data_6EFD # _model_server_result.job_id 80ggn3q8XPznukKe-AxVAw _model_server_result.datetime_utc '2024-12-14 19:33:21' _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 6efd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":505}' # _entry.id 6EFD # _exptl.entry_id 6EFD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method man _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 6EFD _cell.length_a 46.645 _cell.length_b 58.14 _cell.length_c 75.959 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EFD _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 ? 3 C N N ? 3 D N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GAL A2G C1 O1 . O3 HO3 . sing 2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B A2G 1 B 1 A2G K 3 A2G 2 n B GAL 2 B 2 GAL K 2 GAL 2 n B SIA 3 B 3 SIA K 1 SIA # 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 covale ? covale1 B O3 A2G . B A2G 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale2 B O3 GAL . B GAL 2 1_555 B C2 SIA . B SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? metalc ? metalc1 A O GLU 28 A GLU 247 1_555 C NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc2 A OD1 ASP 53 A ASP 272 1_555 C NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc3 A OD2 ASP 53 A ASP 272 1_555 C NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A OD1 ASN 54 A ASN 273 1_555 C NA NA . A NA 504 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc5 A OD2 ASP 127 A ASP 346 1_555 C NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc6 A O ASN 155 A ASN 374 1_555 D NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc7 A O TYR 158 A TYR 377 1_555 D NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc8 A OD1 ASP 217 A ASP 436 1_555 D NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc9 A OD2 ASP 217 A ASP 436 1_555 D NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc10 C NA NA . A NA 504 1_555 E O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc11 D NA NA . A NA 505 1_555 E O HOH . A HOH 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? # _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 6EFD _atom_sites.fract_transf_matrix[1][1] 0.021439 _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] 0.0172 _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] 0.013165 _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 C 3 NA A 1 504 1 NA NA . D 3 NA A 1 505 2 NA NA . E 4 HOH A 1 601 202 HOH HOH . E 4 HOH A 2 602 26 HOH HOH . E 4 HOH A 3 603 117 HOH HOH . E 4 HOH A 4 604 215 HOH HOH . E 4 HOH A 5 605 176 HOH HOH . E 4 HOH A 6 606 126 HOH HOH . E 4 HOH A 7 607 16 HOH HOH . E 4 HOH A 8 608 41 HOH HOH . E 4 HOH A 9 609 17 HOH HOH . E 4 HOH A 10 610 131 HOH HOH . E 4 HOH A 11 611 148 HOH HOH . E 4 HOH A 12 612 14 HOH HOH . E 4 HOH A 13 613 5 HOH HOH . E 4 HOH A 14 614 22 HOH HOH . E 4 HOH A 15 615 71 HOH HOH . E 4 HOH A 16 616 1 HOH HOH . E 4 HOH A 17 617 63 HOH HOH . E 4 HOH A 18 618 81 HOH HOH . E 4 HOH A 19 619 174 HOH HOH . E 4 HOH A 20 620 192 HOH HOH . E 4 HOH A 21 621 219 HOH HOH . E 4 HOH A 22 622 188 HOH HOH . E 4 HOH A 23 623 75 HOH HOH . E 4 HOH A 24 624 48 HOH HOH . E 4 HOH A 25 625 217 HOH HOH . E 4 HOH A 26 626 49 HOH HOH . E 4 HOH A 27 627 44 HOH HOH . E 4 HOH A 28 628 128 HOH HOH . E 4 HOH A 29 629 140 HOH HOH . E 4 HOH A 30 630 100 HOH HOH . E 4 HOH A 31 631 12 HOH HOH . E 4 HOH A 32 632 31 HOH HOH . E 4 HOH A 33 633 73 HOH HOH . E 4 HOH A 34 634 6 HOH HOH . E 4 HOH A 35 635 181 HOH HOH . E 4 HOH A 36 636 90 HOH HOH . E 4 HOH A 37 637 143 HOH HOH . E 4 HOH A 38 638 28 HOH HOH . E 4 HOH A 39 639 10 HOH HOH . E 4 HOH A 40 640 3 HOH HOH . E 4 HOH A 41 641 93 HOH HOH . E 4 HOH A 42 642 70 HOH HOH . E 4 HOH A 43 643 160 HOH HOH . E 4 HOH A 44 644 61 HOH HOH . E 4 HOH A 45 645 158 HOH HOH . E 4 HOH A 46 646 64 HOH HOH . E 4 HOH A 47 647 37 HOH HOH . E 4 HOH A 48 648 96 HOH HOH . E 4 HOH A 49 649 80 HOH HOH . E 4 HOH A 50 650 121 HOH HOH . E 4 HOH A 51 651 164 HOH HOH . E 4 HOH A 52 652 27 HOH HOH . E 4 HOH A 53 653 210 HOH HOH . E 4 HOH A 54 654 216 HOH HOH . E 4 HOH A 55 655 11 HOH HOH . E 4 HOH A 56 656 77 HOH HOH . E 4 HOH A 57 657 13 HOH HOH . E 4 HOH A 58 658 136 HOH HOH . E 4 HOH A 59 659 4 HOH HOH . E 4 HOH A 60 660 134 HOH HOH . E 4 HOH A 61 661 8 HOH HOH . E 4 HOH A 62 662 19 HOH HOH . E 4 HOH A 63 663 95 HOH HOH . E 4 HOH A 64 664 92 HOH HOH . E 4 HOH A 65 665 102 HOH HOH . E 4 HOH A 66 666 185 HOH HOH . E 4 HOH A 67 667 7 HOH HOH . E 4 HOH A 68 668 154 HOH HOH . E 4 HOH A 69 669 222 HOH HOH . E 4 HOH A 70 670 47 HOH HOH . E 4 HOH A 71 671 66 HOH HOH . E 4 HOH A 72 672 94 HOH HOH . E 4 HOH A 73 673 52 HOH HOH . E 4 HOH A 74 674 172 HOH HOH . E 4 HOH A 75 675 55 HOH HOH . E 4 HOH A 76 676 141 HOH HOH . E 4 HOH A 77 677 207 HOH HOH . E 4 HOH A 78 678 97 HOH HOH . E 4 HOH A 79 679 146 HOH HOH . E 4 HOH A 80 680 74 HOH HOH . E 4 HOH A 81 681 68 HOH HOH . E 4 HOH A 82 682 84 HOH HOH . E 4 HOH A 83 683 39 HOH HOH . E 4 HOH A 84 684 132 HOH HOH . E 4 HOH A 85 685 46 HOH HOH . E 4 HOH A 86 686 130 HOH HOH . E 4 HOH A 87 687 153 HOH HOH . E 4 HOH A 88 688 78 HOH HOH . E 4 HOH A 89 689 145 HOH HOH . E 4 HOH A 90 690 38 HOH HOH . E 4 HOH A 91 691 103 HOH HOH . E 4 HOH A 92 692 98 HOH HOH . E 4 HOH A 93 693 23 HOH HOH . E 4 HOH A 94 694 54 HOH HOH . E 4 HOH A 95 695 29 HOH HOH . E 4 HOH A 96 696 225 HOH HOH . E 4 HOH A 97 697 159 HOH HOH . E 4 HOH A 98 698 50 HOH HOH . E 4 HOH A 99 699 220 HOH HOH . E 4 HOH A 100 700 167 HOH HOH . E 4 HOH A 101 701 137 HOH HOH . E 4 HOH A 102 702 67 HOH HOH . E 4 HOH A 103 703 118 HOH HOH . E 4 HOH A 104 704 211 HOH HOH . E 4 HOH A 105 705 133 HOH HOH . E 4 HOH A 106 706 20 HOH HOH . E 4 HOH A 107 707 24 HOH HOH . E 4 HOH A 108 708 112 HOH HOH . E 4 HOH A 109 709 72 HOH HOH . E 4 HOH A 110 710 101 HOH HOH . E 4 HOH A 111 711 88 HOH HOH . E 4 HOH A 112 712 203 HOH HOH . E 4 HOH A 113 713 166 HOH HOH . E 4 HOH A 114 714 65 HOH HOH . E 4 HOH A 115 715 124 HOH HOH . E 4 HOH A 116 716 25 HOH HOH . E 4 HOH A 117 717 85 HOH HOH . E 4 HOH A 118 718 42 HOH HOH . E 4 HOH A 119 719 58 HOH HOH . E 4 HOH A 120 720 86 HOH HOH . E 4 HOH A 121 721 87 HOH HOH . E 4 HOH A 122 722 162 HOH HOH . E 4 HOH A 123 723 105 HOH HOH . E 4 HOH A 124 724 2 HOH HOH . E 4 HOH A 125 725 79 HOH HOH . E 4 HOH A 126 726 9 HOH HOH . E 4 HOH A 127 727 190 HOH HOH . E 4 HOH A 128 728 35 HOH HOH . E 4 HOH A 129 729 139 HOH HOH . E 4 HOH A 130 730 163 HOH HOH . E 4 HOH A 131 731 116 HOH HOH . E 4 HOH A 132 732 170 HOH HOH . E 4 HOH A 133 733 156 HOH HOH . E 4 HOH A 134 734 34 HOH HOH . E 4 HOH A 135 735 45 HOH HOH . E 4 HOH A 136 736 147 HOH HOH . E 4 HOH A 137 737 69 HOH HOH . E 4 HOH A 138 738 201 HOH HOH . E 4 HOH A 139 739 212 HOH HOH . E 4 HOH A 140 740 83 HOH HOH . E 4 HOH A 141 741 200 HOH HOH . E 4 HOH A 142 742 18 HOH HOH . E 4 HOH A 143 743 199 HOH HOH . E 4 HOH A 144 744 189 HOH HOH . E 4 HOH A 145 745 129 HOH HOH . E 4 HOH A 146 746 113 HOH HOH . E 4 HOH A 147 747 187 HOH HOH . E 4 HOH A 148 748 218 HOH HOH . E 4 HOH A 149 749 186 HOH HOH . E 4 HOH A 150 750 108 HOH HOH . E 4 HOH A 151 751 21 HOH HOH . E 4 HOH A 152 752 180 HOH HOH . E 4 HOH A 153 753 182 HOH HOH . E 4 HOH A 154 754 127 HOH HOH . E 4 HOH A 155 755 173 HOH HOH . E 4 HOH A 156 756 122 HOH HOH . E 4 HOH A 157 757 193 HOH HOH . E 4 HOH A 158 758 144 HOH HOH . E 4 HOH A 159 759 53 HOH HOH . E 4 HOH A 160 760 197 HOH HOH . E 4 HOH A 161 761 99 HOH HOH . E 4 HOH A 162 762 33 HOH HOH . E 4 HOH A 163 763 32 HOH HOH . E 4 HOH A 164 764 91 HOH HOH . E 4 HOH A 165 765 115 HOH HOH . E 4 HOH A 166 766 196 HOH HOH . E 4 HOH A 167 767 151 HOH HOH . E 4 HOH A 168 768 221 HOH HOH . E 4 HOH A 169 769 206 HOH HOH . E 4 HOH A 170 770 82 HOH HOH . E 4 HOH A 171 771 15 HOH HOH . E 4 HOH A 172 772 30 HOH HOH . E 4 HOH A 173 773 109 HOH HOH . E 4 HOH A 174 774 107 HOH HOH . E 4 HOH A 175 775 161 HOH HOH . E 4 HOH A 176 776 138 HOH HOH . E 4 HOH A 177 777 89 HOH HOH . E 4 HOH A 178 778 205 HOH HOH . E 4 HOH A 179 779 142 HOH HOH . E 4 HOH A 180 780 149 HOH HOH . E 4 HOH A 181 781 214 HOH HOH . E 4 HOH A 182 782 213 HOH HOH . E 4 HOH A 183 783 40 HOH HOH . E 4 HOH A 184 784 106 HOH HOH . E 4 HOH A 185 785 169 HOH HOH . E 4 HOH A 186 786 114 HOH HOH . E 4 HOH A 187 787 59 HOH HOH . E 4 HOH A 188 788 177 HOH HOH . E 4 HOH A 189 789 104 HOH HOH . E 4 HOH A 190 790 155 HOH HOH . E 4 HOH A 191 791 175 HOH HOH . E 4 HOH A 192 792 60 HOH HOH . E 4 HOH A 193 793 119 HOH HOH . E 4 HOH A 194 794 43 HOH HOH . E 4 HOH A 195 795 110 HOH HOH . E 4 HOH A 196 796 125 HOH HOH . E 4 HOH A 197 797 165 HOH HOH . E 4 HOH A 198 798 51 HOH HOH . E 4 HOH A 199 799 171 HOH HOH . E 4 HOH A 200 800 56 HOH HOH . E 4 HOH A 201 801 123 HOH HOH . E 4 HOH A 202 802 111 HOH HOH . E 4 HOH A 203 803 184 HOH HOH . E 4 HOH A 204 804 183 HOH HOH . E 4 HOH A 205 805 57 HOH HOH . E 4 HOH A 206 806 36 HOH HOH . E 4 HOH A 207 807 209 HOH HOH . E 4 HOH A 208 808 76 HOH HOH . E 4 HOH A 209 809 62 HOH HOH . E 4 HOH A 210 810 150 HOH HOH . E 4 HOH A 211 811 120 HOH HOH . E 4 HOH A 212 812 208 HOH HOH . E 4 HOH A 213 813 179 HOH HOH . E 4 HOH A 214 814 223 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 D _atom_site.label_entity_id 3 _atom_site.Cartn_x 17.869 _atom_site.Cartn_y -10.865 _atom_site.Cartn_z 44.808 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 31.39 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 505 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #