data_4YD2 # _model_server_result.job_id Yq-Z6Z4tWmVHE6EoCpHfiQ _model_server_result.datetime_utc '2024-11-06 23:52:30' _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 4yd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 4YD2 # _exptl.entry_id 4YD2 _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 3 _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 4YD2 _cell.length_a 60.083 _cell.length_b 68.7 _cell.length_c 114.977 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YD2 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,N,O _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 ? 5 E N N ? 5 H N N ? 5 I 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 O THR 113 A THR 241 1_555 I NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc2 A O ILE 115 A ILE 243 1_555 I NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc3 A O VAL 118 A VAL 246 1_555 I NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc4 A OD1 ASP 202 A ASP 330 1_555 E NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc5 A OD1 ASP 202 A ASP 330 1_555 H NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc6 A OD2 ASP 202 A ASP 330 1_555 H NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc7 A OD1 ASP 204 A ASP 332 1_555 E NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc8 A OD2 ASP 204 A ASP 332 1_555 H NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc9 A OD2 ASP 278 A ASP 418 1_555 E NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc10 E NA NA . A NA 501 1_555 C O3' DA 4 P DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc11 E NA NA . A NA 501 1_555 C OP1 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc12 H NA NA . A NA 504 1_555 K O22 PPV . A PPV 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc13 H NA NA . A NA 504 1_555 K O32 PPV . A PPV 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc14 H NA NA . A NA 504 1_555 L O HOH . A HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc15 H NA NA . A NA 504 1_555 C OP1 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc16 I NA NA . A NA 505 1_555 L O HOH . A HOH 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? metalc ? metalc17 I NA NA . A NA 505 1_555 C OP1 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc18 I NA NA . A NA 505 1_555 N O HOH . P HOH 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 T DC 1 1_555 D N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 T DC 1 1_555 D O6 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 T DC 1 1_555 D N2 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 2 T DG 2 1_555 D N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 2 T DG 2 1_555 D O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 2 T DG 2 1_555 D N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DG 3 T DG 3 1_555 D N3 DC 2 D DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 3 T DG 3 1_555 D O2 DC 2 D DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 DG 3 T DG 3 1_555 D N4 DC 2 D DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 4 T DC 4 1_555 D N1 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 4 T DC 4 1_555 D O6 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 4 T DC 4 1_555 D N2 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DA 5 T DA 5 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 5 T DA 5 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 4YD2 _atom_sites.fract_transf_matrix[1][1] 0.016644 _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] 0.014556 _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] 0.008697 _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 E 5 NA A 1 501 1 NA NA . F 6 CL A 1 502 2 CL CL . G 6 CL A 1 503 3 CL CL . H 5 NA A 1 504 4 NA NA . I 5 NA A 1 505 5 NA NA . J 6 CL A 1 506 6 CL CL . K 7 PPV A 1 507 700 PPV PPV . L 8 HOH A 1 601 157 HOH HOH . L 8 HOH A 2 602 33 HOH HOH . L 8 HOH A 3 603 21 HOH HOH . L 8 HOH A 4 604 7 HOH HOH . L 8 HOH A 5 605 62 HOH HOH . L 8 HOH A 6 606 35 HOH HOH . L 8 HOH A 7 607 68 HOH HOH . L 8 HOH A 8 608 116 HOH HOH . L 8 HOH A 9 609 8 HOH HOH . L 8 HOH A 10 610 140 HOH HOH . L 8 HOH A 11 611 83 HOH HOH . L 8 HOH A 12 612 50 HOH HOH . L 8 HOH A 13 613 37 HOH HOH . L 8 HOH A 14 614 77 HOH HOH . L 8 HOH A 15 615 125 HOH HOH . L 8 HOH A 16 616 60 HOH HOH . L 8 HOH A 17 617 39 HOH HOH . L 8 HOH A 18 618 129 HOH HOH . L 8 HOH A 19 619 78 HOH HOH . L 8 HOH A 20 620 30 HOH HOH . L 8 HOH A 21 621 144 HOH HOH . L 8 HOH A 22 622 97 HOH HOH . L 8 HOH A 23 623 110 HOH HOH . L 8 HOH A 24 624 11 HOH HOH . L 8 HOH A 25 625 40 HOH HOH . L 8 HOH A 26 626 143 HOH HOH . L 8 HOH A 27 627 115 HOH HOH . L 8 HOH A 28 628 142 HOH HOH . L 8 HOH A 29 629 104 HOH HOH . L 8 HOH A 30 630 141 HOH HOH . L 8 HOH A 31 631 100 HOH HOH . L 8 HOH A 32 632 1 HOH HOH . L 8 HOH A 33 633 2 HOH HOH . L 8 HOH A 34 634 3 HOH HOH . L 8 HOH A 35 635 4 HOH HOH . L 8 HOH A 36 636 9 HOH HOH . L 8 HOH A 37 637 10 HOH HOH . L 8 HOH A 38 638 12 HOH HOH . L 8 HOH A 39 639 14 HOH HOH . L 8 HOH A 40 640 15 HOH HOH . L 8 HOH A 41 641 17 HOH HOH . L 8 HOH A 42 642 19 HOH HOH . L 8 HOH A 43 643 20 HOH HOH . L 8 HOH A 44 644 22 HOH HOH . L 8 HOH A 45 645 23 HOH HOH . L 8 HOH A 46 646 24 HOH HOH . L 8 HOH A 47 647 25 HOH HOH . L 8 HOH A 48 648 26 HOH HOH . L 8 HOH A 49 649 27 HOH HOH . L 8 HOH A 50 650 29 HOH HOH . L 8 HOH A 51 651 34 HOH HOH . L 8 HOH A 52 652 36 HOH HOH . L 8 HOH A 53 653 38 HOH HOH . L 8 HOH A 54 654 41 HOH HOH . L 8 HOH A 55 655 42 HOH HOH . L 8 HOH A 56 656 43 HOH HOH . L 8 HOH A 57 657 46 HOH HOH . L 8 HOH A 58 658 47 HOH HOH . L 8 HOH A 59 659 48 HOH HOH . L 8 HOH A 60 660 49 HOH HOH . L 8 HOH A 61 661 51 HOH HOH . L 8 HOH A 62 662 52 HOH HOH . L 8 HOH A 63 663 53 HOH HOH . L 8 HOH A 64 664 54 HOH HOH . L 8 HOH A 65 665 55 HOH HOH . L 8 HOH A 66 666 56 HOH HOH . L 8 HOH A 67 667 57 HOH HOH . L 8 HOH A 68 668 58 HOH HOH . L 8 HOH A 69 669 59 HOH HOH . L 8 HOH A 70 670 61 HOH HOH . L 8 HOH A 71 671 63 HOH HOH . L 8 HOH A 72 672 64 HOH HOH . L 8 HOH A 73 673 65 HOH HOH . L 8 HOH A 74 674 66 HOH HOH . L 8 HOH A 75 675 67 HOH HOH . L 8 HOH A 76 676 69 HOH HOH . L 8 HOH A 77 677 71 HOH HOH . L 8 HOH A 78 678 72 HOH HOH . L 8 HOH A 79 679 73 HOH HOH . L 8 HOH A 80 680 74 HOH HOH . L 8 HOH A 81 681 75 HOH HOH . L 8 HOH A 82 682 76 HOH HOH . L 8 HOH A 83 683 79 HOH HOH . L 8 HOH A 84 684 80 HOH HOH . L 8 HOH A 85 685 82 HOH HOH . L 8 HOH A 86 686 84 HOH HOH . L 8 HOH A 87 687 86 HOH HOH . L 8 HOH A 88 688 87 HOH HOH . L 8 HOH A 89 689 88 HOH HOH . L 8 HOH A 90 690 89 HOH HOH . L 8 HOH A 91 691 90 HOH HOH . L 8 HOH A 92 692 91 HOH HOH . L 8 HOH A 93 693 92 HOH HOH . L 8 HOH A 94 694 93 HOH HOH . L 8 HOH A 95 695 96 HOH HOH . L 8 HOH A 96 696 98 HOH HOH . L 8 HOH A 97 697 99 HOH HOH . L 8 HOH A 98 698 101 HOH HOH . L 8 HOH A 99 699 103 HOH HOH . L 8 HOH A 100 700 106 HOH HOH . L 8 HOH A 101 701 107 HOH HOH . L 8 HOH A 102 702 108 HOH HOH . L 8 HOH A 103 703 111 HOH HOH . L 8 HOH A 104 704 112 HOH HOH . L 8 HOH A 105 705 114 HOH HOH . L 8 HOH A 106 706 117 HOH HOH . L 8 HOH A 107 707 118 HOH HOH . L 8 HOH A 108 708 119 HOH HOH . L 8 HOH A 109 709 120 HOH HOH . L 8 HOH A 110 710 123 HOH HOH . L 8 HOH A 111 711 126 HOH HOH . L 8 HOH A 112 712 133 HOH HOH . L 8 HOH A 113 713 135 HOH HOH . L 8 HOH A 114 714 137 HOH HOH . L 8 HOH A 115 715 138 HOH HOH . L 8 HOH A 116 716 139 HOH HOH . L 8 HOH A 117 717 146 HOH HOH . L 8 HOH A 118 718 147 HOH HOH . L 8 HOH A 119 719 148 HOH HOH . L 8 HOH A 120 720 150 HOH HOH . L 8 HOH A 121 721 151 HOH HOH . L 8 HOH A 122 722 152 HOH HOH . L 8 HOH A 123 723 153 HOH HOH . L 8 HOH A 124 724 155 HOH HOH . L 8 HOH A 125 725 156 HOH HOH . L 8 HOH A 126 726 158 HOH HOH . L 8 HOH A 127 727 159 HOH HOH . L 8 HOH A 128 728 160 HOH HOH . L 8 HOH A 129 729 161 HOH HOH . L 8 HOH A 130 730 162 HOH HOH . L 8 HOH A 131 731 163 HOH HOH . L 8 HOH A 132 732 16 HOH HOH . L 8 HOH A 133 733 18 HOH HOH . L 8 HOH A 134 734 70 HOH HOH . L 8 HOH A 135 735 131 HOH HOH . M 8 HOH T 1 101 13 HOH HOH . M 8 HOH T 2 102 45 HOH HOH . M 8 HOH T 3 103 122 HOH HOH . N 8 HOH P 1 101 32 HOH HOH . N 8 HOH P 2 102 102 HOH HOH . N 8 HOH P 3 103 109 HOH HOH . O 8 HOH D 1 101 31 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 1.932 _atom_site.Cartn_y 2.517 _atom_site.Cartn_z -7.669 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 18.65 _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 14 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #