data_4XR9 # _model_server_result.job_id dHaMx29dVPAVaQ01E9U0ng _model_server_result.datetime_utc '2025-09-07 08:37:22' _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 4xr9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 4XR9 # _exptl.entry_id 4XR9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _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 103.59 _cell.angle_gamma 90 _cell.entry_id 4XR9 _cell.length_a 70.682 _cell.length_b 87.04 _cell.length_c 70.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XR9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 O GLY 246 A GLY 243 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 D NA NA . A NA 502 1_555 G O HOH . A HOH 609 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc3 D NA NA . A NA 502 1_555 G O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc4 D NA NA . A NA 502 1_555 G O HOH . A HOH 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc5 D NA NA . A NA 502 1_555 G O HOH . A HOH 651 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? # _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 4XR9 _atom_sites.fract_transf_matrix[1][1] 0.014148 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00342 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011489 _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] 0.01456 _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 2 NAD A 1 501 2 NAD NAD . D 3 NA A 1 502 1 NA NA . E 4 TMP A 1 503 1 TMP TMP . F 5 GOL B 1 501 1 GOL GOL . G 6 HOH A 1 601 107 HOH HOH . G 6 HOH A 2 602 85 HOH HOH . G 6 HOH A 3 603 56 HOH HOH . G 6 HOH A 4 604 59 HOH HOH . G 6 HOH A 5 605 15 HOH HOH . G 6 HOH A 6 606 50 HOH HOH . G 6 HOH A 7 607 102 HOH HOH . G 6 HOH A 8 608 71 HOH HOH . G 6 HOH A 9 609 93 HOH HOH . G 6 HOH A 10 610 77 HOH HOH . G 6 HOH A 11 611 180 HOH HOH . G 6 HOH A 12 612 43 HOH HOH . G 6 HOH A 13 613 4 HOH HOH . G 6 HOH A 14 614 173 HOH HOH . G 6 HOH A 15 615 105 HOH HOH . G 6 HOH A 16 616 65 HOH HOH . G 6 HOH A 17 617 51 HOH HOH . G 6 HOH A 18 618 179 HOH HOH . G 6 HOH A 19 619 18 HOH HOH . G 6 HOH A 20 620 98 HOH HOH . G 6 HOH A 21 621 16 HOH HOH . G 6 HOH A 22 622 33 HOH HOH . G 6 HOH A 23 623 175 HOH HOH . G 6 HOH A 24 624 84 HOH HOH . G 6 HOH A 25 625 3 HOH HOH . G 6 HOH A 26 626 101 HOH HOH . G 6 HOH A 27 627 91 HOH HOH . G 6 HOH A 28 628 106 HOH HOH . G 6 HOH A 29 629 72 HOH HOH . G 6 HOH A 30 630 97 HOH HOH . G 6 HOH A 31 631 77 HOH HOH . G 6 HOH A 32 632 95 HOH HOH . G 6 HOH A 33 633 53 HOH HOH . G 6 HOH A 34 634 69 HOH HOH . G 6 HOH A 35 635 128 HOH HOH . G 6 HOH A 36 636 115 HOH HOH . G 6 HOH A 37 637 91 HOH HOH . G 6 HOH A 38 638 167 HOH HOH . G 6 HOH A 39 639 92 HOH HOH . G 6 HOH A 40 640 44 HOH HOH . G 6 HOH A 41 641 89 HOH HOH . G 6 HOH A 42 642 61 HOH HOH . G 6 HOH A 43 643 168 HOH HOH . G 6 HOH A 44 644 151 HOH HOH . G 6 HOH A 45 645 42 HOH HOH . G 6 HOH A 46 646 100 HOH HOH . G 6 HOH A 47 647 80 HOH HOH . G 6 HOH A 48 648 159 HOH HOH . G 6 HOH A 49 649 58 HOH HOH . G 6 HOH A 50 650 111 HOH HOH . G 6 HOH A 51 651 116 HOH HOH . G 6 HOH A 52 652 3 HOH HOH . G 6 HOH A 53 653 6 HOH HOH . G 6 HOH A 54 654 9 HOH HOH . G 6 HOH A 55 655 11 HOH HOH . G 6 HOH A 56 656 12 HOH HOH . G 6 HOH A 57 657 13 HOH HOH . G 6 HOH A 58 658 17 HOH HOH . G 6 HOH A 59 659 18 HOH HOH . G 6 HOH A 60 660 21 HOH HOH . G 6 HOH A 61 661 22 HOH HOH . G 6 HOH A 62 662 23 HOH HOH . G 6 HOH A 63 663 26 HOH HOH . G 6 HOH A 64 664 27 HOH HOH . G 6 HOH A 65 665 29 HOH HOH . G 6 HOH A 66 666 30 HOH HOH . G 6 HOH A 67 667 31 HOH HOH . G 6 HOH A 68 668 36 HOH HOH . G 6 HOH A 69 669 38 HOH HOH . G 6 HOH A 70 670 40 HOH HOH . G 6 HOH A 71 671 42 HOH HOH . G 6 HOH A 72 672 45 HOH HOH . G 6 HOH A 73 673 46 HOH HOH . G 6 HOH A 74 674 50 HOH HOH . G 6 HOH A 75 675 51 HOH HOH . G 6 HOH A 76 676 54 HOH HOH . G 6 HOH A 77 677 55 HOH HOH . G 6 HOH A 78 678 58 HOH HOH . G 6 HOH A 79 679 59 HOH HOH . G 6 HOH A 80 680 61 HOH HOH . G 6 HOH A 81 681 63 HOH HOH . G 6 HOH A 82 682 64 HOH HOH . G 6 HOH A 83 683 67 HOH HOH . G 6 HOH A 84 684 70 HOH HOH . G 6 HOH A 85 685 71 HOH HOH . G 6 HOH A 86 686 72 HOH HOH . G 6 HOH A 87 687 73 HOH HOH . G 6 HOH A 88 688 74 HOH HOH . G 6 HOH A 89 689 75 HOH HOH . G 6 HOH A 90 690 76 HOH HOH . G 6 HOH A 91 691 81 HOH HOH . G 6 HOH A 92 692 82 HOH HOH . G 6 HOH A 93 693 83 HOH HOH . G 6 HOH A 94 694 84 HOH HOH . G 6 HOH A 95 695 85 HOH HOH . G 6 HOH A 96 696 88 HOH HOH . G 6 HOH A 97 697 92 HOH HOH . G 6 HOH A 98 698 93 HOH HOH . G 6 HOH A 99 699 94 HOH HOH . G 6 HOH A 100 700 96 HOH HOH . G 6 HOH A 101 701 99 HOH HOH . G 6 HOH A 102 702 103 HOH HOH . G 6 HOH A 103 703 104 HOH HOH . G 6 HOH A 104 704 108 HOH HOH . G 6 HOH A 105 705 110 HOH HOH . G 6 HOH A 106 706 113 HOH HOH . G 6 HOH A 107 707 114 HOH HOH . G 6 HOH A 108 708 117 HOH HOH . G 6 HOH A 109 709 121 HOH HOH . G 6 HOH A 110 710 122 HOH HOH . G 6 HOH A 111 711 126 HOH HOH . G 6 HOH A 112 712 127 HOH HOH . G 6 HOH A 113 713 129 HOH HOH . G 6 HOH A 114 714 130 HOH HOH . G 6 HOH A 115 715 131 HOH HOH . G 6 HOH A 116 716 132 HOH HOH . G 6 HOH A 117 717 149 HOH HOH . G 6 HOH A 118 718 150 HOH HOH . G 6 HOH A 119 719 152 HOH HOH . G 6 HOH A 120 720 153 HOH HOH . G 6 HOH A 121 721 169 HOH HOH . G 6 HOH A 122 722 170 HOH HOH . G 6 HOH A 123 723 171 HOH HOH . G 6 HOH A 124 724 174 HOH HOH . G 6 HOH A 125 725 5 HOH HOH . G 6 HOH A 126 726 6 HOH HOH . G 6 HOH A 127 727 7 HOH HOH . G 6 HOH A 128 728 8 HOH HOH . G 6 HOH A 129 729 9 HOH HOH . G 6 HOH A 130 730 10 HOH HOH . G 6 HOH A 131 731 11 HOH HOH . G 6 HOH A 132 732 13 HOH HOH . G 6 HOH A 133 733 14 HOH HOH . G 6 HOH A 134 734 15 HOH HOH . G 6 HOH A 135 735 20 HOH HOH . G 6 HOH A 136 736 21 HOH HOH . G 6 HOH A 137 737 23 HOH HOH . G 6 HOH A 138 738 24 HOH HOH . G 6 HOH A 139 739 25 HOH HOH . G 6 HOH A 140 740 26 HOH HOH . G 6 HOH A 141 741 27 HOH HOH . G 6 HOH A 142 742 29 HOH HOH . G 6 HOH A 143 743 30 HOH HOH . G 6 HOH A 144 744 31 HOH HOH . G 6 HOH A 145 745 32 HOH HOH . G 6 HOH A 146 746 43 HOH HOH . G 6 HOH A 147 747 48 HOH HOH . G 6 HOH A 148 748 49 HOH HOH . G 6 HOH A 149 749 54 HOH HOH . G 6 HOH A 150 750 55 HOH HOH . G 6 HOH A 151 751 56 HOH HOH . G 6 HOH A 152 752 57 HOH HOH . G 6 HOH A 153 753 60 HOH HOH . G 6 HOH A 154 754 65 HOH HOH . G 6 HOH A 155 755 68 HOH HOH . G 6 HOH A 156 756 69 HOH HOH . G 6 HOH A 157 757 70 HOH HOH . G 6 HOH A 158 758 73 HOH HOH . G 6 HOH A 159 759 74 HOH HOH . G 6 HOH A 160 760 75 HOH HOH . G 6 HOH A 161 761 78 HOH HOH . G 6 HOH A 162 762 80 HOH HOH . G 6 HOH A 163 763 81 HOH HOH . G 6 HOH A 164 764 82 HOH HOH . G 6 HOH A 165 765 83 HOH HOH . G 6 HOH A 166 766 86 HOH HOH . G 6 HOH A 167 767 87 HOH HOH . G 6 HOH A 168 768 88 HOH HOH . G 6 HOH A 169 769 102 HOH HOH . G 6 HOH A 170 770 103 HOH HOH . G 6 HOH A 171 771 106 HOH HOH . G 6 HOH A 172 772 107 HOH HOH . G 6 HOH A 173 773 108 HOH HOH . H 6 HOH B 1 601 164 HOH HOH . H 6 HOH B 2 602 98 HOH HOH . H 6 HOH B 3 603 32 HOH HOH . H 6 HOH B 4 604 14 HOH HOH . H 6 HOH B 5 605 143 HOH HOH . H 6 HOH B 6 606 97 HOH HOH . H 6 HOH B 7 607 109 HOH HOH . H 6 HOH B 8 608 52 HOH HOH . H 6 HOH B 9 609 76 HOH HOH . H 6 HOH B 10 610 2 HOH HOH . H 6 HOH B 11 611 133 HOH HOH . H 6 HOH B 12 612 177 HOH HOH . H 6 HOH B 13 613 165 HOH HOH . H 6 HOH B 14 614 48 HOH HOH . H 6 HOH B 15 615 36 HOH HOH . H 6 HOH B 16 616 90 HOH HOH . H 6 HOH B 17 617 24 HOH HOH . H 6 HOH B 18 618 1 HOH HOH . H 6 HOH B 19 619 35 HOH HOH . H 6 HOH B 20 620 62 HOH HOH . H 6 HOH B 21 621 17 HOH HOH . H 6 HOH B 22 622 34 HOH HOH . H 6 HOH B 23 623 161 HOH HOH . H 6 HOH B 24 624 63 HOH HOH . H 6 HOH B 25 625 57 HOH HOH . H 6 HOH B 26 626 160 HOH HOH . H 6 HOH B 27 627 90 HOH HOH . H 6 HOH B 28 628 112 HOH HOH . H 6 HOH B 29 629 12 HOH HOH . H 6 HOH B 30 630 52 HOH HOH . H 6 HOH B 31 631 123 HOH HOH . H 6 HOH B 32 632 37 HOH HOH . H 6 HOH B 33 633 124 HOH HOH . H 6 HOH B 34 634 178 HOH HOH . H 6 HOH B 35 635 4 HOH HOH . H 6 HOH B 36 636 5 HOH HOH . H 6 HOH B 37 637 7 HOH HOH . H 6 HOH B 38 638 8 HOH HOH . H 6 HOH B 39 639 10 HOH HOH . H 6 HOH B 40 640 16 HOH HOH . H 6 HOH B 41 641 19 HOH HOH . H 6 HOH B 42 642 20 HOH HOH . H 6 HOH B 43 643 25 HOH HOH . H 6 HOH B 44 644 28 HOH HOH . H 6 HOH B 45 645 35 HOH HOH . H 6 HOH B 46 646 37 HOH HOH . H 6 HOH B 47 647 39 HOH HOH . H 6 HOH B 48 648 41 HOH HOH . H 6 HOH B 49 649 44 HOH HOH . H 6 HOH B 50 650 47 HOH HOH . H 6 HOH B 51 651 49 HOH HOH . H 6 HOH B 52 652 53 HOH HOH . H 6 HOH B 53 653 60 HOH HOH . H 6 HOH B 54 654 66 HOH HOH . H 6 HOH B 55 655 68 HOH HOH . H 6 HOH B 56 656 78 HOH HOH . H 6 HOH B 57 657 79 HOH HOH . H 6 HOH B 58 658 86 HOH HOH . H 6 HOH B 59 659 87 HOH HOH . H 6 HOH B 60 660 89 HOH HOH . H 6 HOH B 61 661 118 HOH HOH . H 6 HOH B 62 662 119 HOH HOH . H 6 HOH B 63 663 120 HOH HOH . H 6 HOH B 64 664 125 HOH HOH . H 6 HOH B 65 665 134 HOH HOH . H 6 HOH B 66 666 135 HOH HOH . H 6 HOH B 67 667 136 HOH HOH . H 6 HOH B 68 668 137 HOH HOH . H 6 HOH B 69 669 138 HOH HOH . H 6 HOH B 70 670 139 HOH HOH . H 6 HOH B 71 671 140 HOH HOH . H 6 HOH B 72 672 141 HOH HOH . H 6 HOH B 73 673 142 HOH HOH . H 6 HOH B 74 674 144 HOH HOH . H 6 HOH B 75 675 145 HOH HOH . H 6 HOH B 76 676 146 HOH HOH . H 6 HOH B 77 677 147 HOH HOH . H 6 HOH B 78 678 148 HOH HOH . H 6 HOH B 79 679 154 HOH HOH . H 6 HOH B 80 680 155 HOH HOH . H 6 HOH B 81 681 156 HOH HOH . H 6 HOH B 82 682 157 HOH HOH . H 6 HOH B 83 683 158 HOH HOH . H 6 HOH B 84 684 162 HOH HOH . H 6 HOH B 85 685 163 HOH HOH . H 6 HOH B 86 686 166 HOH HOH . H 6 HOH B 87 687 172 HOH HOH . H 6 HOH B 88 688 176 HOH HOH . H 6 HOH B 89 689 1 HOH HOH . H 6 HOH B 90 690 2 HOH HOH . H 6 HOH B 91 691 19 HOH HOH . H 6 HOH B 92 692 22 HOH HOH . H 6 HOH B 93 693 28 HOH HOH . H 6 HOH B 94 694 33 HOH HOH . H 6 HOH B 95 695 34 HOH HOH . H 6 HOH B 96 696 38 HOH HOH . H 6 HOH B 97 697 39 HOH HOH . H 6 HOH B 98 698 40 HOH HOH . H 6 HOH B 99 699 41 HOH HOH . H 6 HOH B 100 700 45 HOH HOH . H 6 HOH B 101 701 46 HOH HOH . H 6 HOH B 102 702 47 HOH HOH . H 6 HOH B 103 703 62 HOH HOH . H 6 HOH B 104 704 64 HOH HOH . H 6 HOH B 105 705 66 HOH HOH . H 6 HOH B 106 706 67 HOH HOH . H 6 HOH B 107 707 79 HOH HOH . H 6 HOH B 108 708 94 HOH HOH . H 6 HOH B 109 709 95 HOH HOH . H 6 HOH B 110 710 96 HOH HOH . H 6 HOH B 111 711 99 HOH HOH . H 6 HOH B 112 712 100 HOH HOH . H 6 HOH B 113 713 101 HOH HOH . H 6 HOH B 114 714 104 HOH HOH . H 6 HOH B 115 715 105 HOH HOH . H 6 HOH B 116 716 109 HOH HOH . H 6 HOH B 117 717 110 HOH HOH . H 6 HOH B 118 718 111 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 33.781 _atom_site.Cartn_y 14.22 _atom_site.Cartn_z -24.877 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 47.69 _atom_site.pdbx_formal_charge 1 _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 502 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #