data_3CYM # _model_server_result.job_id TgrBIWszyomSykP1jI33zg _model_server_result.datetime_utc '2025-08-09 17:40:51' _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 3cym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3CYM # _exptl.entry_id 3CYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 90 _cell.entry_id 3CYM _cell.length_a 42.163 _cell.length_b 94.422 _cell.length_c 113.196 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CYM _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 metalc ? metalc1 A OD2 ASP 44 A ASP 42 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc2 A OD1 ASP 44 A ASP 42 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc3 A OE2 GLU 46 A GLU 44 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc4 A OD2 ASP 172 A ASP 170 1_555 B NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc5 B NA NA . A NA 501 1_555 E O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc6 B NA NA . A NA 501 1_555 E O HOH . A HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc7 B NA NA . A NA 501 1_555 E O HOH . A HOH 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc8 C NA NA . A NA 502 1_555 E O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc9 C NA NA . A NA 502 1_555 E O HOH . A HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc10 C NA NA . A NA 502 1_555 E O HOH . A HOH 748 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc11 C NA NA . A NA 502 1_555 E O HOH . A HOH 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? # _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 3CYM _atom_sites.fract_transf_matrix[1][1] 0.023717 _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] 0.010591 _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] 0.008834 _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 NA A 1 501 1 NA NA . C 2 NA A 1 502 1 NA NA . D 3 GOL A 1 503 1 GOL GOL . E 4 HOH A 1 601 2 HOH HOH . E 4 HOH A 2 602 3 HOH HOH . E 4 HOH A 3 603 4 HOH HOH . E 4 HOH A 4 604 5 HOH HOH . E 4 HOH A 5 605 6 HOH HOH . E 4 HOH A 6 606 7 HOH HOH . E 4 HOH A 7 607 8 HOH HOH . E 4 HOH A 8 608 9 HOH HOH . E 4 HOH A 9 609 10 HOH HOH . E 4 HOH A 10 610 11 HOH HOH . E 4 HOH A 11 611 12 HOH HOH . E 4 HOH A 12 612 13 HOH HOH . E 4 HOH A 13 613 14 HOH HOH . E 4 HOH A 14 614 15 HOH HOH . E 4 HOH A 15 615 16 HOH HOH . E 4 HOH A 16 616 17 HOH HOH . E 4 HOH A 17 617 18 HOH HOH . E 4 HOH A 18 618 19 HOH HOH . E 4 HOH A 19 619 20 HOH HOH . E 4 HOH A 20 620 21 HOH HOH . E 4 HOH A 21 621 22 HOH HOH . E 4 HOH A 22 622 23 HOH HOH . E 4 HOH A 23 623 24 HOH HOH . E 4 HOH A 24 624 25 HOH HOH . E 4 HOH A 25 625 26 HOH HOH . E 4 HOH A 26 626 28 HOH HOH . E 4 HOH A 27 627 29 HOH HOH . E 4 HOH A 28 628 30 HOH HOH . E 4 HOH A 29 629 31 HOH HOH . E 4 HOH A 30 630 32 HOH HOH . E 4 HOH A 31 631 33 HOH HOH . E 4 HOH A 32 632 34 HOH HOH . E 4 HOH A 33 633 35 HOH HOH . E 4 HOH A 34 634 36 HOH HOH . E 4 HOH A 35 635 37 HOH HOH . E 4 HOH A 36 636 38 HOH HOH . E 4 HOH A 37 637 39 HOH HOH . E 4 HOH A 38 638 40 HOH HOH . E 4 HOH A 39 639 41 HOH HOH . E 4 HOH A 40 640 42 HOH HOH . E 4 HOH A 41 641 43 HOH HOH . E 4 HOH A 42 642 44 HOH HOH . E 4 HOH A 43 643 45 HOH HOH . E 4 HOH A 44 644 46 HOH HOH . E 4 HOH A 45 645 47 HOH HOH . E 4 HOH A 46 646 48 HOH HOH . E 4 HOH A 47 647 49 HOH HOH . E 4 HOH A 48 648 50 HOH HOH . E 4 HOH A 49 649 51 HOH HOH . E 4 HOH A 50 650 52 HOH HOH . E 4 HOH A 51 651 53 HOH HOH . E 4 HOH A 52 652 54 HOH HOH . E 4 HOH A 53 653 55 HOH HOH . E 4 HOH A 54 654 56 HOH HOH . E 4 HOH A 55 655 57 HOH HOH . E 4 HOH A 56 656 59 HOH HOH . E 4 HOH A 57 657 60 HOH HOH . E 4 HOH A 58 658 61 HOH HOH . E 4 HOH A 59 659 62 HOH HOH . E 4 HOH A 60 660 63 HOH HOH . E 4 HOH A 61 661 64 HOH HOH . E 4 HOH A 62 662 65 HOH HOH . E 4 HOH A 63 663 66 HOH HOH . E 4 HOH A 64 664 67 HOH HOH . E 4 HOH A 65 665 68 HOH HOH . E 4 HOH A 66 666 69 HOH HOH . E 4 HOH A 67 667 71 HOH HOH . E 4 HOH A 68 668 72 HOH HOH . E 4 HOH A 69 669 73 HOH HOH . E 4 HOH A 70 670 74 HOH HOH . E 4 HOH A 71 671 75 HOH HOH . E 4 HOH A 72 672 76 HOH HOH . E 4 HOH A 73 673 77 HOH HOH . E 4 HOH A 74 674 78 HOH HOH . E 4 HOH A 75 675 79 HOH HOH . E 4 HOH A 76 676 80 HOH HOH . E 4 HOH A 77 677 81 HOH HOH . E 4 HOH A 78 678 82 HOH HOH . E 4 HOH A 79 679 83 HOH HOH . E 4 HOH A 80 680 84 HOH HOH . E 4 HOH A 81 681 85 HOH HOH . E 4 HOH A 82 682 87 HOH HOH . E 4 HOH A 83 683 88 HOH HOH . E 4 HOH A 84 684 89 HOH HOH . E 4 HOH A 85 685 90 HOH HOH . E 4 HOH A 86 686 91 HOH HOH . E 4 HOH A 87 687 92 HOH HOH . E 4 HOH A 88 688 93 HOH HOH . E 4 HOH A 89 689 94 HOH HOH . E 4 HOH A 90 690 95 HOH HOH . E 4 HOH A 91 691 96 HOH HOH . E 4 HOH A 92 692 97 HOH HOH . E 4 HOH A 93 693 98 HOH HOH . E 4 HOH A 94 694 99 HOH HOH . E 4 HOH A 95 695 101 HOH HOH . E 4 HOH A 96 696 102 HOH HOH . E 4 HOH A 97 697 103 HOH HOH . E 4 HOH A 98 698 104 HOH HOH . E 4 HOH A 99 699 105 HOH HOH . E 4 HOH A 100 700 106 HOH HOH . E 4 HOH A 101 701 107 HOH HOH . E 4 HOH A 102 702 108 HOH HOH . E 4 HOH A 103 703 110 HOH HOH . E 4 HOH A 104 704 112 HOH HOH . E 4 HOH A 105 705 113 HOH HOH . E 4 HOH A 106 706 115 HOH HOH . E 4 HOH A 107 707 116 HOH HOH . E 4 HOH A 108 708 117 HOH HOH . E 4 HOH A 109 709 118 HOH HOH . E 4 HOH A 110 710 119 HOH HOH . E 4 HOH A 111 711 120 HOH HOH . E 4 HOH A 112 712 122 HOH HOH . E 4 HOH A 113 713 123 HOH HOH . E 4 HOH A 114 714 124 HOH HOH . E 4 HOH A 115 715 125 HOH HOH . E 4 HOH A 116 716 126 HOH HOH . E 4 HOH A 117 717 127 HOH HOH . E 4 HOH A 118 718 128 HOH HOH . E 4 HOH A 119 719 130 HOH HOH . E 4 HOH A 120 720 131 HOH HOH . E 4 HOH A 121 721 132 HOH HOH . E 4 HOH A 122 722 133 HOH HOH . E 4 HOH A 123 723 134 HOH HOH . E 4 HOH A 124 724 135 HOH HOH . E 4 HOH A 125 725 136 HOH HOH . E 4 HOH A 126 726 137 HOH HOH . E 4 HOH A 127 727 138 HOH HOH . E 4 HOH A 128 728 140 HOH HOH . E 4 HOH A 129 729 141 HOH HOH . E 4 HOH A 130 730 142 HOH HOH . E 4 HOH A 131 731 144 HOH HOH . E 4 HOH A 132 732 145 HOH HOH . E 4 HOH A 133 733 146 HOH HOH . E 4 HOH A 134 734 147 HOH HOH . E 4 HOH A 135 735 148 HOH HOH . E 4 HOH A 136 736 149 HOH HOH . E 4 HOH A 137 737 150 HOH HOH . E 4 HOH A 138 738 151 HOH HOH . E 4 HOH A 139 739 152 HOH HOH . E 4 HOH A 140 740 154 HOH HOH . E 4 HOH A 141 741 156 HOH HOH . E 4 HOH A 142 742 158 HOH HOH . E 4 HOH A 143 743 159 HOH HOH . E 4 HOH A 144 744 161 HOH HOH . E 4 HOH A 145 745 162 HOH HOH . E 4 HOH A 146 746 163 HOH HOH . E 4 HOH A 147 747 164 HOH HOH . E 4 HOH A 148 748 165 HOH HOH . E 4 HOH A 149 749 166 HOH HOH . E 4 HOH A 150 750 167 HOH HOH . E 4 HOH A 151 751 168 HOH HOH . E 4 HOH A 152 752 169 HOH HOH . E 4 HOH A 153 753 170 HOH HOH . E 4 HOH A 154 754 171 HOH HOH . E 4 HOH A 155 755 172 HOH HOH . E 4 HOH A 156 756 173 HOH HOH . E 4 HOH A 157 757 174 HOH HOH . E 4 HOH A 158 758 175 HOH HOH . E 4 HOH A 159 759 176 HOH HOH . E 4 HOH A 160 760 177 HOH HOH . E 4 HOH A 161 761 178 HOH HOH . E 4 HOH A 162 762 179 HOH HOH . E 4 HOH A 163 763 180 HOH HOH . E 4 HOH A 164 764 181 HOH HOH . E 4 HOH A 165 765 182 HOH HOH . E 4 HOH A 166 766 183 HOH HOH . E 4 HOH A 167 767 184 HOH HOH . E 4 HOH A 168 768 185 HOH HOH . E 4 HOH A 169 769 186 HOH HOH . E 4 HOH A 170 770 187 HOH HOH . E 4 HOH A 171 771 188 HOH HOH . E 4 HOH A 172 772 189 HOH HOH . E 4 HOH A 173 773 191 HOH HOH . E 4 HOH A 174 774 192 HOH HOH . E 4 HOH A 175 775 193 HOH HOH . E 4 HOH A 176 776 194 HOH HOH . E 4 HOH A 177 777 195 HOH HOH . E 4 HOH A 178 778 196 HOH HOH . E 4 HOH A 179 779 197 HOH HOH . E 4 HOH A 180 780 198 HOH HOH . E 4 HOH A 181 781 199 HOH HOH . E 4 HOH A 182 782 200 HOH HOH . E 4 HOH A 183 783 203 HOH HOH . E 4 HOH A 184 784 204 HOH HOH . E 4 HOH A 185 785 205 HOH HOH . E 4 HOH A 186 786 206 HOH HOH . E 4 HOH A 187 787 207 HOH HOH . E 4 HOH A 188 788 208 HOH HOH . E 4 HOH A 189 789 209 HOH HOH . E 4 HOH A 190 790 210 HOH HOH . E 4 HOH A 191 791 211 HOH HOH . E 4 HOH A 192 792 212 HOH HOH . E 4 HOH A 193 793 213 HOH HOH . E 4 HOH A 194 794 214 HOH HOH . E 4 HOH A 195 795 215 HOH HOH . E 4 HOH A 196 796 216 HOH HOH . E 4 HOH A 197 797 217 HOH HOH . E 4 HOH A 198 798 218 HOH HOH . E 4 HOH A 199 799 219 HOH HOH . E 4 HOH A 200 800 220 HOH HOH . E 4 HOH A 201 801 221 HOH HOH . E 4 HOH A 202 802 222 HOH HOH . E 4 HOH A 203 803 223 HOH HOH . E 4 HOH A 204 804 229 HOH HOH . E 4 HOH A 205 805 230 HOH HOH . E 4 HOH A 206 806 231 HOH HOH . E 4 HOH A 207 807 232 HOH HOH . E 4 HOH A 208 808 233 HOH HOH . E 4 HOH A 209 809 234 HOH HOH . E 4 HOH A 210 810 236 HOH HOH . E 4 HOH A 211 811 237 HOH HOH . E 4 HOH A 212 812 238 HOH HOH . E 4 HOH A 213 813 239 HOH HOH . E 4 HOH A 214 814 240 HOH HOH . E 4 HOH A 215 815 241 HOH HOH . E 4 HOH A 216 816 242 HOH HOH . E 4 HOH A 217 817 243 HOH HOH . E 4 HOH A 218 818 244 HOH HOH . E 4 HOH A 219 819 245 HOH HOH . E 4 HOH A 220 820 246 HOH HOH . E 4 HOH A 221 821 247 HOH HOH . E 4 HOH A 222 822 248 HOH HOH . E 4 HOH A 223 823 249 HOH HOH . E 4 HOH A 224 824 250 HOH HOH . E 4 HOH A 225 825 251 HOH HOH . E 4 HOH A 226 826 252 HOH HOH . E 4 HOH A 227 827 253 HOH HOH . E 4 HOH A 228 828 254 HOH HOH . E 4 HOH A 229 829 256 HOH HOH . E 4 HOH A 230 830 257 HOH HOH . E 4 HOH A 231 831 258 HOH HOH . E 4 HOH A 232 832 259 HOH HOH . E 4 HOH A 233 833 261 HOH HOH . E 4 HOH A 234 834 262 HOH HOH . E 4 HOH A 235 835 263 HOH HOH . E 4 HOH A 236 836 264 HOH HOH . E 4 HOH A 237 837 265 HOH HOH . E 4 HOH A 238 838 267 HOH HOH . E 4 HOH A 239 839 268 HOH HOH . E 4 HOH A 240 840 269 HOH HOH . E 4 HOH A 241 841 270 HOH HOH . E 4 HOH A 242 842 271 HOH HOH . E 4 HOH A 243 843 272 HOH HOH . E 4 HOH A 244 844 273 HOH HOH . E 4 HOH A 245 845 274 HOH HOH . E 4 HOH A 246 846 275 HOH HOH . E 4 HOH A 247 847 276 HOH HOH . E 4 HOH A 248 848 277 HOH HOH . E 4 HOH A 249 849 279 HOH HOH . E 4 HOH A 250 850 280 HOH HOH . E 4 HOH A 251 851 281 HOH HOH . E 4 HOH A 252 852 282 HOH HOH . E 4 HOH A 253 853 283 HOH HOH . E 4 HOH A 254 854 284 HOH HOH . E 4 HOH A 255 855 285 HOH HOH . E 4 HOH A 256 856 286 HOH HOH . E 4 HOH A 257 857 287 HOH HOH . E 4 HOH A 258 858 288 HOH HOH . E 4 HOH A 259 859 289 HOH HOH . E 4 HOH A 260 860 290 HOH HOH . E 4 HOH A 261 861 291 HOH HOH . E 4 HOH A 262 862 292 HOH HOH . E 4 HOH A 263 863 293 HOH HOH . E 4 HOH A 264 864 294 HOH HOH . E 4 HOH A 265 865 295 HOH HOH . E 4 HOH A 266 866 296 HOH HOH . E 4 HOH A 267 867 297 HOH HOH . E 4 HOH A 268 868 298 HOH HOH . E 4 HOH A 269 869 299 HOH HOH . E 4 HOH A 270 870 300 HOH HOH . E 4 HOH A 271 871 301 HOH HOH . E 4 HOH A 272 872 302 HOH HOH . E 4 HOH A 273 873 303 HOH HOH . E 4 HOH A 274 874 304 HOH HOH . E 4 HOH A 275 875 305 HOH HOH . E 4 HOH A 276 876 306 HOH HOH . E 4 HOH A 277 877 307 HOH HOH . E 4 HOH A 278 878 308 HOH HOH . E 4 HOH A 279 879 309 HOH HOH . E 4 HOH A 280 880 310 HOH HOH . E 4 HOH A 281 881 311 HOH HOH . E 4 HOH A 282 882 312 HOH HOH . E 4 HOH A 283 883 313 HOH HOH . E 4 HOH A 284 884 314 HOH HOH . E 4 HOH A 285 885 315 HOH HOH . E 4 HOH A 286 886 316 HOH HOH . E 4 HOH A 287 887 317 HOH HOH . E 4 HOH A 288 888 318 HOH HOH . E 4 HOH A 289 889 319 HOH HOH . E 4 HOH A 290 890 320 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 B _atom_site.label_entity_id 2 _atom_site.Cartn_x 5.355 _atom_site.Cartn_y -6.416 _atom_site.Cartn_z 96.964 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 14.97 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 501 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #