOH . M 9 HOH A 223 923 95 HOH HOH . M 9 HOH A 224 924 193 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id L _atom_site.label_entity_id 8 _atom_site.Cartn_x -16.06 _atom_site.Cartn_y 71.674 _atom_site.Cartn_z 17.868 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 54.52 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 611 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #