data_3PDG
#
_model_server_result.job_id            nXWA6u9Aut3uv0k8uASQ5Q 
_model_server_result.datetime_utc      '2024-11-29 08:11:27' 
_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          3pdg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":99}' 
#
_entry.id    3PDG 
#
_exptl.entry_id    3PDG 
_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            3PDG 
_cell.length_a            42.316 
_cell.length_b            42.316 
_cell.length_c            116.756 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PDG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 46 A ASP 46 1_555 B NA NA . A NA 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc2 A OD1 ASP 46 A ASP 46 1_555 B NA NA . A NA 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? 
metalc ? metalc3 A O THR 48 A THR 48 1_555 B NA NA . A NA 99 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc4 A O THR 48 A THR 48 1_555 B NA NA . A NA 99 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc5 A O PRO 50 A PRO 50 1_555 B NA NA . A NA 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc6 B NA NA . A NA 99 1_555 D O HOH . A HOH 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc7 B NA NA . A NA 99 1_555 D O HOH . A HOH 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc8 B NA NA . A NA 99 1_555 D O HOH . A HOH 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc9 C NA NA . A NA 100 1_555 D O HOH . A HOH 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.12 ? 
#
_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                     3PDG 
_atom_sites.fract_transf_matrix[1][1]    0.023632 
_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]    0.023632 
_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]    0.008565 
_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 99 1 NA NA . 
C 2 NA A 1 100 2 NA NA . 
D 3 HOH A 1 101 101 HOH HOH . 
D 3 HOH A 2 102 102 HOH HOH . 
D 3 HOH A 3 103 103 HOH HOH . 
D 3 HOH A 4 104 104 HOH HOH . 
D 3 HOH A 5 105 105 HOH HOH . 
D 3 HOH A 6 106 106 HOH HOH . 
D 3 HOH A 7 107 107 HOH HOH . 
D 3 HOH A 8 108 108 HOH HOH . 
D 3 HOH A 9 109 1 HOH HOH . 
D 3 HOH A 10 110 3 HOH HOH . 
D 3 HOH A 11 111 4 HOH HOH . 
D 3 HOH A 12 112 5 HOH HOH . 
D 3 HOH A 13 113 6 HOH HOH . 
D 3 HOH A 14 114 7 HOH HOH . 
D 3 HOH A 15 115 8 HOH HOH . 
D 3 HOH A 16 116 9 HOH HOH . 
D 3 HOH A 17 117 10 HOH HOH . 
D 3 HOH A 18 118 11 HOH HOH . 
D 3 HOH A 19 119 12 HOH HOH . 
D 3 HOH A 20 120 13 HOH HOH . 
D 3 HOH A 21 121 14 HOH HOH . 
D 3 HOH A 22 122 15 HOH HOH . 
D 3 HOH A 23 123 16 HOH HOH . 
D 3 HOH A 24 124 17 HOH HOH . 
D 3 HOH A 25 125 18 HOH HOH . 
D 3 HOH A 26 126 20 HOH HOH . 
D 3 HOH A 27 127 21 HOH HOH . 
D 3 HOH A 28 128 22 HOH HOH . 
D 3 HOH A 29 129 24 HOH HOH . 
D 3 HOH A 30 130 25 HOH HOH . 
D 3 HOH A 31 131 26 HOH HOH . 
D 3 HOH A 32 132 27 HOH HOH . 
D 3 HOH A 33 133 29 HOH HOH . 
D 3 HOH A 34 134 30 HOH HOH . 
D 3 HOH A 35 135 31 HOH HOH . 
D 3 HOH A 36 136 33 HOH HOH . 
D 3 HOH A 37 137 34 HOH HOH . 
D 3 HOH A 38 138 35 HOH HOH . 
D 3 HOH A 39 139 36 HOH HOH . 
D 3 HOH A 40 140 37 HOH HOH . 
D 3 HOH A 41 141 38 HOH HOH . 
D 3 HOH A 42 142 41 HOH HOH . 
D 3 HOH A 43 143 43 HOH HOH . 
D 3 HOH A 44 144 44 HOH HOH . 
D 3 HOH A 45 145 45 HOH HOH . 
D 3 HOH A 46 146 46 HOH HOH . 
D 3 HOH A 47 147 47 HOH HOH . 
D 3 HOH A 48 148 48 HOH HOH . 
D 3 HOH A 49 149 50 HOH HOH . 
D 3 HOH A 50 150 51 HOH HOH . 
D 3 HOH A 51 151 53 HOH HOH . 
D 3 HOH A 52 152 54 HOH HOH . 
D 3 HOH A 53 153 56 HOH HOH . 
D 3 HOH A 54 154 58 HOH HOH . 
D 3 HOH A 55 155 59 HOH HOH . 
D 3 HOH A 56 156 60 HOH HOH . 
D 3 HOH A 57 157 61 HOH HOH . 
D 3 HOH A 58 158 62 HOH HOH . 
D 3 HOH A 59 159 63 HOH HOH . 
D 3 HOH A 60 160 64 HOH HOH . 
D 3 HOH A 61 161 65 HOH HOH . 
D 3 HOH A 62 162 66 HOH HOH . 
D 3 HOH A 63 163 67 HOH HOH . 
D 3 HOH A 64 164 68 HOH HOH . 
D 3 HOH A 65 165 70 HOH HOH . 
D 3 HOH A 66 166 71 HOH HOH . 
D 3 HOH A 67 167 72 HOH HOH . 
D 3 HOH A 68 168 74 HOH HOH . 
D 3 HOH A 69 169 75 HOH HOH . 
D 3 HOH A 70 170 77 HOH HOH . 
D 3 HOH A 71 171 78 HOH HOH . 
D 3 HOH A 72 172 79 HOH HOH . 
D 3 HOH A 73 173 80 HOH HOH . 
D 3 HOH A 74 174 81 HOH HOH . 
D 3 HOH A 75 175 82 HOH HOH . 
D 3 HOH A 76 176 83 HOH HOH . 
D 3 HOH A 77 177 84 HOH HOH . 
D 3 HOH A 78 178 85 HOH HOH . 
D 3 HOH A 79 179 86 HOH HOH . 
D 3 HOH A 80 180 87 HOH HOH . 
D 3 HOH A 81 181 88 HOH HOH . 
D 3 HOH A 82 182 89 HOH HOH . 
D 3 HOH A 83 183 90 HOH HOH . 
D 3 HOH A 84 184 91 HOH HOH . 
D 3 HOH A 85 185 92 HOH HOH . 
D 3 HOH A 86 186 93 HOH HOH . 
D 3 HOH A 87 187 94 HOH HOH . 
D 3 HOH A 88 188 95 HOH HOH . 
D 3 HOH A 89 189 96 HOH HOH . 
D 3 HOH A 90 190 97 HOH HOH . 
D 3 HOH A 91 191 98 HOH HOH . 
D 3 HOH A 92 192 99 HOH HOH . 
D 3 HOH A 93 193 100 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               -23.901 
_atom_site.Cartn_y               -1.979 
_atom_site.Cartn_z               -13.883 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        23.1 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           99 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#