data_3SK5
#
_model_server_result.job_id            iqeiiaZCv3HTXqhODRGCKg 
_model_server_result.datetime_utc      '2024-10-11 10:25:10' 
_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          3sk5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":150}' 
#
_entry.id    3SK5 
#
_exptl.entry_id    3SK5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-3',5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          92.92 
_cell.angle_gamma         90 
_cell.entry_id            3SK5 
_cell.length_a            31.11 
_cell.length_b            60.666 
_cell.length_c            38.269 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3SK5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 21 A ASP 21 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? 
metalc ? metalc5 B O5P THP . A THP 150 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? 
metalc ? metalc6 C CA CA . A CA 151 1_555 D O HOH . A HOH 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? 
metalc ? metalc7 C CA CA . A CA 151 1_555 D O HOH . A HOH 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? 
metalc ? metalc8 C CA CA . A CA 151 1_555 D O HOH . A HOH 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                THP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-3',5'-DIPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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
P2 O4P THP doub 277 n n 
P2 O5P THP sing 278 n n 
P2 O6P THP sing 279 n n 
P2 O5' THP sing 280 n n 
O5P HOP5 THP sing 281 n n 
O6P HOP6 THP sing 282 n n 
P1 O1P THP doub 283 n n 
P1 O2P THP sing 284 n n 
P1 O3P THP sing 285 n n 
P1 O3' THP sing 286 n n 
O2P HOP2 THP sing 287 n n 
O3P HOP3 THP sing 288 n n 
O5' C5' THP sing 289 n n 
C5' C4' THP sing 290 n n 
C5' "H5'1" THP sing 291 n n 
C5' "H5'2" THP sing 292 n n 
C4' O4' THP sing 293 n n 
C4' C3' THP sing 294 n n 
C4' H4' THP sing 295 n n 
O4' C1' THP sing 296 n n 
C3' O3' THP sing 297 n n 
C3' C2' THP sing 298 n n 
C3' H3' THP sing 299 n n 
C2' C1' THP sing 300 n n 
C2' "H2'1" THP sing 301 n n 
C2' "H2'2" THP sing 302 n n 
C1' N1 THP sing 303 n n 
C1' H1' THP sing 304 n n 
N1 C2 THP sing 305 n n 
N1 C6 THP sing 306 n n 
C2 O2 THP doub 307 n n 
C2 N3 THP sing 308 n n 
N3 C4 THP sing 309 n n 
N3 H3 THP sing 310 n n 
C4 O4 THP doub 311 n n 
C4 C5 THP sing 312 n n 
C5 C5M THP sing 313 n n 
C5 C6 THP doub 314 n n 
C5M H51 THP sing 315 n n 
C5M H52 THP sing 316 n n 
C5M H53 THP sing 317 n n 
C6 H6 THP sing 318 n n 
#
_atom_sites.entry_id                     3SK5 
_atom_sites.fract_transf_matrix[1][1]    0.032144 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00164 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016484 
_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]    0.026165 
_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 THP A 1 150 150 THP THP . 
C 3 CA A 1 151 151 CA CA . 
D 4 HOH A 1 152 152 HOH HOH . 
D 4 HOH A 2 153 153 HOH HOH . 
D 4 HOH A 3 155 155 HOH HOH . 
D 4 HOH A 4 156 156 HOH HOH . 
D 4 HOH A 5 157 157 HOH HOH . 
D 4 HOH A 6 158 158 HOH HOH . 
D 4 HOH A 7 159 159 HOH HOH . 
D 4 HOH A 8 160 160 HOH HOH . 
D 4 HOH A 9 161 161 HOH HOH . 
D 4 HOH A 10 162 162 HOH HOH . 
D 4 HOH A 11 163 163 HOH HOH . 
D 4 HOH A 12 164 164 HOH HOH . 
D 4 HOH A 13 165 165 HOH HOH . 
D 4 HOH A 14 166 166 HOH HOH . 
D 4 HOH A 15 167 167 HOH HOH . 
D 4 HOH A 16 168 168 HOH HOH . 
D 4 HOH A 17 169 169 HOH HOH . 
D 4 HOH A 18 170 170 HOH HOH . 
D 4 HOH A 19 171 171 HOH HOH . 
D 4 HOH A 20 172 172 HOH HOH . 
D 4 HOH A 21 173 173 HOH HOH . 
D 4 HOH A 22 174 174 HOH HOH . 
D 4 HOH A 23 175 175 HOH HOH . 
D 4 HOH A 24 176 176 HOH HOH . 
D 4 HOH A 25 177 177 HOH HOH . 
D 4 HOH A 26 178 178 HOH HOH . 
D 4 HOH A 27 179 179 HOH HOH . 
D 4 HOH A 28 180 180 HOH HOH . 
D 4 HOH A 29 181 181 HOH HOH . 
D 4 HOH A 30 182 182 HOH HOH . 
D 4 HOH A 31 183 183 HOH HOH . 
D 4 HOH A 32 184 184 HOH HOH . 
D 4 HOH A 33 185 185 HOH HOH . 
D 4 HOH A 34 186 186 HOH HOH . 
D 4 HOH A 35 187 187 HOH HOH . 
D 4 HOH A 36 188 188 HOH HOH . 
D 4 HOH A 37 189 189 HOH HOH . 
D 4 HOH A 38 190 190 HOH HOH . 
D 4 HOH A 39 191 191 HOH HOH . 
D 4 HOH A 40 192 192 HOH HOH . 
D 4 HOH A 41 193 193 HOH HOH . 
D 4 HOH A 42 194 194 HOH HOH . 
D 4 HOH A 43 195 195 HOH HOH . 
D 4 HOH A 44 196 196 HOH HOH . 
D 4 HOH A 45 197 197 HOH HOH . 
D 4 HOH A 46 198 198 HOH HOH . 
D 4 HOH A 47 199 199 HOH HOH . 
D 4 HOH A 48 200 200 HOH HOH . 
D 4 HOH A 49 201 201 HOH HOH . 
D 4 HOH A 50 202 202 HOH HOH . 
D 4 HOH A 51 203 203 HOH HOH . 
D 4 HOH A 52 204 204 HOH HOH . 
D 4 HOH A 53 205 205 HOH HOH . 
D 4 HOH A 54 206 206 HOH HOH . 
D 4 HOH A 55 207 207 HOH HOH . 
D 4 HOH A 56 208 208 HOH HOH . 
D 4 HOH A 57 209 209 HOH HOH . 
D 4 HOH A 58 210 210 HOH HOH . 
D 4 HOH A 59 211 211 HOH HOH . 
D 4 HOH A 60 212 212 HOH HOH . 
D 4 HOH A 61 213 213 HOH HOH . 
D 4 HOH A 62 214 214 HOH HOH . 
D 4 HOH A 63 215 215 HOH HOH . 
D 4 HOH A 64 216 216 HOH HOH . 
D 4 HOH A 65 217 217 HOH HOH . 
D 4 HOH A 66 218 218 HOH HOH . 
D 4 HOH A 67 219 219 HOH HOH . 
D 4 HOH A 68 220 220 HOH HOH . 
D 4 HOH A 69 221 221 HOH HOH . 
D 4 HOH A 70 222 222 HOH HOH . 
D 4 HOH A 71 223 223 HOH HOH . 
D 4 HOH A 72 224 224 HOH HOH . 
D 4 HOH A 73 225 225 HOH HOH . 
D 4 HOH A 74 226 226 HOH HOH . 
D 4 HOH A 75 227 227 HOH HOH . 
D 4 HOH A 76 228 228 HOH HOH . 
D 4 HOH A 77 229 229 HOH HOH . 
D 4 HOH A 78 230 230 HOH HOH . 
D 4 HOH A 79 231 231 HOH HOH . 
D 4 HOH A 80 232 232 HOH HOH . 
D 4 HOH A 81 233 233 HOH HOH . 
D 4 HOH A 82 234 234 HOH HOH . 
D 4 HOH A 83 235 235 HOH HOH . 
D 4 HOH A 84 236 236 HOH HOH . 
D 4 HOH A 85 237 237 HOH HOH . 
D 4 HOH A 86 238 238 HOH HOH . 
D 4 HOH A 87 239 239 HOH HOH . 
D 4 HOH A 88 240 240 HOH HOH . 
D 4 HOH A 89 241 241 HOH HOH . 
D 4 HOH A 90 242 242 HOH HOH . 
D 4 HOH A 91 243 243 HOH HOH . 
D 4 HOH A 92 244 244 HOH HOH . 
D 4 HOH A 93 245 245 HOH HOH . 
D 4 HOH A 94 246 246 HOH HOH . 
D 4 HOH A 95 247 247 HOH HOH . 
D 4 HOH A 96 248 248 HOH HOH . 
D 4 HOH A 97 249 249 HOH HOH . 
D 4 HOH A 98 250 250 HOH HOH . 
D 4 HOH A 99 251 251 HOH HOH . 
D 4 HOH A 100 252 252 HOH HOH . 
D 4 HOH A 101 253 253 HOH HOH . 
D 4 HOH A 102 254 254 HOH HOH . 
D 4 HOH A 103 255 255 HOH HOH . 
D 4 HOH A 104 256 256 HOH HOH . 
D 4 HOH A 105 257 257 HOH HOH . 
D 4 HOH A 106 258 258 HOH HOH . 
D 4 HOH A 107 259 259 HOH HOH . 
D 4 HOH A 108 260 260 HOH HOH . 
D 4 HOH A 109 261 261 HOH HOH . 
D 4 HOH A 110 262 262 HOH HOH . 
D 4 HOH A 111 263 263 HOH HOH . 
D 4 HOH A 112 264 264 HOH HOH . 
D 4 HOH A 113 265 265 HOH HOH . 
D 4 HOH A 114 266 266 HOH HOH . 
D 4 HOH A 115 268 268 HOH HOH . 
D 4 HOH A 116 270 270 HOH HOH . 
D 4 HOH A 117 277 277 HOH HOH . 
D 4 HOH A 118 278 278 HOH HOH . 
D 4 HOH A 119 280 280 HOH HOH . 
D 4 HOH A 120 281 281 HOH HOH . 
D 4 HOH A 121 282 282 HOH HOH . 
D 4 HOH A 122 283 283 HOH HOH . 
D 4 HOH A 123 284 284 HOH HOH . 
D 4 HOH A 124 285 285 HOH HOH . 
D 4 HOH A 125 286 286 HOH HOH . 
D 4 HOH A 126 287 287 HOH HOH . 
D 4 HOH A 127 288 288 HOH HOH . 
D 4 HOH A 128 289 289 HOH HOH . 
D 4 HOH A 129 291 291 HOH HOH . 
D 4 HOH A 130 292 292 HOH HOH . 
D 4 HOH A 131 295 295 HOH HOH . 
D 4 HOH A 132 298 298 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 P P2 THP . . . B 2 17.914 8.465 4.736 1 10.3 ? P2 THP 150 A 1 
HETATM 2 O O4P THP . . . B 2 17.939 7.001 5.047 1 11.05 ? O4P THP 150 A 1 
HETATM 3 O O5P THP . . . B 2 16.636 9.215 5.273 1 10.39 ? O5P THP 150 A 1 
HETATM 4 O O6P THP . . . B 2 19.179 9.19 5.31 1 13.42 ? O6P THP 150 A 1 
HETATM 5 P P1 THP . . . B 2 21.244 11.908 0.924 1 12.42 ? P1 THP 150 A 1 
HETATM 6 O O1P THP . . . B 2 22.222 12.532 -0.043 1 14.41 ? O1P THP 150 A 1 
HETATM 7 O O2P THP . . . B 2 21.962 10.739 1.698 1 14.1 ? O2P THP 150 A 1 
HETATM 8 O O3P THP . . . B 2 20.588 12.909 1.904 1 12.94 ? O3P THP 150 A 1 
HETATM 9 O O5' THP . . . B 2 17.873 8.492 3.189 1 9.25 ? O5' THP 150 A 1 
HETATM 10 C C5' THP . . . B 2 17.966 9.806 2.521 1 12.36 ? C5' THP 150 A 1 
HETATM 11 C C4' THP . . . B 2 18.885 9.675 1.315 1 10.33 ? C4' THP 150 A 1 
HETATM 12 O O4' THP . . . B 2 18.605 8.552 0.44 1 11.22 ? O4' THP 150 A 1 
HETATM 13 C C3' THP . . . B 2 18.885 10.955 0.386 1 10.09 ? C3' THP 150 A 1 
HETATM 14 O O3' THP . . . B 2 20.237 11.231 -0.118 1 10.42 ? O3' THP 150 A 1 
HETATM 15 C C2' THP . . . B 2 18.025 10.448 -0.8 1 10.37 ? C2' THP 150 A 1 
HETATM 16 C C1' THP . . . B 2 18.224 8.898 -0.868 1 10.76 ? C1' THP 150 A 1 
HETATM 17 N N1 THP . . . B 2 16.915 8.263 -1.21 1 9.59 ? N1 THP 150 A 1 
HETATM 18 C C2 THP . . . B 2 16.607 8.063 -2.519 1 11.71 ? C2 THP 150 A 1 
HETATM 19 O O2 THP . . . B 2 17.436 8.406 -3.396 1 14.45 ? O2 THP 150 A 1 
HETATM 20 N N3 THP . . . B 2 15.41 7.532 -2.92 1 8.57 ? N3 THP 150 A 1 
HETATM 21 C C4 THP . . . B 2 14.482 7.301 -1.909 1 7.24 ? C4 THP 150 A 1 
HETATM 22 O O4 THP . . . B 2 13.378 6.885 -2.27 1 10.79 ? O4 THP 150 A 1 
HETATM 23 C C5 THP . . . B 2 14.832 7.465 -0.547 1 7.88 ? C5 THP 150 A 1 
HETATM 24 C C5M THP . . . B 2 13.787 7.127 0.53 1 8.98 ? C5M THP 150 A 1 
HETATM 25 C C6 THP . . . B 2 16.047 7.994 -0.145 1 8.82 ? C6 THP 150 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#