data_5D4B
#
_model_server_result.job_id            DouIxjH0BMrZiF63DG8aRA 
_model_server_result.datetime_utc      '2024-10-18 16:20:48' 
_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          5d4b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":602}' 
#
_entry.id    5D4B 
#
_exptl.entry_id    5D4B 
_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    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            5D4B 
_cell.length_a            56.73 
_cell.length_b            71.45 
_cell.length_c            198.17 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5D4B 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,H,I,J,Q,R,S,U,W,X 1 1 
B,D,E,F,K,L,M,N,O,P,T,V,W,X 2 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 H N N 
? 5 L 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 143 A THR 253 1_555 H NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc2 A O VAL 145 A VAL 255 1_555 H NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc3 A O VAL 148 A VAL 258 1_555 H NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc4 A OD1 ASP 233 A ASP 343 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc5 A OD2 ASP 235 A ASP 345 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc6 G MG MG . A MG 601 1_555 C OP1 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc7 G MG MG . A MG 601 1_555 Q O2 SO4 . C SO4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc8 H NA NA . A NA 602 1_555 C OP1 DA 4 C DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc9 B O THR 143 B THR 253 1_555 L NA NA . B NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc10 B O VAL 148 B VAL 258 1_555 L NA NA . B NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc11 B OD1 ASP 233 B ASP 343 1_555 K MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
metalc ? metalc12 B OD2 ASP 235 B ASP 345 1_555 K MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
metalc ? metalc13 K MG MG . B MG 601 1_555 M O4 SO4 . B SO4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc14 K MG MG . B MG 601 1_555 T O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc15 K MG MG . B MG 601 1_555 D OP1 DC 6 D DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc16 L NA NA . B NA 602 1_555 D OP1 DA 4 D DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
hydrog WATSON-CRICK hydrog1 D N3 DC 6 D DC 6 1_555 F N1 DG 6 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 D N4 DC 6 D DC 6 1_555 F O6 DG 6 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 D O2 DC 6 D DC 6 1_555 F N2 DG 6 F DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 E N1 DA 1 E DA 1 1_555 F N3 DT 5 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 E N6 DA 1 E DA 1 1_555 F O4 DT 5 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 E N1 DA 2 E DA 2 1_555 F N3 DT 4 F DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 E N6 DA 2 E DA 2 1_555 F O4 DT 4 F DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 E N1 DA 3 E DA 3 1_555 F N3 DT 3 F DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 E N6 DA 3 E DA 3 1_555 F O4 DT 3 F DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 E N1 DA 4 E DA 4 1_555 F N3 DT 2 F DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 E N6 DA 4 E DA 4 1_555 F O4 DT 2 F DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 E N1 DA 5 E DA 5 1_555 F N3 DT 1 F DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 E N6 DA 5 E DA 5 1_555 F O4 DT 1 F DT 1 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                     5D4B 
_atom_sites.fract_transf_matrix[1][1]    0.017627 
_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]    0.013996 
_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]    0.005046 
_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
G 4 MG A 1 601 1 MG MG . 
H 5 NA A 1 602 201 NA NA . 
I 6 SO4 A 1 603 6 SO4 SO4 . 
J 6 SO4 A 1 604 7 SO4 SO4 . 
K 4 MG B 1 601 101 MG MG . 
L 5 NA B 1 602 301 NA NA . 
M 6 SO4 B 1 603 501 SO4 SO4 . 
N 6 SO4 B 1 604 3 SO4 SO4 . 
O 6 SO4 B 1 605 4 SO4 SO4 . 
P 6 SO4 B 1 606 5 SO4 SO4 . 
Q 6 SO4 C 1 401 401 SO4 SO4 . 
R 6 SO4 C 1 402 2 SO4 SO4 . 
S 7 HOH A 1 701 10 HOH HOH . 
S 7 HOH A 2 702 108 HOH HOH . 
S 7 HOH A 3 703 15 HOH HOH . 
S 7 HOH A 4 704 39 HOH HOH . 
S 7 HOH A 5 705 157 HOH HOH . 
S 7 HOH A 6 706 25 HOH HOH . 
S 7 HOH A 7 707 106 HOH HOH . 
S 7 HOH A 8 708 148 HOH HOH . 
S 7 HOH A 9 709 105 HOH HOH . 
S 7 HOH A 10 710 107 HOH HOH . 
S 7 HOH A 11 711 69 HOH HOH . 
S 7 HOH A 12 712 72 HOH HOH . 
S 7 HOH A 13 713 43 HOH HOH . 
S 7 HOH A 14 714 26 HOH HOH . 
S 7 HOH A 15 715 21 HOH HOH . 
S 7 HOH A 16 716 53 HOH HOH . 
S 7 HOH A 17 717 73 HOH HOH . 
S 7 HOH A 18 718 99 HOH HOH . 
S 7 HOH A 19 719 41 HOH HOH . 
S 7 HOH A 20 720 125 HOH HOH . 
S 7 HOH A 21 721 56 HOH HOH . 
S 7 HOH A 22 722 67 HOH HOH . 
S 7 HOH A 23 723 76 HOH HOH . 
S 7 HOH A 24 724 140 HOH HOH . 
S 7 HOH A 25 725 24 HOH HOH . 
S 7 HOH A 26 726 20 HOH HOH . 
S 7 HOH A 27 727 50 HOH HOH . 
S 7 HOH A 28 728 65 HOH HOH . 
S 7 HOH A 29 729 144 HOH HOH . 
S 7 HOH A 30 730 127 HOH HOH . 
S 7 HOH A 31 731 96 HOH HOH . 
S 7 HOH A 32 732 37 HOH HOH . 
S 7 HOH A 33 733 133 HOH HOH . 
S 7 HOH A 34 734 138 HOH HOH . 
S 7 HOH A 35 735 34 HOH HOH . 
S 7 HOH A 36 736 13 HOH HOH . 
S 7 HOH A 37 737 68 HOH HOH . 
S 7 HOH A 38 738 87 HOH HOH . 
S 7 HOH A 39 739 90 HOH HOH . 
S 7 HOH A 40 740 58 HOH HOH . 
S 7 HOH A 41 741 14 HOH HOH . 
S 7 HOH A 42 742 88 HOH HOH . 
S 7 HOH A 43 743 130 HOH HOH . 
S 7 HOH A 44 744 151 HOH HOH . 
S 7 HOH A 45 745 71 HOH HOH . 
S 7 HOH A 46 746 35 HOH HOH . 
S 7 HOH A 47 747 146 HOH HOH . 
S 7 HOH A 48 748 4 HOH HOH . 
S 7 HOH A 49 749 126 HOH HOH . 
S 7 HOH A 50 750 77 HOH HOH . 
S 7 HOH A 51 751 103 HOH HOH . 
S 7 HOH A 52 752 92 HOH HOH . 
S 7 HOH A 53 753 132 HOH HOH . 
S 7 HOH A 54 754 102 HOH HOH . 
S 7 HOH A 55 755 98 HOH HOH . 
S 7 HOH A 56 756 3 HOH HOH . 
S 7 HOH A 57 757 120 HOH HOH . 
S 7 HOH A 58 758 11 HOH HOH . 
S 7 HOH A 59 759 59 HOH HOH . 
S 7 HOH A 60 760 47 HOH HOH . 
S 7 HOH A 61 761 100 HOH HOH . 
S 7 HOH A 62 762 129 HOH HOH . 
S 7 HOH A 63 763 160 HOH HOH . 
S 7 HOH A 64 764 147 HOH HOH . 
T 7 HOH B 1 701 5 HOH HOH . 
T 7 HOH B 2 702 135 HOH HOH . 
T 7 HOH B 3 703 18 HOH HOH . 
T 7 HOH B 4 704 79 HOH HOH . 
T 7 HOH B 5 705 85 HOH HOH . 
T 7 HOH B 6 706 74 HOH HOH . 
T 7 HOH B 7 707 134 HOH HOH . 
T 7 HOH B 8 708 17 HOH HOH . 
T 7 HOH B 9 709 156 HOH HOH . 
T 7 HOH B 10 710 91 HOH HOH . 
T 7 HOH B 11 711 8 HOH HOH . 
T 7 HOH B 12 712 30 HOH HOH . 
T 7 HOH B 13 713 154 HOH HOH . 
T 7 HOH B 14 714 112 HOH HOH . 
T 7 HOH B 15 715 28 HOH HOH . 
T 7 HOH B 16 716 122 HOH HOH . 
T 7 HOH B 17 717 153 HOH HOH . 
T 7 HOH B 18 718 123 HOH HOH . 
T 7 HOH B 19 719 109 HOH HOH . 
T 7 HOH B 20 720 111 HOH HOH . 
T 7 HOH B 21 721 114 HOH HOH . 
T 7 HOH B 22 722 155 HOH HOH . 
T 7 HOH B 23 723 27 HOH HOH . 
T 7 HOH B 24 724 9 HOH HOH . 
T 7 HOH B 25 725 62 HOH HOH . 
T 7 HOH B 26 726 136 HOH HOH . 
T 7 HOH B 27 727 89 HOH HOH . 
T 7 HOH B 28 728 49 HOH HOH . 
T 7 HOH B 29 729 80 HOH HOH . 
T 7 HOH B 30 730 19 HOH HOH . 
T 7 HOH B 31 731 118 HOH HOH . 
T 7 HOH B 32 732 78 HOH HOH . 
T 7 HOH B 33 733 55 HOH HOH . 
T 7 HOH B 34 734 54 HOH HOH . 
T 7 HOH B 35 735 84 HOH HOH . 
T 7 HOH B 36 736 63 HOH HOH . 
T 7 HOH B 37 737 36 HOH HOH . 
T 7 HOH B 38 738 44 HOH HOH . 
T 7 HOH B 39 739 42 HOH HOH . 
T 7 HOH B 40 740 128 HOH HOH . 
T 7 HOH B 41 741 119 HOH HOH . 
T 7 HOH B 42 742 139 HOH HOH . 
T 7 HOH B 43 743 23 HOH HOH . 
T 7 HOH B 44 744 142 HOH HOH . 
T 7 HOH B 45 745 131 HOH HOH . 
T 7 HOH B 46 746 12 HOH HOH . 
T 7 HOH B 47 747 32 HOH HOH . 
T 7 HOH B 48 748 137 HOH HOH . 
T 7 HOH B 49 749 7 HOH HOH . 
T 7 HOH B 50 750 48 HOH HOH . 
T 7 HOH B 51 751 93 HOH HOH . 
T 7 HOH B 52 752 143 HOH HOH . 
T 7 HOH B 53 753 161 HOH HOH . 
T 7 HOH B 54 754 31 HOH HOH . 
T 7 HOH B 55 755 40 HOH HOH . 
T 7 HOH B 56 756 158 HOH HOH . 
T 7 HOH B 57 757 64 HOH HOH . 
T 7 HOH B 58 758 46 HOH HOH . 
T 7 HOH B 59 759 145 HOH HOH . 
T 7 HOH B 60 760 97 HOH HOH . 
T 7 HOH B 61 761 94 HOH HOH . 
T 7 HOH B 62 762 70 HOH HOH . 
T 7 HOH B 63 763 104 HOH HOH . 
T 7 HOH B 64 764 95 HOH HOH . 
T 7 HOH B 65 765 141 HOH HOH . 
U 7 HOH C 1 501 110 HOH HOH . 
U 7 HOH C 2 502 150 HOH HOH . 
U 7 HOH C 3 503 121 HOH HOH . 
U 7 HOH C 4 504 149 HOH HOH . 
U 7 HOH C 5 505 159 HOH HOH . 
U 7 HOH C 6 506 75 HOH HOH . 
V 7 HOH D 1 101 33 HOH HOH . 
V 7 HOH D 2 102 81 HOH HOH . 
V 7 HOH D 3 103 60 HOH HOH . 
V 7 HOH D 4 104 16 HOH HOH . 
V 7 HOH D 5 105 29 HOH HOH . 
V 7 HOH D 6 106 52 HOH HOH . 
V 7 HOH D 7 107 61 HOH HOH . 
V 7 HOH D 8 108 82 HOH HOH . 
W 7 HOH E 1 101 57 HOH HOH . 
W 7 HOH E 2 102 66 HOH HOH . 
W 7 HOH E 3 103 115 HOH HOH . 
W 7 HOH E 4 104 152 HOH HOH . 
W 7 HOH E 5 105 117 HOH HOH . 
X 7 HOH F 1 101 116 HOH HOH . 
X 7 HOH F 2 102 101 HOH HOH . 
X 7 HOH F 3 103 45 HOH HOH . 
X 7 HOH F 4 104 86 HOH HOH . 
X 7 HOH F 5 105 38 HOH HOH . 
X 7 HOH F 6 106 83 HOH HOH . 
X 7 HOH F 7 107 113 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         L 
_atom_site.label_entity_id       5 
_atom_site.Cartn_x               41.064 
_atom_site.Cartn_y               -1.054 
_atom_site.Cartn_z               30.933 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        67.07 
_atom_site.pdbx_formal_charge    1 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           602 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#