data_1KD4
#
_model_server_result.job_id            V7Pn8X8XQ_ppH87JWtIUKw 
_model_server_result.datetime_utc      '2024-10-18 14:29:19' 
_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          1kd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    1KD4 
#
_exptl.entry_id    1KD4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              137.327 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'BARIUM 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            1KD4 
_cell.length_a            39.99 
_cell.length_b            39.99 
_cell.length_c            52.62 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KD4 
_symmetry.cell_setting             tetragonal 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 C N N 
? 2 D 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 O6 G 2 A G 2 1_555 C BA BA . A BA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? 
metalc ? metalc2 A O4 U 3 A U 3 1_555 C BA BA . A BA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc3 A O6 G 8 A G 8 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? 
metalc ? metalc4 E O HOH . A HOH 70 1_555 C BA BA . A BA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc5 E O HOH . A HOH 73 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? 
metalc ? metalc6 E O HOH . A HOH 81 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? 
metalc ? metalc7 E O HOH . A HOH 147 1_555 C BA BA . A BA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? 
metalc ? metalc8 E O HOH . A HOH 174 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc9 E O HOH . A HOH 175 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
metalc ? metalc10 C BA BA . A BA 502 1_555 B O6 G 8 B G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc11 C BA BA . A BA 502 1_555 F O HOH . B HOH 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
metalc ? metalc12 C BA BA . A BA 502 1_555 F O HOH . B HOH 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
metalc ? metalc13 C BA BA . A BA 502 1_555 F O HOH . B HOH 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? 
metalc ? metalc14 C BA BA . A BA 502 1_555 F O HOH . B HOH 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc15 B O6 G 2 B G 2 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? 
metalc ? metalc16 B O4 U 3 B U 3 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc17 F O HOH . B HOH 84 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc18 F O HOH . B HOH 134 1_555 D BA BA . B BA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 1 1_555 B N3 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 1 1_555 B O2 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 1 1_555 B N4 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 2 1_555 B N3 C 9 B C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 2 1_555 B O2 C 9 B C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 2 1_555 B N4 C 9 B C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog7 A N3 U 3 A U 3 1_555 B O6 G 8 B G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog8 A O2 U 3 A U 3 1_555 B N1 G 8 B G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-A MISPAIR' hydrog9 A O2 C 4 A C 4 1_555 B N6 A 7 B A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_25_PAIR hydrog10 A N6 A 5 A A 5 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_25_PAIR hydrog11 A N7 A 5 A A 5 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_25_PAIR hydrog12 A N3 C 6 A C 6 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_25_PAIR hydrog13 A N4 C 6 A C 6 1_555 B N7 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'A-C MISPAIR' hydrog14 A N6 A 7 A A 7 1_555 B O2 C 4 B C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog15 A N1 G 8 A G 8 1_555 B O2 U 3 B U 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog TYPE_28_PAIR hydrog16 A O6 G 8 A G 8 1_555 B N3 U 3 B U 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N3 C 9 A C 9 1_555 B N1 G 2 B G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A N4 C 9 A C 9 1_555 B O6 G 2 B G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A O2 C 9 A C 9 1_555 B N2 G 2 B G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A N3 C 10 A C 10 1_555 B N1 G 1 B G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N4 C 10 A C 10 1_555 B O6 G 1 B G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A O2 C 10 A C 10 1_555 B N2 G 1 B G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'Ba 2' 
_chem_comp.formula_weight    137.327 
_chem_comp.id                BA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'BARIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     1KD4 
_atom_sites.fract_transf_matrix[1][1]    0.025006 
_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]    0.025006 
_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]    0.019004 
_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 BA A 1 502 502 BA BA . 
D 2 BA B 1 501 501 BA BA . 
E 3 HOH A 1 70 70 HOH HOH . 
E 3 HOH A 2 73 73 HOH HOH . 
E 3 HOH A 3 74 74 HOH HOH . 
E 3 HOH A 4 76 76 HOH HOH . 
E 3 HOH A 5 77 77 HOH HOH . 
E 3 HOH A 6 78 78 HOH HOH . 
E 3 HOH A 7 81 81 HOH HOH . 
E 3 HOH A 8 85 85 HOH HOH . 
E 3 HOH A 9 87 87 HOH HOH . 
E 3 HOH A 10 90 90 HOH HOH . 
E 3 HOH A 11 94 94 HOH HOH . 
E 3 HOH A 12 97 97 HOH HOH . 
E 3 HOH A 13 98 98 HOH HOH . 
E 3 HOH A 14 102 102 HOH HOH . 
E 3 HOH A 15 107 107 HOH HOH . 
E 3 HOH A 16 114 114 HOH HOH . 
E 3 HOH A 17 122 122 HOH HOH . 
E 3 HOH A 18 128 128 HOH HOH . 
E 3 HOH A 19 138 138 HOH HOH . 
E 3 HOH A 20 139 139 HOH HOH . 
E 3 HOH A 21 142 142 HOH HOH . 
E 3 HOH A 22 147 147 HOH HOH . 
E 3 HOH A 23 156 156 HOH HOH . 
E 3 HOH A 24 158 158 HOH HOH . 
E 3 HOH A 25 162 162 HOH HOH . 
E 3 HOH A 26 163 163 HOH HOH . 
E 3 HOH A 27 166 166 HOH HOH . 
E 3 HOH A 28 168 168 HOH HOH . 
E 3 HOH A 29 170 170 HOH HOH . 
E 3 HOH A 30 174 174 HOH HOH . 
E 3 HOH A 31 175 175 HOH HOH . 
F 3 HOH B 1 71 71 HOH HOH . 
F 3 HOH B 2 72 72 HOH HOH . 
F 3 HOH B 3 75 75 HOH HOH . 
F 3 HOH B 4 79 79 HOH HOH . 
F 3 HOH B 5 80 80 HOH HOH . 
F 3 HOH B 6 82 82 HOH HOH . 
F 3 HOH B 7 83 83 HOH HOH . 
F 3 HOH B 8 84 84 HOH HOH . 
F 3 HOH B 9 86 86 HOH HOH . 
F 3 HOH B 10 88 88 HOH HOH . 
F 3 HOH B 11 91 91 HOH HOH . 
F 3 HOH B 12 92 92 HOH HOH . 
F 3 HOH B 13 93 93 HOH HOH . 
F 3 HOH B 14 95 95 HOH HOH . 
F 3 HOH B 15 96 96 HOH HOH . 
F 3 HOH B 16 99 99 HOH HOH . 
F 3 HOH B 17 103 103 HOH HOH . 
F 3 HOH B 18 106 106 HOH HOH . 
F 3 HOH B 19 127 127 HOH HOH . 
F 3 HOH B 20 134 134 HOH HOH . 
F 3 HOH B 21 135 135 HOH HOH . 
F 3 HOH B 22 137 137 HOH HOH . 
F 3 HOH B 23 141 141 HOH HOH . 
F 3 HOH B 24 143 143 HOH HOH . 
F 3 HOH B 25 144 144 HOH HOH . 
F 3 HOH B 26 146 146 HOH HOH . 
F 3 HOH B 27 148 148 HOH HOH . 
F 3 HOH B 28 153 153 HOH HOH . 
F 3 HOH B 29 155 155 HOH HOH . 
F 3 HOH B 30 160 160 HOH HOH . 
F 3 HOH B 31 161 161 HOH HOH . 
F 3 HOH B 32 164 164 HOH HOH . 
F 3 HOH B 33 165 165 HOH HOH . 
F 3 HOH B 34 167 167 HOH HOH . 
F 3 HOH B 35 169 169 HOH HOH . 
F 3 HOH B 36 171 171 HOH HOH . 
F 3 HOH B 37 172 172 HOH HOH . 
F 3 HOH B 38 173 173 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           BA 
_atom_site.label_atom_id         BA 
_atom_site.label_comp_id         BA 
_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       2 
_atom_site.Cartn_x               12.129 
_atom_site.Cartn_y               16.03 
_atom_site.Cartn_z               85.684 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        26.91 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          BA 
_atom_site.auth_comp_id          BA 
_atom_site.auth_seq_id           501 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#