data_3U8T # _model_server_result.job_id 4NJ_VPHK1ZMPJCb0Im8_iQ _model_server_result.datetime_utc '2024-11-30 16:22:16' _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 3u8t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 3U8T # _exptl.entry_id 3U8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _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 90 _cell.entry_id 3U8T _cell.length_a 51.8 _cell.length_b 77.1 _cell.length_c 83.43 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U8T _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 3 L CYS 293 1_555 B SG CYS 119 H CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf2 B SG CYS 28 H CYS 348 1_555 B SG CYS 44 H CYS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf3 B SG CYS 173 H CYS 493 1_555 B SG CYS 187 H CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 201 H CYS 521 1_555 B SG CYS 231 H CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? covale ? covale1 B ND2 ASN 53 H ASN 373 1_555 D C1 NAG . H NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 C C DPN 1 I DPN 1 1_555 C N PRO 2 I PRO 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 sing covale ? covale3 C C PRO 2 I PRO 2 1_555 C N DAR 3 I DAR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 sing covale ? covale4 C C DAR 3 I DAR 3 1_555 C N CYS 4 I CYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 sing covale ? covale5 C C CYS 4 I CYS 4 1_555 C N NH2 5 I NH2 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 sing metalc ? metalc1 B O ARG 233 H ARG 553 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc2 B O LYS 236 H LYS 556 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc3 E NA NA . H NA 602 1_555 J O HOH . H HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc4 E NA NA . H NA 602 1_555 J O HOH . H HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc5 E NA NA . H NA 602 1_555 J O HOH . H HOH 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc6 E NA NA . H NA 602 1_555 J O HOH . H HOH 738 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? # _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 3U8T _atom_sites.fract_transf_matrix[1][1] 0.019305 _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] 0.01297 _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] 0.011986 _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 D 4 NAG H 1 601 1373 NAG NAG . E 5 NA H 1 602 1 NA NA . F 6 IOD H 1 603 2 IOD I . G 7 CL H 1 604 3 CL CL . H 8 MPD H 1 605 700 MPD MPD . I 9 HOH L 1 401 16 HOH HOH . I 9 HOH L 2 402 41 HOH HOH . I 9 HOH L 3 403 46 HOH HOH . I 9 HOH L 4 404 54 HOH HOH . I 9 HOH L 5 405 56 HOH HOH . I 9 HOH L 6 406 66 HOH HOH . I 9 HOH L 7 407 68 HOH HOH . I 9 HOH L 8 408 75 HOH HOH . I 9 HOH L 9 409 80 HOH HOH . I 9 HOH L 10 410 85 HOH HOH . I 9 HOH L 11 411 88 HOH HOH . I 9 HOH L 12 412 92 HOH HOH . I 9 HOH L 13 413 93 HOH HOH . I 9 HOH L 14 414 94 HOH HOH . I 9 HOH L 15 415 99 HOH HOH . I 9 HOH L 16 416 110 HOH HOH . I 9 HOH L 17 417 121 HOH HOH . I 9 HOH L 18 418 122 HOH HOH . I 9 HOH L 19 419 131 HOH HOH . I 9 HOH L 20 420 139 HOH HOH . I 9 HOH L 21 421 145 HOH HOH . I 9 HOH L 22 422 146 HOH HOH . I 9 HOH L 23 423 147 HOH HOH . I 9 HOH L 24 424 159 HOH HOH . I 9 HOH L 25 425 162 HOH HOH . I 9 HOH L 26 426 167 HOH HOH . I 9 HOH L 27 427 168 HOH HOH . I 9 HOH L 28 428 175 HOH HOH . I 9 HOH L 29 429 177 HOH HOH . I 9 HOH L 30 430 178 HOH HOH . I 9 HOH L 31 431 183 HOH HOH . I 9 HOH L 32 432 202 HOH HOH . I 9 HOH L 33 433 205 HOH HOH . I 9 HOH L 34 434 228 HOH HOH . I 9 HOH L 35 435 266 HOH HOH . J 9 HOH H 1 701 4 HOH HOH . J 9 HOH H 2 702 5 HOH HOH . J 9 HOH H 3 703 6 HOH HOH . J 9 HOH H 4 704 7 HOH HOH . J 9 HOH H 5 705 8 HOH HOH . J 9 HOH H 6 706 9 HOH HOH . J 9 HOH H 7 707 10 HOH HOH . J 9 HOH H 8 708 11 HOH HOH . J 9 HOH H 9 709 12 HOH HOH . J 9 HOH H 10 710 13 HOH HOH . J 9 HOH H 11 711 14 HOH HOH . J 9 HOH H 12 712 15 HOH HOH . J 9 HOH H 13 713 17 HOH HOH . J 9 HOH H 14 714 18 HOH HOH . J 9 HOH H 15 715 19 HOH HOH . J 9 HOH H 16 716 20 HOH HOH . J 9 HOH H 17 717 21 HOH HOH . J 9 HOH H 18 718 22 HOH HOH . J 9 HOH H 19 719 23 HOH HOH . J 9 HOH H 20 720 24 HOH HOH . J 9 HOH H 21 721 25 HOH HOH . J 9 HOH H 22 722 26 HOH HOH . J 9 HOH H 23 723 27 HOH HOH . J 9 HOH H 24 724 28 HOH HOH . J 9 HOH H 25 725 29 HOH HOH . J 9 HOH H 26 726 30 HOH HOH . J 9 HOH H 27 727 31 HOH HOH . J 9 HOH H 28 728 32 HOH HOH . J 9 HOH H 29 729 33 HOH HOH . J 9 HOH H 30 730 34 HOH HOH . J 9 HOH H 31 731 35 HOH HOH . J 9 HOH H 32 732 36 HOH HOH . J 9 HOH H 33 733 37 HOH HOH . J 9 HOH H 34 734 38 HOH HOH . J 9 HOH H 35 735 39 HOH HOH . J 9 HOH H 36 736 40 HOH HOH . J 9 HOH H 37 737 42 HOH HOH . J 9 HOH H 38 738 43 HOH HOH . J 9 HOH H 39 739 44 HOH HOH . J 9 HOH H 40 740 45 HOH HOH . J 9 HOH H 41 741 47 HOH HOH . J 9 HOH H 42 742 48 HOH HOH . J 9 HOH H 43 743 49 HOH HOH . J 9 HOH H 44 744 50 HOH HOH . J 9 HOH H 45 745 51 HOH HOH . J 9 HOH H 46 746 52 HOH HOH . J 9 HOH H 47 747 53 HOH HOH . J 9 HOH H 48 748 55 HOH HOH . J 9 HOH H 49 749 57 HOH HOH . J 9 HOH H 50 750 58 HOH HOH . J 9 HOH H 51 751 59 HOH HOH . J 9 HOH H 52 752 60 HOH HOH . J 9 HOH H 53 753 61 HOH HOH . J 9 HOH H 54 754 62 HOH HOH . J 9 HOH H 55 755 63 HOH HOH . J 9 HOH H 56 756 64 HOH HOH . J 9 HOH H 57 757 65 HOH HOH . J 9 HOH H 58 758 67 HOH HOH . J 9 HOH H 59 759 69 HOH HOH . J 9 HOH H 60 760 70 HOH HOH . J 9 HOH H 61 761 71 HOH HOH . J 9 HOH H 62 762 72 HOH HOH . J 9 HOH H 63 763 73 HOH HOH . J 9 HOH H 64 764 74 HOH HOH . J 9 HOH H 65 765 76 HOH HOH . J 9 HOH H 66 766 77 HOH HOH . J 9 HOH H 67 767 78 HOH HOH . J 9 HOH H 68 768 79 HOH HOH . J 9 HOH H 69 769 81 HOH HOH . J 9 HOH H 70 770 82 HOH HOH . J 9 HOH H 71 771 83 HOH HOH . J 9 HOH H 72 772 84 HOH HOH . J 9 HOH H 73 773 86 HOH HOH . J 9 HOH H 74 774 87 HOH HOH . J 9 HOH H 75 775 89 HOH HOH . J 9 HOH H 76 776 90 HOH HOH . J 9 HOH H 77 777 91 HOH HOH . J 9 HOH H 78 778 95 HOH HOH . J 9 HOH H 79 779 96 HOH HOH . J 9 HOH H 80 780 97 HOH HOH . J 9 HOH H 81 781 98 HOH HOH . J 9 HOH H 82 782 100 HOH HOH . J 9 HOH H 83 783 101 HOH HOH . J 9 HOH H 84 784 102 HOH HOH . J 9 HOH H 85 785 103 HOH HOH . J 9 HOH H 86 786 104 HOH HOH . J 9 HOH H 87 787 105 HOH HOH . J 9 HOH H 88 788 106 HOH HOH . J 9 HOH H 89 789 107 HOH HOH . J 9 HOH H 90 790 108 HOH HOH . J 9 HOH H 91 791 109 HOH HOH . J 9 HOH H 92 792 111 HOH HOH . J 9 HOH H 93 793 112 HOH HOH . J 9 HOH H 94 794 113 HOH HOH . J 9 HOH H 95 795 114 HOH HOH . J 9 HOH H 96 796 115 HOH HOH . J 9 HOH H 97 797 116 HOH HOH . J 9 HOH H 98 798 117 HOH HOH . J 9 HOH H 99 799 118 HOH HOH . J 9 HOH H 100 800 119 HOH HOH . J 9 HOH H 101 801 120 HOH HOH . J 9 HOH H 102 802 123 HOH HOH . J 9 HOH H 103 803 124 HOH HOH . J 9 HOH H 104 804 125 HOH HOH . J 9 HOH H 105 805 126 HOH HOH . J 9 HOH H 106 806 127 HOH HOH . J 9 HOH H 107 807 128 HOH HOH . J 9 HOH H 108 808 129 HOH HOH . J 9 HOH H 109 809 130 HOH HOH . J 9 HOH H 110 810 132 HOH HOH . J 9 HOH H 111 811 133 HOH HOH . J 9 HOH H 112 812 134 HOH HOH . J 9 HOH H 113 813 135 HOH HOH . J 9 HOH H 114 814 136 HOH HOH . J 9 HOH H 115 815 137 HOH HOH . J 9 HOH H 116 816 138 HOH HOH . J 9 HOH H 117 817 140 HOH HOH . J 9 HOH H 118 818 141 HOH HOH . J 9 HOH H 119 819 142 HOH HOH . J 9 HOH H 120 820 143 HOH HOH . J 9 HOH H 121 821 144 HOH HOH . J 9 HOH H 122 822 148 HOH HOH . J 9 HOH H 123 823 149 HOH HOH . J 9 HOH H 124 824 150 HOH HOH . J 9 HOH H 125 825 151 HOH HOH . J 9 HOH H 126 826 152 HOH HOH . J 9 HOH H 127 827 153 HOH HOH . J 9 HOH H 128 828 154 HOH HOH . J 9 HOH H 129 829 155 HOH HOH . J 9 HOH H 130 830 156 HOH HOH . J 9 HOH H 131 831 157 HOH HOH . J 9 HOH H 132 832 158 HOH HOH . J 9 HOH H 133 833 160 HOH HOH . J 9 HOH H 134 834 161 HOH HOH . J 9 HOH H 135 835 163 HOH HOH . J 9 HOH H 136 836 164 HOH HOH . J 9 HOH H 137 837 165 HOH HOH . J 9 HOH H 138 838 166 HOH HOH . J 9 HOH H 139 839 169 HOH HOH . J 9 HOH H 140 840 170 HOH HOH . J 9 HOH H 141 841 171 HOH HOH . J 9 HOH H 142 842 172 HOH HOH . J 9 HOH H 143 843 173 HOH HOH . J 9 HOH H 144 844 174 HOH HOH . J 9 HOH H 145 845 176 HOH HOH . J 9 HOH H 146 846 179 HOH HOH . J 9 HOH H 147 847 180 HOH HOH . J 9 HOH H 148 848 181 HOH HOH . J 9 HOH H 149 849 182 HOH HOH . J 9 HOH H 150 850 184 HOH HOH . J 9 HOH H 151 851 185 HOH HOH . J 9 HOH H 152 852 186 HOH HOH . J 9 HOH H 153 853 187 HOH HOH . J 9 HOH H 154 854 188 HOH HOH . J 9 HOH H 155 855 189 HOH HOH . J 9 HOH H 156 856 190 HOH HOH . J 9 HOH H 157 857 191 HOH HOH . J 9 HOH H 158 858 192 HOH HOH . J 9 HOH H 159 859 193 HOH HOH . J 9 HOH H 160 860 194 HOH HOH . J 9 HOH H 161 861 195 HOH HOH . J 9 HOH H 162 862 196 HOH HOH . J 9 HOH H 163 863 197 HOH HOH . J 9 HOH H 164 864 198 HOH HOH . J 9 HOH H 165 865 199 HOH HOH . J 9 HOH H 166 866 200 HOH HOH . J 9 HOH H 167 867 201 HOH HOH . J 9 HOH H 168 868 203 HOH HOH . J 9 HOH H 169 869 204 HOH HOH . J 9 HOH H 170 870 206 HOH HOH . J 9 HOH H 171 871 207 HOH HOH . J 9 HOH H 172 872 208 HOH HOH . J 9 HOH H 173 873 209 HOH HOH . J 9 HOH H 174 874 210 HOH HOH . J 9 HOH H 175 875 211 HOH HOH . J 9 HOH H 176 876 212 HOH HOH . J 9 HOH H 177 877 213 HOH HOH . J 9 HOH H 178 878 214 HOH HOH . J 9 HOH H 179 879 215 HOH HOH . J 9 HOH H 180 880 216 HOH HOH . J 9 HOH H 181 881 217 HOH HOH . J 9 HOH H 182 882 218 HOH HOH . J 9 HOH H 183 883 219 HOH HOH . J 9 HOH H 184 884 220 HOH HOH . J 9 HOH H 185 885 221 HOH HOH . J 9 HOH H 186 886 222 HOH HOH . J 9 HOH H 187 887 223 HOH HOH . J 9 HOH H 188 888 224 HOH HOH . J 9 HOH H 189 889 225 HOH HOH . J 9 HOH H 190 890 226 HOH HOH . J 9 HOH H 191 891 227 HOH HOH . J 9 HOH H 192 892 230 HOH HOH . J 9 HOH H 193 893 231 HOH HOH . J 9 HOH H 194 894 232 HOH HOH . J 9 HOH H 195 895 233 HOH HOH . J 9 HOH H 196 896 234 HOH HOH . J 9 HOH H 197 897 235 HOH HOH . J 9 HOH H 198 898 237 HOH HOH . J 9 HOH H 199 899 238 HOH HOH . J 9 HOH H 200 900 239 HOH HOH . J 9 HOH H 201 901 240 HOH HOH . J 9 HOH H 202 902 241 HOH HOH . J 9 HOH H 203 903 242 HOH HOH . J 9 HOH H 204 904 243 HOH HOH . J 9 HOH H 205 905 244 HOH HOH . J 9 HOH H 206 906 245 HOH HOH . J 9 HOH H 207 907 246 HOH HOH . J 9 HOH H 208 908 247 HOH HOH . J 9 HOH H 209 909 248 HOH HOH . J 9 HOH H 210 910 249 HOH HOH . J 9 HOH H 211 911 250 HOH HOH . J 9 HOH H 212 912 251 HOH HOH . J 9 HOH H 213 913 252 HOH HOH . J 9 HOH H 214 914 253 HOH HOH . J 9 HOH H 215 915 254 HOH HOH . J 9 HOH H 216 916 255 HOH HOH . J 9 HOH H 217 917 256 HOH HOH . J 9 HOH H 218 918 257 HOH HOH . J 9 HOH H 219 919 258 HOH HOH . J 9 HOH H 220 920 259 HOH HOH . J 9 HOH H 221 921 260 HOH HOH . J 9 HOH H 222 922 261 HOH HOH . J 9 HOH H 223 923 262 HOH HOH . J 9 HOH H 224 924 263 HOH HOH . J 9 HOH H 225 925 264 HOH HOH . J 9 HOH H 226 926 265 HOH HOH . J 9 HOH H 227 927 267 HOH HOH . K 9 HOH I 1 101 229 HOH HOH . K 9 HOH I 2 102 236 HOH HOH . K 9 HOH I 3 103 268 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 E _atom_site.label_entity_id 5 _atom_site.Cartn_x 7.998 _atom_site.Cartn_y -25.005 _atom_site.Cartn_z -9.23 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 17.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 602 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 479 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 1 #