data_1SYD
#
_model_server_result.job_id            5JUgHXNO5FDL-NLxRijtEg 
_model_server_result.datetime_utc      '2024-10-20 03:43:50' 
_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          1syd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":180}' 
#
_entry.id    1SYD 
#
_exptl.entry_id    1SYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1SYD 
_cell.length_a            48.5 
_cell.length_b            48.5 
_cell.length_c            63.5 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1SYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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                      3 
_struct_asym.id                             C 
_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 B CA CA . A CA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? 
metalc ? metalc4 C O5P THP . A THP 180 1_555 B CA CA . A CA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? 
metalc ? metalc5 B CA CA . A CA 190 1_555 D O HOH . A HOH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? 
metalc ? metalc6 B CA CA . A CA 190 1_555 D O HOH . A HOH 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc7 B CA CA . A CA 190 1_555 D O HOH . A HOH 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
#
_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                     1SYD 
_atom_sites.fract_transf_matrix[1][1]    0.020619 
_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]    0.020619 
_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]    0.015748 
_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 CA A 1 190 190 CA CA . 
C 3 THP A 1 180 180 THP PTP . 
D 4 HOH A 1 201 201 HOH HOH . 
D 4 HOH A 2 202 202 HOH HOH . 
D 4 HOH A 3 203 203 HOH HOH . 
D 4 HOH A 4 204 204 HOH HOH . 
D 4 HOH A 5 205 205 HOH HOH . 
D 4 HOH A 6 206 206 HOH HOH . 
D 4 HOH A 7 207 207 HOH HOH . 
D 4 HOH A 8 208 208 HOH HOH . 
D 4 HOH A 9 209 209 HOH HOH . 
D 4 HOH A 10 210 210 HOH HOH . 
D 4 HOH A 11 211 211 HOH HOH . 
D 4 HOH A 12 212 212 HOH HOH . 
D 4 HOH A 13 213 213 HOH HOH . 
D 4 HOH A 14 214 214 HOH HOH . 
D 4 HOH A 15 215 215 HOH HOH . 
D 4 HOH A 16 216 216 HOH HOH . 
D 4 HOH A 17 217 217 HOH HOH . 
D 4 HOH A 18 218 218 HOH HOH . 
D 4 HOH A 19 219 219 HOH HOH . 
D 4 HOH A 20 220 220 HOH HOH . 
D 4 HOH A 21 221 221 HOH HOH . 
D 4 HOH A 22 222 222 HOH HOH . 
D 4 HOH A 23 223 223 HOH HOH . 
D 4 HOH A 24 224 224 HOH HOH . 
D 4 HOH A 25 225 225 HOH HOH . 
D 4 HOH A 26 226 226 HOH HOH . 
D 4 HOH A 27 227 227 HOH HOH . 
D 4 HOH A 28 228 228 HOH HOH . 
D 4 HOH A 29 229 229 HOH HOH . 
D 4 HOH A 30 230 230 HOH HOH . 
D 4 HOH A 31 231 231 HOH HOH . 
D 4 HOH A 32 232 232 HOH HOH . 
D 4 HOH A 33 233 233 HOH HOH . 
D 4 HOH A 34 234 234 HOH HOH . 
D 4 HOH A 35 235 235 HOH HOH . 
D 4 HOH A 36 236 236 HOH HOH . 
D 4 HOH A 37 237 237 HOH HOH . 
D 4 HOH A 38 238 238 HOH HOH . 
D 4 HOH A 39 239 239 HOH HOH . 
D 4 HOH A 40 240 240 HOH HOH . 
D 4 HOH A 41 241 241 HOH HOH . 
D 4 HOH A 42 242 242 HOH HOH . 
D 4 HOH A 43 243 243 HOH HOH . 
D 4 HOH A 44 244 244 HOH HOH . 
D 4 HOH A 45 245 245 HOH HOH . 
D 4 HOH A 46 246 246 HOH HOH . 
D 4 HOH A 47 247 247 HOH HOH . 
D 4 HOH A 48 248 248 HOH HOH . 
D 4 HOH A 49 249 249 HOH HOH . 
D 4 HOH A 50 250 250 HOH HOH . 
D 4 HOH A 51 251 251 HOH HOH . 
D 4 HOH A 52 252 252 HOH HOH . 
D 4 HOH A 53 253 253 HOH HOH . 
D 4 HOH A 54 254 254 HOH HOH . 
D 4 HOH A 55 255 255 HOH HOH . 
D 4 HOH A 56 256 256 HOH HOH . 
D 4 HOH A 57 257 257 HOH HOH . 
D 4 HOH A 58 258 258 HOH HOH . 
D 4 HOH A 59 259 259 HOH HOH . 
D 4 HOH A 60 260 260 HOH HOH . 
D 4 HOH A 61 261 261 HOH HOH . 
D 4 HOH A 62 262 262 HOH HOH . 
D 4 HOH A 63 263 263 HOH HOH . 
D 4 HOH A 64 264 264 HOH HOH . 
D 4 HOH A 65 265 265 HOH HOH . 
D 4 HOH A 66 266 266 HOH HOH . 
D 4 HOH A 67 267 267 HOH HOH . 
D 4 HOH A 68 268 268 HOH HOH . 
D 4 HOH A 69 269 269 HOH HOH . 
D 4 HOH A 70 270 270 HOH HOH . 
D 4 HOH A 71 271 271 HOH HOH . 
D 4 HOH A 72 272 272 HOH HOH . 
D 4 HOH A 73 273 273 HOH HOH . 
D 4 HOH A 74 274 274 HOH HOH . 
D 4 HOH A 75 275 275 HOH HOH . 
D 4 HOH A 76 276 276 HOH HOH . 
D 4 HOH A 77 277 277 HOH HOH . 
D 4 HOH A 78 278 278 HOH HOH . 
D 4 HOH A 79 279 279 HOH HOH . 
D 4 HOH A 80 280 280 HOH HOH . 
D 4 HOH A 81 281 281 HOH HOH . 
D 4 HOH A 82 282 282 HOH HOH . 
D 4 HOH A 83 283 283 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 . . . C 3 6.144 14.325 20.517 1 30.17 ? P2 THP 180 A 1 
HETATM 2 O O4P THP . . . C 3 6.494 12.928 20.994 1 30.07 ? O4P THP 180 A 1 
HETATM 3 O O5P THP . . . C 3 5.161 14.315 19.347 1 29.71 ? O5P THP 180 A 1 
HETATM 4 O O6P THP . . . C 3 7.498 14.971 20.185 1 28.35 ? O6P THP 180 A 1 
HETATM 5 P P1 THP . . . C 3 4.939 12.151 26.331 1 38.99 ? P1 THP 180 A 1 
HETATM 6 O O1P THP . . . C 3 6.309 12.013 25.695 1 38.86 ? O1P THP 180 A 1 
HETATM 7 O O2P THP . . . C 3 4.89 11.816 27.799 1 39.81 ? O2P THP 180 A 1 
HETATM 8 O O3P THP . . . C 3 3.838 11.524 25.457 1 38.98 ? O3P THP 180 A 1 
HETATM 9 O O5' THP . . . C 3 5.581 15.147 21.686 1 30.23 ? O5' THP 180 A 1 
HETATM 10 C C5' THP . . . C 3 4.459 14.62 22.498 1 31.37 ? C5' THP 180 A 1 
HETATM 11 C C4' THP . . . C 3 4.957 14.542 23.931 1 32.65 ? C4' THP 180 A 1 
HETATM 12 O O4' THP . . . C 3 5.371 15.883 24.357 1 32.38 ? O4' THP 180 A 1 
HETATM 13 C C3' THP . . . C 3 3.867 14.188 24.976 1 33.82 ? C3' THP 180 A 1 
HETATM 14 O O3' THP . . . C 3 4.608 13.677 26.167 1 36.87 ? O3' THP 180 A 1 
HETATM 15 C C2' THP . . . C 3 3.122 15.507 25.291 1 32.48 ? C2' THP 180 A 1 
HETATM 16 C C1' THP . . . C 3 4.316 16.512 25.099 1 31.65 ? C1' THP 180 A 1 
HETATM 17 N N1 THP . . . C 3 3.797 17.807 24.621 1 30.44 ? N1 THP 180 A 1 
HETATM 18 C C2 THP . . . C 3 3.426 18.636 25.651 1 29.81 ? C2 THP 180 A 1 
HETATM 19 O O2 THP . . . C 3 3.614 18.319 26.83 1 29.29 ? O2 THP 180 A 1 
HETATM 20 N N3 THP . . . C 3 2.848 19.843 25.369 1 29.1 ? N3 THP 180 A 1 
HETATM 21 C C4 THP . . . C 3 2.642 20.183 24.138 1 28.67 ? C4 THP 180 A 1 
HETATM 22 O O4 THP . . . C 3 2.069 21.301 23.891 1 29.16 ? O4 THP 180 A 1 
HETATM 23 C C5 THP . . . C 3 3.019 19.346 23.033 1 28.12 ? C5 THP 180 A 1 
HETATM 24 C C5M THP . . . C 3 2.776 19.803 21.611 1 26.99 ? C5M THP 180 A 1 
HETATM 25 C C6 THP . . . C 3 3.586 18.118 23.327 1 28.77 ? C6 THP 180 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           25 
#