data_1JTK
#
_model_server_result.job_id            366KXnOZ6q2HaPLO2jebUQ 
_model_server_result.datetime_utc      '2025-02-18 09:08:23' 
_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          1jtk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1138}' 
#
_entry.id    1JTK 
#
_exptl.entry_id    1JTK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              230.218 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            TETRAHYDRODEOXYURIDINE 
_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          115.92 
_cell.angle_gamma         90 
_cell.entry_id            1JTK 
_cell.length_a            75.086 
_cell.length_b            66.142 
_cell.length_c            55.476 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JTK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_657 -x+1,y,-z+2 -1 0 0 0 1 0 0 0 -1 26.587131 0 99.790811 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 SG CYS 53 A CYS 53 1_555 C ZN ZN . A ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc2 A SG CYS 86 A CYS 86 1_555 C ZN ZN . A ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc3 A SG CYS 89 A CYS 89 1_555 C ZN ZN . A ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc4 C ZN ZN . A ZN 137 1_555 D O4 THU . A THU 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc5 B SG CYS 53 B CYS 53 1_555 E ZN ZN . B ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc6 B SG CYS 86 B CYS 86 1_555 E ZN ZN . B ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc7 B SG CYS 89 B CYS 89 1_555 E ZN ZN . B ZN 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc8 E ZN ZN . B ZN 137 1_555 F O4 THU . B THU 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
#
_chem_comp.formula           'C9 H14 N2 O5' 
_chem_comp.formula_weight    230.218 
_chem_comp.id                THU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              TETRAHYDRODEOXYURIDINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N1 C2 THU sing 306 n n 
N1 C6 THU sing 307 n n 
N1 C1' THU sing 308 n n 
C2 O2 THU doub 309 n n 
C2 N3 THU sing 310 n n 
N3 C4 THU sing 311 n n 
N3 HN3 THU sing 312 n n 
C4 O4 THU doub 313 n n 
C4 C5 THU sing 314 n n 
C5 C6 THU sing 315 n n 
C5 H51 THU sing 316 n n 
C5 H52 THU sing 317 n n 
C6 H61 THU sing 318 n n 
C6 H62 THU sing 319 n n 
C1' C2' THU sing 320 n n 
C1' O4' THU sing 321 n n 
C1' H1' THU sing 322 n n 
C2' C3' THU sing 323 n n 
C2' "H2'1" THU sing 324 n n 
C2' "H2'2" THU sing 325 n n 
C3' O3' THU sing 326 n n 
C3' C4' THU sing 327 n n 
C3' H3' THU sing 328 n n 
O3' HO3' THU sing 329 n n 
C4' O4' THU sing 330 n n 
C4' C5' THU sing 331 n n 
C4' H4' THU sing 332 n n 
C5' O5' THU sing 333 n n 
C5' "H5'1" THU sing 334 n n 
C5' "H5'2" THU sing 335 n n 
O5' HO5' THU sing 336 n n 
#
_atom_sites.entry_id                     1JTK 
_atom_sites.fract_transf_matrix[1][1]    0.013318 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.006472 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015119 
_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]    0.020042 
_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 ZN A 1 137 137 ZN ZN . 
D 3 THU A 1 138 138 THU THU . 
E 2 ZN B 1 137 137 ZN ZN . 
F 3 THU B 1 1138 138 THU THU . 
G 4 HOH A 1 139 139 HOH HOH . 
G 4 HOH A 2 140 140 HOH HOH . 
G 4 HOH A 3 141 141 HOH HOH . 
G 4 HOH A 4 142 142 HOH HOH . 
G 4 HOH A 5 143 143 HOH HOH . 
G 4 HOH A 6 144 144 HOH HOH . 
G 4 HOH A 7 145 145 HOH HOH . 
G 4 HOH A 8 146 146 HOH HOH . 
G 4 HOH A 9 147 147 HOH HOH . 
G 4 HOH A 10 148 148 HOH HOH . 
G 4 HOH A 11 149 149 HOH HOH . 
G 4 HOH A 12 150 150 HOH HOH . 
G 4 HOH A 13 151 151 HOH HOH . 
G 4 HOH A 14 152 152 HOH HOH . 
G 4 HOH A 15 153 153 HOH HOH . 
G 4 HOH A 16 154 154 HOH HOH . 
G 4 HOH A 17 155 155 HOH HOH . 
G 4 HOH A 18 156 156 HOH HOH . 
G 4 HOH A 19 157 157 HOH HOH . 
G 4 HOH A 20 158 158 HOH HOH . 
G 4 HOH A 21 159 159 HOH HOH . 
G 4 HOH A 22 160 160 HOH HOH . 
G 4 HOH A 23 161 161 HOH HOH . 
G 4 HOH A 24 162 162 HOH HOH . 
G 4 HOH A 25 163 163 HOH HOH . 
G 4 HOH A 26 164 164 HOH HOH . 
G 4 HOH A 27 165 165 HOH HOH . 
G 4 HOH A 28 166 166 HOH HOH . 
G 4 HOH A 29 167 167 HOH HOH . 
G 4 HOH A 30 168 168 HOH HOH . 
G 4 HOH A 31 169 169 HOH HOH . 
G 4 HOH A 32 170 170 HOH HOH . 
G 4 HOH A 33 171 171 HOH HOH . 
G 4 HOH A 34 172 172 HOH HOH . 
G 4 HOH A 35 173 173 HOH HOH . 
G 4 HOH A 36 174 174 HOH HOH . 
G 4 HOH A 37 175 175 HOH HOH . 
G 4 HOH A 38 176 176 HOH HOH . 
G 4 HOH A 39 177 177 HOH HOH . 
G 4 HOH A 40 178 178 HOH HOH . 
G 4 HOH A 41 179 179 HOH HOH . 
G 4 HOH A 42 180 180 HOH HOH . 
G 4 HOH A 43 181 181 HOH HOH . 
G 4 HOH A 44 182 182 HOH HOH . 
G 4 HOH A 45 183 183 HOH HOH . 
G 4 HOH A 46 184 184 HOH HOH . 
G 4 HOH A 47 185 185 HOH HOH . 
G 4 HOH A 48 186 186 HOH HOH . 
G 4 HOH A 49 187 187 HOH HOH . 
G 4 HOH A 50 188 188 HOH HOH . 
G 4 HOH A 51 189 189 HOH HOH . 
G 4 HOH A 52 190 190 HOH HOH . 
G 4 HOH A 53 2003 3 HOH HOH . 
G 4 HOH A 54 2054 54 HOH HOH . 
G 4 HOH A 55 2063 63 HOH HOH . 
G 4 HOH A 56 2075 75 HOH HOH . 
G 4 HOH A 57 2087 87 HOH HOH . 
G 4 HOH A 58 2089 89 HOH HOH . 
G 4 HOH A 59 2094 94 HOH HOH . 
G 4 HOH A 60 2097 97 HOH HOH . 
G 4 HOH A 61 2109 109 HOH HOH . 
G 4 HOH A 62 2110 110 HOH HOH . 
G 4 HOH A 63 2115 115 HOH HOH . 
G 4 HOH A 64 2116 116 HOH HOH . 
G 4 HOH A 65 2122 122 HOH HOH . 
G 4 HOH A 66 2123 123 HOH HOH . 
G 4 HOH A 67 2125 125 HOH HOH . 
G 4 HOH A 68 2129 129 HOH HOH . 
G 4 HOH A 69 2131 131 HOH HOH . 
G 4 HOH A 70 2140 140 HOH HOH . 
G 4 HOH A 71 2141 141 HOH HOH . 
G 4 HOH A 72 2147 147 HOH HOH . 
G 4 HOH A 73 2149 149 HOH HOH . 
G 4 HOH A 74 2150 150 HOH HOH . 
G 4 HOH A 75 2153 153 HOH HOH . 
G 4 HOH A 76 2154 154 HOH HOH . 
G 4 HOH A 77 2157 157 HOH HOH . 
G 4 HOH A 78 2159 159 HOH HOH . 
G 4 HOH A 79 2163 163 HOH HOH . 
G 4 HOH A 80 2164 164 HOH HOH . 
G 4 HOH A 81 2166 166 HOH HOH . 
G 4 HOH A 82 2167 167 HOH HOH . 
G 4 HOH A 83 2170 170 HOH HOH . 
G 4 HOH A 84 2171 171 HOH HOH . 
G 4 HOH A 85 2174 174 HOH HOH . 
G 4 HOH A 86 2177 177 HOH HOH . 
G 4 HOH A 87 2179 179 HOH HOH . 
G 4 HOH A 88 2180 180 HOH HOH . 
G 4 HOH A 89 2181 181 HOH HOH . 
G 4 HOH A 90 2182 182 HOH HOH . 
H 4 HOH B 1 1139 139 HOH HOH . 
H 4 HOH B 2 1140 140 HOH HOH . 
H 4 HOH B 3 1141 141 HOH HOH . 
H 4 HOH B 4 1142 142 HOH HOH . 
H 4 HOH B 5 1143 143 HOH HOH . 
H 4 HOH B 6 1144 144 HOH HOH . 
H 4 HOH B 7 1145 145 HOH HOH . 
H 4 HOH B 8 1146 146 HOH HOH . 
H 4 HOH B 9 1147 147 HOH HOH . 
H 4 HOH B 10 1148 148 HOH HOH . 
H 4 HOH B 11 1149 149 HOH HOH . 
H 4 HOH B 12 1150 150 HOH HOH . 
H 4 HOH B 13 1151 151 HOH HOH . 
H 4 HOH B 14 1152 152 HOH HOH . 
H 4 HOH B 15 1153 153 HOH HOH . 
H 4 HOH B 16 1154 154 HOH HOH . 
H 4 HOH B 17 1155 155 HOH HOH . 
H 4 HOH B 18 1156 156 HOH HOH . 
H 4 HOH B 19 1157 157 HOH HOH . 
H 4 HOH B 20 1158 158 HOH HOH . 
H 4 HOH B 21 1159 159 HOH HOH . 
H 4 HOH B 22 1160 160 HOH HOH . 
H 4 HOH B 23 1161 161 HOH HOH . 
H 4 HOH B 24 1162 162 HOH HOH . 
H 4 HOH B 25 1163 163 HOH HOH . 
H 4 HOH B 26 1164 164 HOH HOH . 
H 4 HOH B 27 1165 165 HOH HOH . 
H 4 HOH B 28 1166 166 HOH HOH . 
H 4 HOH B 29 1167 167 HOH HOH . 
H 4 HOH B 30 1168 168 HOH HOH . 
H 4 HOH B 31 1169 169 HOH HOH . 
H 4 HOH B 32 1170 170 HOH HOH . 
H 4 HOH B 33 1171 171 HOH HOH . 
H 4 HOH B 34 1172 172 HOH HOH . 
H 4 HOH B 35 1173 173 HOH HOH . 
H 4 HOH B 36 1174 174 HOH HOH . 
H 4 HOH B 37 1175 175 HOH HOH . 
H 4 HOH B 38 1176 176 HOH HOH . 
H 4 HOH B 39 1177 177 HOH HOH . 
H 4 HOH B 40 1178 178 HOH HOH . 
H 4 HOH B 41 1179 179 HOH HOH . 
H 4 HOH B 42 1180 180 HOH HOH . 
H 4 HOH B 43 1181 181 HOH HOH . 
H 4 HOH B 44 1182 182 HOH HOH . 
H 4 HOH B 45 1183 183 HOH HOH . 
H 4 HOH B 46 1184 184 HOH HOH . 
H 4 HOH B 47 1185 185 HOH HOH . 
H 4 HOH B 48 1186 186 HOH HOH . 
H 4 HOH B 49 1187 187 HOH HOH . 
H 4 HOH B 50 1188 188 HOH HOH . 
H 4 HOH B 51 1189 189 HOH HOH . 
H 4 HOH B 52 1190 190 HOH HOH . 
H 4 HOH B 53 2015 15 HOH HOH . 
H 4 HOH B 54 2024 24 HOH HOH . 
H 4 HOH B 55 2050 50 HOH HOH . 
H 4 HOH B 56 2058 58 HOH HOH . 
H 4 HOH B 57 2068 68 HOH HOH . 
H 4 HOH B 58 2069 69 HOH HOH . 
H 4 HOH B 59 2070 70 HOH HOH . 
H 4 HOH B 60 2079 79 HOH HOH . 
H 4 HOH B 61 2080 80 HOH HOH . 
H 4 HOH B 62 2082 82 HOH HOH . 
H 4 HOH B 63 2088 88 HOH HOH . 
H 4 HOH B 64 2091 91 HOH HOH . 
H 4 HOH B 65 2092 92 HOH HOH . 
H 4 HOH B 66 2093 93 HOH HOH . 
H 4 HOH B 67 2095 95 HOH HOH . 
H 4 HOH B 68 2096 96 HOH HOH . 
H 4 HOH B 69 2101 101 HOH HOH . 
H 4 HOH B 70 2105 105 HOH HOH . 
H 4 HOH B 71 2106 106 HOH HOH . 
H 4 HOH B 72 2107 107 HOH HOH . 
H 4 HOH B 73 2113 113 HOH HOH . 
H 4 HOH B 74 2119 119 HOH HOH . 
H 4 HOH B 75 2124 124 HOH HOH . 
H 4 HOH B 76 2128 128 HOH HOH . 
H 4 HOH B 77 2134 134 HOH HOH . 
H 4 HOH B 78 2135 135 HOH HOH . 
H 4 HOH B 79 2138 138 HOH HOH . 
H 4 HOH B 80 2142 142 HOH HOH . 
H 4 HOH B 81 2152 152 HOH HOH . 
H 4 HOH B 82 2155 155 HOH HOH . 
H 4 HOH B 83 2156 156 HOH HOH . 
H 4 HOH B 84 2158 158 HOH HOH . 
H 4 HOH B 85 2160 160 HOH HOH . 
H 4 HOH B 86 2161 161 HOH HOH . 
H 4 HOH B 87 2162 162 HOH HOH . 
H 4 HOH B 88 2165 165 HOH HOH . 
H 4 HOH B 89 2172 172 HOH HOH . 
H 4 HOH B 90 2175 175 HOH HOH . 
H 4 HOH B 91 2176 176 HOH HOH . 
H 4 HOH B 92 2178 178 HOH HOH . 
H 4 HOH B 93 2183 183 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N1 THU . . . F 3 22.385 52.625 56.984 1 8.05 ? N1 THU 1138 B 1 
HETATM 2 C C2 THU . . . F 3 21.682 51.468 57.072 1 7.65 ? C2 THU 1138 B 1 
HETATM 3 O O2 THU . . . F 3 21.751 50.607 56.208 1 7.06 ? O2 THU 1138 B 1 
HETATM 4 N N3 THU . . . F 3 20.899 51.278 58.164 1 8.01 ? N3 THU 1138 B 1 
HETATM 5 C C4 THU . . . F 3 20.786 52.271 59.229 1 7.01 ? C4 THU 1138 B 1 
HETATM 6 O O4 THU . . . F 3 19.473 52.784 59.39 1 7.09 ? O4 THU 1138 B 1 
HETATM 7 C C5 THU . . . F 3 21.718 53.504 59.106 1 7.17 ? C5 THU 1138 B 1 
HETATM 8 C C6 THU . . . F 3 21.975 53.802 57.62 1 6.99 ? C6 THU 1138 B 1 
HETATM 9 C C1' THU . . . F 3 22.789 53.098 55.47 1 7.64 ? C1' THU 1138 B 1 
HETATM 10 C C2' THU . . . F 3 22.241 53.401 54.115 1 8.14 ? C2' THU 1138 B 1 
HETATM 11 C C3' THU . . . F 3 23.478 53.839 53.433 1 7.55 ? C3' THU 1138 B 1 
HETATM 12 O O3' THU . . . F 3 23.808 52.985 52.381 1 7.98 ? O3' THU 1138 B 1 
HETATM 13 C C4' THU . . . F 3 24.62 53.897 54.464 1 7.56 ? C4' THU 1138 B 1 
HETATM 14 O O4' THU . . . F 3 24.191 53.285 55.674 1 7.52 ? O4' THU 1138 B 1 
HETATM 15 C C5' THU . . . F 3 25.184 55.276 54.681 1 7.03 ? C5' THU 1138 B 1 
HETATM 16 O O5' THU . . . F 3 24.13 56.083 55.222 1 6.99 ? O5' THU 1138 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           16 
#