data_4O9E # _model_server_result.job_id xk3qgBxmD_YwLLlXRVtoWQ _model_server_result.datetime_utc '2024-11-26 18:23:21' _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 4o9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4O9E # _exptl.entry_id 4O9E _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-5'-DIPHOSPHATE" _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 4O9E _cell.length_a 95.788 _cell.length_b 95.788 _cell.length_c 94.679 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O9E _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _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,G,H _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 E N N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 409 n n PA O2A TYD sing 410 n n PA O3A TYD sing 411 n n PA O5' TYD sing 412 n n O2A HOA2 TYD sing 413 n n O3A PB TYD sing 414 n n PB O1B TYD doub 415 n n PB O2B TYD sing 416 n n PB O3B TYD sing 417 n n O2B HOB2 TYD sing 418 n n O3B HOB3 TYD sing 419 n n O5' C5' TYD sing 420 n n C5' C4' TYD sing 421 n n C5' "H5'1" TYD sing 422 n n C5' "H5'2" TYD sing 423 n n C4' O4' TYD sing 424 n n C4' C3' TYD sing 425 n n C4' H4' TYD sing 426 n n O4' C1' TYD sing 427 n n C3' O3' TYD sing 428 n n C3' C2' TYD sing 429 n n C3' H3' TYD sing 430 n n O3' HO3' TYD sing 431 n n C2' C1' TYD sing 432 n n C2' "H2'1" TYD sing 433 n n C2' "H2'2" TYD sing 434 n n C1' N1 TYD sing 435 n n C1' H1' TYD sing 436 n n N1 C2 TYD sing 437 n y N1 C6 TYD sing 438 n y C2 O2 TYD doub 439 n n C2 N3 TYD sing 440 n y N3 C4 TYD sing 441 n y N3 HN3 TYD sing 442 n n C4 O4 TYD doub 443 n n C4 C5 TYD sing 444 n y C5 C5M TYD sing 445 n n C5 C6 TYD doub 446 n y C5M H51 TYD sing 447 n n C5M H52 TYD sing 448 n n C5M H53 TYD sing 449 n n C6 H6 TYD sing 450 n n # _atom_sites.entry_id 4O9E _atom_sites.fract_transf_matrix[1][1] 0.01044 _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] 0.01044 _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] 0.010562 _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 TYD A 1 201 1 TYD TYD . D 3 TDR A 1 202 1 TDR TDR . E 2 TYD B 1 201 1 TYD TYD . F 4 4TD B 1 202 1 4TD X21 . G 5 HOH A 1 301 2 HOH HOH . G 5 HOH A 2 302 3 HOH HOH . G 5 HOH A 3 303 4 HOH HOH . G 5 HOH A 4 304 8 HOH HOH . G 5 HOH A 5 305 9 HOH HOH . G 5 HOH A 6 306 10 HOH HOH . G 5 HOH A 7 307 16 HOH HOH . G 5 HOH A 8 308 17 HOH HOH . G 5 HOH A 9 309 20 HOH HOH . G 5 HOH A 10 310 25 HOH HOH . G 5 HOH A 11 311 27 HOH HOH . G 5 HOH A 12 312 28 HOH HOH . G 5 HOH A 13 313 29 HOH HOH . G 5 HOH A 14 314 33 HOH HOH . G 5 HOH A 15 315 34 HOH HOH . G 5 HOH A 16 316 36 HOH HOH . G 5 HOH A 17 317 40 HOH HOH . G 5 HOH A 18 318 48 HOH HOH . G 5 HOH A 19 319 49 HOH HOH . G 5 HOH A 20 320 55 HOH HOH . G 5 HOH A 21 321 58 HOH HOH . G 5 HOH A 22 322 76 HOH HOH . G 5 HOH A 23 323 100 HOH HOH . G 5 HOH A 24 324 121 HOH HOH . G 5 HOH A 25 325 122 HOH HOH . G 5 HOH A 26 326 123 HOH HOH . G 5 HOH A 27 327 127 HOH HOH . G 5 HOH A 28 328 128 HOH HOH . G 5 HOH A 29 329 129 HOH HOH . G 5 HOH A 30 330 130 HOH HOH . G 5 HOH A 31 331 131 HOH HOH . G 5 HOH A 32 332 141 HOH HOH . G 5 HOH A 33 333 142 HOH HOH . G 5 HOH A 34 334 143 HOH HOH . G 5 HOH A 35 335 144 HOH HOH . G 5 HOH A 36 336 145 HOH HOH . G 5 HOH A 37 337 146 HOH HOH . G 5 HOH A 38 338 147 HOH HOH . G 5 HOH A 39 339 148 HOH HOH . G 5 HOH A 40 340 150 HOH HOH . G 5 HOH A 41 341 152 HOH HOH . G 5 HOH A 42 342 153 HOH HOH . G 5 HOH A 43 343 154 HOH HOH . G 5 HOH A 44 344 155 HOH HOH . G 5 HOH A 45 345 156 HOH HOH . G 5 HOH A 46 346 158 HOH HOH . G 5 HOH A 47 347 159 HOH HOH . G 5 HOH A 48 348 160 HOH HOH . G 5 HOH A 49 349 161 HOH HOH . G 5 HOH A 50 350 162 HOH HOH . G 5 HOH A 51 351 163 HOH HOH . G 5 HOH A 52 352 164 HOH HOH . G 5 HOH A 53 353 165 HOH HOH . G 5 HOH A 54 354 169 HOH HOH . G 5 HOH A 55 355 170 HOH HOH . G 5 HOH A 56 356 171 HOH HOH . G 5 HOH A 57 357 173 HOH HOH . G 5 HOH A 58 358 183 HOH HOH . G 5 HOH A 59 359 184 HOH HOH . G 5 HOH A 60 360 185 HOH HOH . G 5 HOH A 61 361 191 HOH HOH . G 5 HOH A 62 362 192 HOH HOH . G 5 HOH A 63 363 193 HOH HOH . G 5 HOH A 64 364 194 HOH HOH . G 5 HOH A 65 365 195 HOH HOH . G 5 HOH A 66 366 196 HOH HOH . G 5 HOH A 67 367 201 HOH HOH . G 5 HOH A 68 368 174 HOH HOH . G 5 HOH A 69 369 186 HOH HOH . H 5 HOH B 1 301 1 HOH HOH . H 5 HOH B 2 302 5 HOH HOH . H 5 HOH B 3 303 6 HOH HOH . H 5 HOH B 4 304 7 HOH HOH . H 5 HOH B 5 305 11 HOH HOH . H 5 HOH B 6 306 13 HOH HOH . H 5 HOH B 7 307 14 HOH HOH . H 5 HOH B 8 308 15 HOH HOH . H 5 HOH B 9 309 18 HOH HOH . H 5 HOH B 10 310 23 HOH HOH . H 5 HOH B 11 311 24 HOH HOH . H 5 HOH B 12 312 26 HOH HOH . H 5 HOH B 13 313 30 HOH HOH . H 5 HOH B 14 314 32 HOH HOH . H 5 HOH B 15 315 39 HOH HOH . H 5 HOH B 16 316 45 HOH HOH . H 5 HOH B 17 317 46 HOH HOH . H 5 HOH B 18 318 52 HOH HOH . H 5 HOH B 19 319 57 HOH HOH . H 5 HOH B 20 320 124 HOH HOH . H 5 HOH B 21 321 125 HOH HOH . H 5 HOH B 22 322 126 HOH HOH . H 5 HOH B 23 323 132 HOH HOH . H 5 HOH B 24 324 133 HOH HOH . H 5 HOH B 25 325 134 HOH HOH . H 5 HOH B 26 326 135 HOH HOH . H 5 HOH B 27 327 136 HOH HOH . H 5 HOH B 28 328 137 HOH HOH . H 5 HOH B 29 329 138 HOH HOH . H 5 HOH B 30 330 139 HOH HOH . H 5 HOH B 31 331 140 HOH HOH . H 5 HOH B 32 332 149 HOH HOH . H 5 HOH B 33 333 151 HOH HOH . H 5 HOH B 34 334 157 HOH HOH . H 5 HOH B 35 335 172 HOH HOH . H 5 HOH B 36 336 175 HOH HOH . H 5 HOH B 37 337 176 HOH HOH . H 5 HOH B 38 338 177 HOH HOH . H 5 HOH B 39 339 178 HOH HOH . H 5 HOH B 40 340 179 HOH HOH . H 5 HOH B 41 341 180 HOH HOH . H 5 HOH B 42 342 181 HOH HOH . H 5 HOH B 43 343 182 HOH HOH . H 5 HOH B 44 344 187 HOH HOH . H 5 HOH B 45 345 188 HOH HOH . H 5 HOH B 46 346 189 HOH HOH . H 5 HOH B 47 347 190 HOH HOH . H 5 HOH B 48 348 197 HOH HOH . H 5 HOH B 49 349 198 HOH HOH . H 5 HOH B 50 350 199 HOH HOH . H 5 HOH B 51 351 200 HOH HOH . H 5 HOH B 52 352 202 HOH HOH . H 5 HOH B 53 353 203 HOH HOH . H 5 HOH B 54 354 204 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 PA TYD . . . C 2 -1.183 -22.104 -39.339 1 53.07 ? PA TYD 201 A 1 HETATM 2 O O1A TYD . . . C 2 -1.454 -22.228 -40.811 1 50.04 ? O1A TYD 201 A 1 HETATM 3 O O2A TYD . . . C 2 -1.72 -23.088 -38.315 1 41 ? O2A TYD 201 A 1 HETATM 4 O O3A TYD . . . C 2 -1.169 -20.633 -38.674 1 51.6 ? O3A TYD 201 A 1 HETATM 5 P PB TYD . . . C 2 -2.371 -19.785 -37.999 1 48.56 ? PB TYD 201 A 1 HETATM 6 O O1B TYD . . . C 2 -2.696 -18.801 -39.112 1 46.07 ? O1B TYD 201 A 1 HETATM 7 O O2B TYD . . . C 2 -1.679 -19.142 -36.835 1 37.3 ? O2B TYD 201 A 1 HETATM 8 O O3B TYD . . . C 2 -3.503 -20.715 -37.615 1 51.23 ? O3B TYD 201 A 1 HETATM 9 O O5' TYD . . . C 2 0.402 -22.282 -39.504 1 45.84 ? O5' TYD 201 A 1 HETATM 10 C C5' TYD . . . C 2 1.369 -21.461 -40.141 1 52.75 ? C5' TYD 201 A 1 HETATM 11 C C4' TYD . . . C 2 2.478 -22.407 -40.599 1 47.53 ? C4' TYD 201 A 1 HETATM 12 O O4' TYD . . . C 2 3.143 -23.111 -39.547 1 49.68 ? O4' TYD 201 A 1 HETATM 13 C C3' TYD . . . C 2 1.954 -23.513 -41.499 1 50.84 ? C3' TYD 201 A 1 HETATM 14 O O3' TYD . . . C 2 2.831 -23.523 -42.62 1 52.29 ? O3' TYD 201 A 1 HETATM 15 C C2' TYD . . . C 2 2.167 -24.863 -40.827 1 48.72 ? C2' TYD 201 A 1 HETATM 16 C C1' TYD . . . C 2 3.203 -24.526 -39.764 1 51.21 ? C1' TYD 201 A 1 HETATM 17 N N1 TYD . . . C 2 2.955 -25.263 -38.521 1 44.85 ? N1 TYD 201 A 1 HETATM 18 C C2 TYD . . . C 2 3.749 -26.258 -38.118 1 39.52 ? C2 TYD 201 A 1 HETATM 19 O O2 TYD . . . C 2 4.748 -26.572 -38.787 1 40.85 ? O2 TYD 201 A 1 HETATM 20 N N3 TYD . . . C 2 3.558 -26.885 -36.943 1 36.6 ? N3 TYD 201 A 1 HETATM 21 C C4 TYD . . . C 2 2.468 -26.591 -36.21 1 37.08 ? C4 TYD 201 A 1 HETATM 22 O O4 TYD . . . C 2 2.254 -27.237 -35.173 1 31.7 ? O4 TYD 201 A 1 HETATM 23 C C5 TYD . . . C 2 1.605 -25.586 -36.617 1 39.16 ? C5 TYD 201 A 1 HETATM 24 C C5M TYD . . . C 2 0.417 -25.15 -35.81 1 35.71 ? C5M TYD 201 A 1 HETATM 25 C C6 TYD . . . C 2 1.89 -24.913 -37.795 1 41.33 ? C6 TYD 201 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #