data_4N9P # _model_server_result.job_id A7wUsBZdWgck24KEt-6TWw _model_server_result.datetime_utc '2024-10-11 10:22:33' _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 4n9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4N9P # _exptl.entry_id 4N9P _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 94.72 _cell.angle_gamma 90 _cell.entry_id 4N9P _cell.length_a 31.234 _cell.length_b 60.133 _cell.length_c 38.34 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N9P _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 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 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc5 B CA CA . A CA 201 1_555 C O5P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.177 ? metalc ? metalc6 B CA CA . A CA 201 1_555 D O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc7 B CA CA . A CA 201 1_555 D O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? # _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 4N9P _atom_sites.fract_transf_matrix[1][1] 0.032016 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002641 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01663 _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] 0.026171 _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 1 201 1 CA CA . C 3 THP A 1 202 1 THP THP . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 36 HOH HOH . D 4 HOH A 36 336 37 HOH HOH . D 4 HOH A 37 337 38 HOH HOH . D 4 HOH A 38 338 39 HOH HOH . D 4 HOH A 39 339 40 HOH HOH . D 4 HOH A 40 340 41 HOH HOH . D 4 HOH A 41 341 42 HOH HOH . D 4 HOH A 42 342 43 HOH HOH . D 4 HOH A 43 343 44 HOH HOH . D 4 HOH A 44 344 45 HOH HOH . D 4 HOH A 45 345 46 HOH HOH . D 4 HOH A 46 346 47 HOH HOH . D 4 HOH A 47 347 48 HOH HOH . D 4 HOH A 48 348 49 HOH HOH . D 4 HOH A 49 349 50 HOH HOH . D 4 HOH A 50 350 51 HOH HOH . D 4 HOH A 51 351 52 HOH HOH . D 4 HOH A 52 352 53 HOH HOH . D 4 HOH A 53 353 54 HOH HOH . D 4 HOH A 54 354 55 HOH HOH . D 4 HOH A 55 355 56 HOH HOH . D 4 HOH A 56 356 57 HOH HOH . D 4 HOH A 57 357 58 HOH HOH . D 4 HOH A 58 358 59 HOH HOH . D 4 HOH A 59 359 60 HOH HOH . D 4 HOH A 60 360 61 HOH HOH . D 4 HOH A 61 361 62 HOH HOH . D 4 HOH A 62 362 63 HOH HOH . D 4 HOH A 63 363 65 HOH HOH . D 4 HOH A 64 364 66 HOH HOH . D 4 HOH A 65 365 67 HOH HOH . D 4 HOH A 66 366 68 HOH HOH . D 4 HOH A 67 367 69 HOH HOH . D 4 HOH A 68 368 70 HOH HOH . D 4 HOH A 69 369 71 HOH HOH . D 4 HOH A 70 370 73 HOH HOH . D 4 HOH A 71 371 74 HOH HOH . D 4 HOH A 72 372 75 HOH HOH . D 4 HOH A 73 373 76 HOH HOH . D 4 HOH A 74 374 77 HOH HOH . D 4 HOH A 75 375 78 HOH HOH . D 4 HOH A 76 376 80 HOH HOH . D 4 HOH A 77 377 81 HOH HOH . D 4 HOH A 78 378 82 HOH HOH . D 4 HOH A 79 379 83 HOH HOH . D 4 HOH A 80 380 84 HOH HOH . D 4 HOH A 81 381 85 HOH HOH . D 4 HOH A 82 382 86 HOH HOH . D 4 HOH A 83 383 87 HOH HOH . D 4 HOH A 84 384 88 HOH HOH . D 4 HOH A 85 385 89 HOH HOH . D 4 HOH A 86 386 90 HOH HOH . D 4 HOH A 87 387 91 HOH HOH . D 4 HOH A 88 388 93 HOH HOH . D 4 HOH A 89 389 94 HOH HOH . D 4 HOH A 90 390 95 HOH HOH . D 4 HOH A 91 391 97 HOH HOH . D 4 HOH A 92 392 98 HOH HOH . D 4 HOH A 93 393 99 HOH HOH . D 4 HOH A 94 394 100 HOH HOH . D 4 HOH A 95 395 101 HOH HOH . D 4 HOH A 96 396 102 HOH HOH . D 4 HOH A 97 397 103 HOH HOH . D 4 HOH A 98 398 104 HOH HOH . D 4 HOH A 99 399 105 HOH HOH . D 4 HOH A 100 400 106 HOH HOH . D 4 HOH A 101 401 108 HOH HOH . D 4 HOH A 102 402 109 HOH HOH . D 4 HOH A 103 403 110 HOH HOH . D 4 HOH A 104 404 111 HOH HOH . D 4 HOH A 105 405 112 HOH HOH . D 4 HOH A 106 406 113 HOH HOH . D 4 HOH A 107 407 114 HOH HOH . D 4 HOH A 108 408 115 HOH HOH . D 4 HOH A 109 409 116 HOH HOH . D 4 HOH A 110 410 117 HOH HOH . D 4 HOH A 111 411 118 HOH HOH . D 4 HOH A 112 412 119 HOH HOH . D 4 HOH A 113 413 120 HOH HOH . D 4 HOH A 114 414 121 HOH HOH . D 4 HOH A 115 415 122 HOH HOH . D 4 HOH A 116 416 123 HOH HOH . D 4 HOH A 117 417 124 HOH HOH . D 4 HOH A 118 418 125 HOH HOH . D 4 HOH A 119 419 126 HOH HOH . D 4 HOH A 120 420 127 HOH HOH . D 4 HOH A 121 421 128 HOH HOH . D 4 HOH A 122 422 129 HOH HOH . D 4 HOH A 123 423 130 HOH HOH . D 4 HOH A 124 424 131 HOH HOH . D 4 HOH A 125 425 132 HOH HOH . D 4 HOH A 126 426 133 HOH HOH . D 4 HOH A 127 427 134 HOH HOH . D 4 HOH A 128 428 135 HOH HOH . D 4 HOH A 129 429 136 HOH HOH . D 4 HOH A 130 430 137 HOH HOH . D 4 HOH A 131 431 138 HOH HOH . D 4 HOH A 132 432 139 HOH HOH . D 4 HOH A 133 433 140 HOH HOH . D 4 HOH A 134 434 141 HOH HOH . D 4 HOH A 135 435 142 HOH HOH . D 4 HOH A 136 436 143 HOH HOH . D 4 HOH A 137 437 144 HOH HOH . D 4 HOH A 138 438 145 HOH HOH . D 4 HOH A 139 439 146 HOH HOH . D 4 HOH A 140 440 147 HOH HOH . D 4 HOH A 141 441 148 HOH HOH . D 4 HOH A 142 442 149 HOH HOH . D 4 HOH A 143 443 150 HOH HOH . D 4 HOH A 144 444 151 HOH HOH . D 4 HOH A 145 445 152 HOH HOH . D 4 HOH A 146 446 153 HOH HOH . D 4 HOH A 147 447 154 HOH HOH . D 4 HOH A 148 448 155 HOH HOH . D 4 HOH A 149 449 156 HOH HOH . D 4 HOH A 150 450 157 HOH HOH . D 4 HOH A 151 451 158 HOH HOH . D 4 HOH A 152 452 159 HOH HOH . D 4 HOH A 153 453 160 HOH HOH . D 4 HOH A 154 454 161 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 17.897 10.928 5.075 1 12.21 ? P2 THP 202 A 1 HETATM 2 O O4P THP . . . C 3 17.872 9.419 5.273 1 13.11 ? O4P THP 202 A 1 HETATM 3 O O5P THP . . . C 3 16.648 11.613 5.536 1 11.51 ? O5P THP 202 A 1 HETATM 4 O O6P THP . . . C 3 19.102 11.636 5.607 1 14.7 ? O6P THP 202 A 1 HETATM 5 P P1 THP . . . C 3 21.167 14.434 1.31 1 13.1 ? P1 THP 202 A 1 HETATM 6 O O1P THP . . . C 3 22.145 15.124 0.401 1 14.72 ? O1P THP 202 A 1 HETATM 7 O O2P THP . . . C 3 21.832 13.27 2.055 1 15.21 ? O2P THP 202 A 1 HETATM 8 O O3P THP . . . C 3 20.474 15.313 2.273 1 14.42 ? O3P THP 202 A 1 HETATM 9 O O5' THP . . . C 3 17.897 10.994 3.551 1 12.62 ? O5' THP 202 A 1 HETATM 10 C C5' THP . . . C 3 17.87 12.28 2.86 1 14.76 ? C5' THP 202 A 1 HETATM 11 C C4' THP . . . C 3 18.797 12.185 1.635 1 10.6 ? C4' THP 202 A 1 HETATM 12 O O4' THP . . . C 3 18.393 11.127 0.79 1 12.01 ? O4' THP 202 A 1 HETATM 13 C C3' THP . . . C 3 18.719 13.43 0.777 1 13.31 ? C3' THP 202 A 1 HETATM 14 O O3' THP . . . C 3 20.041 13.795 0.308 1 12.95 ? O3' THP 202 A 1 HETATM 15 C C2' THP . . . C 3 17.868 13.088 -0.399 1 13.16 ? C2' THP 202 A 1 HETATM 16 C C1' THP . . . C 3 18.036 11.546 -0.487 1 11.46 ? C1' THP 202 A 1 HETATM 17 N N1 THP . . . C 3 16.77 10.896 -0.893 1 10.32 ? N1 THP 202 A 1 HETATM 18 C C2 THP . . . C 3 16.547 10.744 -2.226 1 12.32 ? C2 THP 202 A 1 HETATM 19 O O2 THP . . . C 3 17.43 11.064 -3.107 1 13.59 ? O2 THP 202 A 1 HETATM 20 N N3 THP . . . C 3 15.409 10.203 -2.697 1 11.86 ? N3 THP 202 A 1 HETATM 21 C C4 THP . . . C 3 14.388 9.933 -1.814 1 11.17 ? C4 THP 202 A 1 HETATM 22 O O4 THP . . . C 3 13.306 9.532 -2.237 1 11.57 ? O4 THP 202 A 1 HETATM 23 C C5 THP . . . C 3 14.628 10.099 -0.41 1 10.21 ? C5 THP 202 A 1 HETATM 24 C C5M THP . . . C 3 13.62 9.749 0.653 1 11.19 ? C5M THP 202 A 1 HETATM 25 C C6 THP . . . C 3 15.855 10.575 0.011 1 12.14 ? C6 THP 202 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #