data_6VCP # _model_server_result.job_id '_dUIp7xuRPo5j51ngQPawg' _model_server_result.datetime_utc '2024-11-14 03:13:08' _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 6vcp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 6VCP # _exptl.entry_id 6VCP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _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 101.007 _cell.angle_gamma 90 _cell.entry_id 6VCP _cell.length_a 78.783 _cell.length_b 38.739 _cell.length_c 58.757 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VCP _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _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 UTP doub 358 n n PA O2A UTP sing 359 n n PA O3A UTP sing 360 n n PA O5' UTP sing 361 n n O2A H2A UTP sing 362 n n O3A PB UTP sing 363 n n O5' C5' UTP sing 364 n n PB O1B UTP sing 365 n n PB O2B UTP doub 366 n n PB O3B UTP sing 367 n n O1B H1B UTP sing 368 n n O3B PG UTP sing 369 n n PG O1G UTP sing 370 n n PG O2G UTP doub 371 n n PG O3G UTP sing 372 n n O1G H1G UTP sing 373 n n O3G H3G UTP sing 374 n n C5' C4' UTP sing 375 n n C5' "H5'1" UTP sing 376 n n C5' "H5'2" UTP sing 377 n n C4' O4' UTP sing 378 n n C4' C3' UTP sing 379 n n C4' H4' UTP sing 380 n n O4' C1' UTP sing 381 n n C1' C2' UTP sing 382 n n C1' N1 UTP sing 383 n n C1' H1' UTP sing 384 n n C2' O2' UTP sing 385 n n C2' C3' UTP sing 386 n n C2' H2' UTP sing 387 n n O2' HA UTP sing 388 n n C3' O3' UTP sing 389 n n C3' H3' UTP sing 390 n n O3' HB UTP sing 391 n n N1 C6 UTP sing 392 n y N1 C2 UTP sing 393 n y C6 C5 UTP doub 394 n y C6 H6 UTP sing 395 n n C2 O2 UTP doub 396 n n C2 N3 UTP sing 397 n y N3 C4 UTP sing 398 n y N3 H3 UTP sing 399 n n C4 O4 UTP doub 400 n n C4 C5 UTP sing 401 n y C5 H5 UTP sing 402 n n # _atom_sites.entry_id 6VCP _atom_sites.fract_transf_matrix[1][1] 0.012693 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002469 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025814 _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] 0.017338 _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 UTP A 1 201 1 UTP UTP . C 2 UTP A 1 202 2 UTP UTP . D 3 HOH A 1 301 115 HOH HOH . D 3 HOH A 2 302 92 HOH HOH . D 3 HOH A 3 303 81 HOH HOH . D 3 HOH A 4 304 78 HOH HOH . D 3 HOH A 5 305 16 HOH HOH . D 3 HOH A 6 306 122 HOH HOH . D 3 HOH A 7 307 42 HOH HOH . D 3 HOH A 8 308 9 HOH HOH . D 3 HOH A 9 309 114 HOH HOH . D 3 HOH A 10 310 50 HOH HOH . D 3 HOH A 11 311 32 HOH HOH . D 3 HOH A 12 312 131 HOH HOH . D 3 HOH A 13 313 26 HOH HOH . D 3 HOH A 14 314 3 HOH HOH . D 3 HOH A 15 315 83 HOH HOH . D 3 HOH A 16 316 84 HOH HOH . D 3 HOH A 17 317 66 HOH HOH . D 3 HOH A 18 318 36 HOH HOH . D 3 HOH A 19 319 116 HOH HOH . D 3 HOH A 20 320 31 HOH HOH . D 3 HOH A 21 321 73 HOH HOH . D 3 HOH A 22 322 90 HOH HOH . D 3 HOH A 23 323 118 HOH HOH . D 3 HOH A 24 324 68 HOH HOH . D 3 HOH A 25 325 45 HOH HOH . D 3 HOH A 26 326 23 HOH HOH . D 3 HOH A 27 327 93 HOH HOH . D 3 HOH A 28 328 39 HOH HOH . D 3 HOH A 29 329 97 HOH HOH . D 3 HOH A 30 330 80 HOH HOH . D 3 HOH A 31 331 52 HOH HOH . D 3 HOH A 32 332 11 HOH HOH . D 3 HOH A 33 333 121 HOH HOH . D 3 HOH A 34 334 64 HOH HOH . D 3 HOH A 35 335 17 HOH HOH . D 3 HOH A 36 336 4 HOH HOH . D 3 HOH A 37 337 54 HOH HOH . D 3 HOH A 38 338 58 HOH HOH . D 3 HOH A 39 339 8 HOH HOH . D 3 HOH A 40 340 59 HOH HOH . D 3 HOH A 41 341 22 HOH HOH . D 3 HOH A 42 342 61 HOH HOH . D 3 HOH A 43 343 18 HOH HOH . D 3 HOH A 44 344 34 HOH HOH . D 3 HOH A 45 345 28 HOH HOH . D 3 HOH A 46 346 166 HOH HOH . D 3 HOH A 47 347 170 HOH HOH . D 3 HOH A 48 348 15 HOH HOH . D 3 HOH A 49 349 43 HOH HOH . D 3 HOH A 50 350 72 HOH HOH . D 3 HOH A 51 351 21 HOH HOH . D 3 HOH A 52 352 49 HOH HOH . D 3 HOH A 53 353 86 HOH HOH . D 3 HOH A 54 354 47 HOH HOH . D 3 HOH A 55 355 117 HOH HOH . D 3 HOH A 56 356 7 HOH HOH . D 3 HOH A 57 357 100 HOH HOH . D 3 HOH A 58 358 76 HOH HOH . D 3 HOH A 59 359 132 HOH HOH . D 3 HOH A 60 360 130 HOH HOH . D 3 HOH A 61 361 37 HOH HOH . D 3 HOH A 62 362 5 HOH HOH . D 3 HOH A 63 363 20 HOH HOH . D 3 HOH A 64 364 158 HOH HOH . D 3 HOH A 65 365 24 HOH HOH . D 3 HOH A 66 366 89 HOH HOH . D 3 HOH A 67 367 125 HOH HOH . D 3 HOH A 68 368 19 HOH HOH . D 3 HOH A 69 369 71 HOH HOH . D 3 HOH A 70 370 146 HOH HOH . D 3 HOH A 71 371 35 HOH HOH . D 3 HOH A 72 372 12 HOH HOH . D 3 HOH A 73 373 57 HOH HOH . D 3 HOH A 74 374 2 HOH HOH . D 3 HOH A 75 375 142 HOH HOH . D 3 HOH A 76 376 27 HOH HOH . D 3 HOH A 77 377 13 HOH HOH . D 3 HOH A 78 378 25 HOH HOH . D 3 HOH A 79 379 6 HOH HOH . D 3 HOH A 80 380 88 HOH HOH . D 3 HOH A 81 381 103 HOH HOH . D 3 HOH A 82 382 56 HOH HOH . D 3 HOH A 83 383 46 HOH HOH . D 3 HOH A 84 384 94 HOH HOH . D 3 HOH A 85 385 30 HOH HOH . D 3 HOH A 86 386 82 HOH HOH . D 3 HOH A 87 387 44 HOH HOH . D 3 HOH A 88 388 10 HOH HOH . D 3 HOH A 89 389 55 HOH HOH . D 3 HOH A 90 390 63 HOH HOH . D 3 HOH A 91 391 119 HOH HOH . D 3 HOH A 92 392 14 HOH HOH . D 3 HOH A 93 393 67 HOH HOH . D 3 HOH A 94 394 111 HOH HOH . D 3 HOH A 95 395 139 HOH HOH . D 3 HOH A 96 396 163 HOH HOH . D 3 HOH A 97 397 29 HOH HOH . D 3 HOH A 98 398 33 HOH HOH . D 3 HOH A 99 399 51 HOH HOH . D 3 HOH A 100 400 155 HOH HOH . D 3 HOH A 101 401 87 HOH HOH . D 3 HOH A 102 402 48 HOH HOH . D 3 HOH A 103 403 159 HOH HOH . D 3 HOH A 104 404 154 HOH HOH . D 3 HOH A 105 405 85 HOH HOH . D 3 HOH A 106 406 62 HOH HOH . D 3 HOH A 107 407 126 HOH HOH . D 3 HOH A 108 408 60 HOH HOH . D 3 HOH A 109 409 162 HOH HOH . D 3 HOH A 110 410 74 HOH HOH . D 3 HOH A 111 411 70 HOH HOH . D 3 HOH A 112 412 53 HOH HOH . D 3 HOH A 113 413 124 HOH HOH . D 3 HOH A 114 414 79 HOH HOH . D 3 HOH A 115 415 1 HOH HOH . D 3 HOH A 116 416 149 HOH HOH . D 3 HOH A 117 417 157 HOH HOH . D 3 HOH A 118 418 105 HOH HOH . D 3 HOH A 119 419 161 HOH HOH . D 3 HOH A 120 420 106 HOH HOH . D 3 HOH A 121 421 172 HOH HOH . D 3 HOH A 122 422 134 HOH HOH . D 3 HOH A 123 423 75 HOH HOH . D 3 HOH A 124 424 133 HOH HOH . D 3 HOH A 125 425 136 HOH HOH . D 3 HOH A 126 426 151 HOH HOH . D 3 HOH A 127 427 69 HOH HOH . D 3 HOH A 128 428 153 HOH HOH . D 3 HOH A 129 429 156 HOH HOH . D 3 HOH A 130 430 65 HOH HOH . D 3 HOH A 131 431 171 HOH HOH . D 3 HOH A 132 432 129 HOH HOH . D 3 HOH A 133 433 104 HOH HOH . D 3 HOH A 134 434 41 HOH HOH . D 3 HOH A 135 435 123 HOH HOH . D 3 HOH A 136 436 147 HOH HOH . D 3 HOH A 137 437 110 HOH HOH . D 3 HOH A 138 438 144 HOH HOH . D 3 HOH A 139 439 127 HOH HOH . D 3 HOH A 140 440 109 HOH HOH . D 3 HOH A 141 441 91 HOH HOH . D 3 HOH A 142 442 99 HOH HOH . D 3 HOH A 143 443 38 HOH HOH . D 3 HOH A 144 444 107 HOH HOH . D 3 HOH A 145 445 98 HOH HOH . D 3 HOH A 146 446 120 HOH HOH . D 3 HOH A 147 447 138 HOH HOH . D 3 HOH A 148 448 40 HOH HOH . D 3 HOH A 149 449 164 HOH HOH . D 3 HOH A 150 450 160 HOH HOH . D 3 HOH A 151 451 145 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 UTP . . . C 2 14.635 -19.666 13.915 1 33.53 ? PA UTP 202 A 1 HETATM 2 O O1A UTP . . . C 2 13.699 -18.805 13.065 1 32.37 ? O1A UTP 202 A 1 HETATM 3 O O2A UTP . . . C 2 14.805 -19.202 15.323 1 35.67 ? O2A UTP 202 A 1 HETATM 4 O O3A UTP . . . C 2 13.874 -21.147 13.958 1 38.14 ? O3A UTP 202 A 1 HETATM 5 O O5' UTP . . . C 2 16.055 -19.797 13.213 1 29.77 ? O5' UTP 202 A 1 HETATM 6 P PB UTP . . . C 2 14.045 -22.45 14.961 1 37.65 ? PB UTP 202 A 1 HETATM 7 O O1B UTP . . . C 2 15.558 -22.651 15.074 1 43.71 ? O1B UTP 202 A 1 HETATM 8 O O2B UTP . . . C 2 13.42 -23.669 14.356 1 38.75 ? O2B UTP 202 A 1 HETATM 9 O O3B UTP . . . C 2 13.455 -22.13 16.472 1 82.32 ? O3B UTP 202 A 1 HETATM 10 P PG UTP . . . C 2 11.968 -21.906 17.015 1 84.96 ? PG UTP 202 A 1 HETATM 11 O O1G UTP . . . C 2 11.83 -22.603 18.369 1 84.48 ? O1G UTP 202 A 1 HETATM 12 O O2G UTP . . . C 2 11.04 -22.527 15.986 1 84.9 ? O2G UTP 202 A 1 HETATM 13 O O3G UTP . . . C 2 11.712 -20.42 17.119 1 85.49 ? O3G UTP 202 A 1 HETATM 14 C C5' UTP . . . C 2 17.21 -20.019 14.004 1 26.61 ? C5' UTP 202 A 1 HETATM 15 C C4' UTP . . . C 2 18.27 -19.092 13.42 1 30.6 ? C4' UTP 202 A 1 HETATM 16 O O4' UTP . . . C 2 18.451 -19.379 12.031 1 30.35 ? O4' UTP 202 A 1 HETATM 17 C C1' UTP . . . C 2 18.823 -18.18 11.366 1 31.65 ? C1' UTP 202 A 1 HETATM 18 C C2' UTP . . . C 2 18.66 -17.027 12.36 1 27.15 ? C2' UTP 202 A 1 HETATM 19 O O2' UTP . . . C 2 19.949 -16.754 12.933 1 31.16 ? O2' UTP 202 A 1 HETATM 20 C C3' UTP . . . C 2 17.76 -17.651 13.428 1 29.14 ? C3' UTP 202 A 1 HETATM 21 O O3' UTP . . . C 2 17.917 -17.047 14.717 1 30.29 ? O3' UTP 202 A 1 HETATM 22 N N1 UTP . . . C 2 17.959 -18.078 10.172 1 28.8 ? N1 UTP 202 A 1 HETATM 23 C C6 UTP . . . C 2 16.611 -18.645 10.342 1 28.43 ? C6 UTP 202 A 1 HETATM 24 C C2 UTP . . . C 2 18.491 -17.51 9.067 1 24.9 ? C2 UTP 202 A 1 HETATM 25 O O2 UTP . . . C 2 19.632 -17.051 9.026 1 29.11 ? O2 UTP 202 A 1 HETATM 26 N N3 UTP . . . C 2 17.703 -17.46 7.956 1 24.05 ? N3 UTP 202 A 1 HETATM 27 C C4 UTP . . . C 2 16.41 -17.899 7.844 1 25.16 ? C4 UTP 202 A 1 HETATM 28 O O4 UTP . . . C 2 15.776 -17.802 6.792 1 25.45 ? O4 UTP 202 A 1 HETATM 29 C C5 UTP . . . C 2 15.804 -18.536 9.06 1 28.61 ? C5 UTP 202 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 29 #