data_1SB9 # _model_server_result.job_id JdqX_lwd0PXtQWetnppZkQ _model_server_result.datetime_utc '2024-11-28 03:24:36' _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 1sb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":343}' # _entry.id 1SB9 # _exptl.entry_id 1SB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 1SB9 _cell.length_a 60.989 _cell.length_b 95.704 _cell.length_c 141.165 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SB9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 141.165 # _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 # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 433 n n N1 C6 UPG sing 434 n n N1 C1C UPG sing 435 n n C2 N3 UPG sing 436 n n C2 O2 UPG doub 437 n n N3 C4 UPG sing 438 n n N3 HN3 UPG sing 439 n n C4 C5 UPG sing 440 n n C4 O4 UPG doub 441 n n C5 C6 UPG doub 442 n n C5 H5 UPG sing 443 n n C6 H6 UPG sing 444 n n C1C C2C UPG sing 445 n n C1C O4C UPG sing 446 n n C1C H1C UPG sing 447 n n C2C O2C UPG sing 448 n n C2C C3C UPG sing 449 n n C2C H2C UPG sing 450 n n O2C HO2C UPG sing 451 n n C3C C4C UPG sing 452 n n C3C O3C UPG sing 453 n n C3C H3C UPG sing 454 n n C4C O4C UPG sing 455 n n C4C C5C UPG sing 456 n n C4C H4C UPG sing 457 n n O3C HO3C UPG sing 458 n n C5C O5C UPG sing 459 n n C5C H5C1 UPG sing 460 n n C5C H5C2 UPG sing 461 n n O5C PA UPG sing 462 n n PA O1A UPG doub 463 n n PA O2A UPG sing 464 n n PA O3A UPG sing 465 n n O2A HOA2 UPG sing 466 n n O3A PB UPG sing 467 n n PB O1B UPG doub 468 n n PB O2B UPG sing 469 n n PB O3B UPG sing 470 n n O2B HOB2 UPG sing 471 n n O3B C1' UPG sing 472 n n C1' C2' UPG sing 473 n n C1' O5' UPG sing 474 n n C1' H1' UPG sing 475 n n C2' C3' UPG sing 476 n n C2' O2' UPG sing 477 n n C2' H2' UPG sing 478 n n C3' C4' UPG sing 479 n n C3' O3' UPG sing 480 n n C3' H3' UPG sing 481 n n C4' C5' UPG sing 482 n n C4' O4' UPG sing 483 n n C4' H4' UPG sing 484 n n C5' C6' UPG sing 485 n n C5' O5' UPG sing 486 n n C5' H5' UPG sing 487 n n C6' O6' UPG sing 488 n n C6' "H6'1" UPG sing 489 n n C6' "H6'2" UPG sing 490 n n O2' HO2' UPG sing 491 n n O3' HO3' UPG sing 492 n n O4' HO4' UPG sing 493 n n O6' HO6' UPG sing 494 n n # _atom_sites.entry_id 1SB9 _atom_sites.fract_transf_matrix[1][1] 0.016396 _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] 0.010449 _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] 0.007084 _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 NAD A 1 342 342 NAD NAD . C 3 UPG A 1 343 343 UPG UPG . D 4 HOH A 1 344 1 HOH WAT . D 4 HOH A 2 345 2 HOH WAT . D 4 HOH A 3 346 3 HOH WAT . D 4 HOH A 4 347 4 HOH WAT . D 4 HOH A 5 348 5 HOH WAT . D 4 HOH A 6 349 6 HOH WAT . D 4 HOH A 7 350 7 HOH WAT . D 4 HOH A 8 351 8 HOH WAT . D 4 HOH A 9 352 9 HOH WAT . D 4 HOH A 10 353 10 HOH WAT . D 4 HOH A 11 354 11 HOH WAT . D 4 HOH A 12 355 12 HOH WAT . D 4 HOH A 13 356 13 HOH WAT . D 4 HOH A 14 357 14 HOH WAT . D 4 HOH A 15 358 15 HOH WAT . D 4 HOH A 16 359 16 HOH WAT . D 4 HOH A 17 360 17 HOH WAT . D 4 HOH A 18 361 18 HOH WAT . D 4 HOH A 19 362 19 HOH WAT . D 4 HOH A 20 363 20 HOH WAT . D 4 HOH A 21 364 21 HOH WAT . D 4 HOH A 22 365 22 HOH WAT . D 4 HOH A 23 366 23 HOH WAT . D 4 HOH A 24 367 24 HOH WAT . D 4 HOH A 25 368 25 HOH WAT . D 4 HOH A 26 369 26 HOH WAT . D 4 HOH A 27 370 27 HOH WAT . D 4 HOH A 28 371 28 HOH WAT . D 4 HOH A 29 372 29 HOH WAT . D 4 HOH A 30 373 30 HOH WAT . D 4 HOH A 31 374 31 HOH WAT . D 4 HOH A 32 375 32 HOH WAT . D 4 HOH A 33 376 33 HOH WAT . D 4 HOH A 34 377 34 HOH WAT . D 4 HOH A 35 378 35 HOH WAT . D 4 HOH A 36 379 36 HOH WAT . D 4 HOH A 37 380 37 HOH WAT . D 4 HOH A 38 381 38 HOH WAT . D 4 HOH A 39 382 39 HOH WAT . D 4 HOH A 40 383 40 HOH WAT . D 4 HOH A 41 384 41 HOH WAT . D 4 HOH A 42 385 42 HOH WAT . D 4 HOH A 43 386 43 HOH WAT . D 4 HOH A 44 387 44 HOH WAT . D 4 HOH A 45 388 45 HOH WAT . D 4 HOH A 46 389 46 HOH WAT . D 4 HOH A 47 390 47 HOH WAT . D 4 HOH A 48 391 48 HOH WAT . D 4 HOH A 49 392 49 HOH WAT . D 4 HOH A 50 393 50 HOH WAT . D 4 HOH A 51 394 51 HOH WAT . D 4 HOH A 52 395 52 HOH WAT . D 4 HOH A 53 396 53 HOH WAT . D 4 HOH A 54 397 54 HOH WAT . D 4 HOH A 55 398 55 HOH WAT . D 4 HOH A 56 399 56 HOH WAT . D 4 HOH A 57 400 57 HOH WAT . D 4 HOH A 58 401 58 HOH WAT . D 4 HOH A 59 402 59 HOH WAT . D 4 HOH A 60 403 60 HOH WAT . D 4 HOH A 61 404 61 HOH WAT . D 4 HOH A 62 405 62 HOH WAT . D 4 HOH A 63 406 63 HOH WAT . D 4 HOH A 64 407 64 HOH WAT . D 4 HOH A 65 408 66 HOH WAT . D 4 HOH A 66 409 67 HOH WAT . D 4 HOH A 67 410 68 HOH WAT . D 4 HOH A 68 411 70 HOH WAT . D 4 HOH A 69 412 71 HOH WAT . D 4 HOH A 70 413 73 HOH WAT . D 4 HOH A 71 414 75 HOH WAT . D 4 HOH A 72 415 76 HOH WAT . D 4 HOH A 73 416 77 HOH WAT . D 4 HOH A 74 417 78 HOH WAT . D 4 HOH A 75 418 79 HOH WAT . D 4 HOH A 76 419 80 HOH WAT . D 4 HOH A 77 420 81 HOH WAT . D 4 HOH A 78 421 82 HOH WAT . D 4 HOH A 79 422 83 HOH WAT . D 4 HOH A 80 423 84 HOH WAT . D 4 HOH A 81 424 85 HOH WAT . D 4 HOH A 82 425 86 HOH WAT . D 4 HOH A 83 426 87 HOH WAT . D 4 HOH A 84 427 89 HOH WAT . D 4 HOH A 85 428 90 HOH WAT . D 4 HOH A 86 429 91 HOH WAT . D 4 HOH A 87 430 92 HOH WAT . D 4 HOH A 88 431 93 HOH WAT . D 4 HOH A 89 432 94 HOH WAT . D 4 HOH A 90 433 95 HOH WAT . D 4 HOH A 91 434 96 HOH WAT . D 4 HOH A 92 435 97 HOH WAT . D 4 HOH A 93 436 98 HOH WAT . D 4 HOH A 94 437 99 HOH WAT . D 4 HOH A 95 438 101 HOH WAT . D 4 HOH A 96 439 103 HOH WAT . D 4 HOH A 97 440 104 HOH WAT . D 4 HOH A 98 441 105 HOH WAT . D 4 HOH A 99 442 108 HOH WAT . D 4 HOH A 100 443 109 HOH WAT . D 4 HOH A 101 444 110 HOH WAT . D 4 HOH A 102 445 111 HOH WAT . D 4 HOH A 103 446 112 HOH WAT . D 4 HOH A 104 447 113 HOH WAT . D 4 HOH A 105 448 114 HOH WAT . D 4 HOH A 106 449 115 HOH WAT . D 4 HOH A 107 450 118 HOH WAT . D 4 HOH A 108 451 119 HOH WAT . D 4 HOH A 109 452 120 HOH WAT . D 4 HOH A 110 453 121 HOH WAT . D 4 HOH A 111 454 122 HOH WAT . D 4 HOH A 112 455 123 HOH WAT . D 4 HOH A 113 456 124 HOH WAT . D 4 HOH A 114 457 125 HOH WAT . D 4 HOH A 115 458 126 HOH WAT . D 4 HOH A 116 459 129 HOH WAT . D 4 HOH A 117 460 130 HOH WAT . D 4 HOH A 118 461 131 HOH WAT . D 4 HOH A 119 462 132 HOH WAT . D 4 HOH A 120 463 134 HOH WAT . D 4 HOH A 121 464 135 HOH WAT . D 4 HOH A 122 465 137 HOH WAT . D 4 HOH A 123 466 138 HOH WAT . D 4 HOH A 124 467 139 HOH WAT . D 4 HOH A 125 468 140 HOH WAT . D 4 HOH A 126 469 141 HOH WAT . D 4 HOH A 127 470 142 HOH WAT . D 4 HOH A 128 471 143 HOH WAT . D 4 HOH A 129 472 144 HOH WAT . D 4 HOH A 130 473 145 HOH WAT . D 4 HOH A 131 474 146 HOH WAT . D 4 HOH A 132 475 147 HOH WAT . D 4 HOH A 133 476 148 HOH WAT . D 4 HOH A 134 477 149 HOH WAT . D 4 HOH A 135 478 156 HOH WAT . D 4 HOH A 136 479 157 HOH WAT . D 4 HOH A 137 480 158 HOH WAT . D 4 HOH A 138 481 159 HOH WAT . D 4 HOH A 139 482 160 HOH WAT . D 4 HOH A 140 483 161 HOH WAT . D 4 HOH A 141 484 163 HOH WAT . D 4 HOH A 142 485 164 HOH WAT . # 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 N N1 UPG . . . C 3 40.119 11.535 94.484 1 31.17 ? N1 UPG 343 A 1 HETATM 2 C C2 UPG . . . C 3 40.04 12.606 95.379 1 29.78 ? C2 UPG 343 A 1 HETATM 3 N N3 UPG . . . C 3 41.197 12.955 96.04 1 30.75 ? N3 UPG 343 A 1 HETATM 4 C C4 UPG . . . C 3 42.432 12.338 95.899 1 30.68 ? C4 UPG 343 A 1 HETATM 5 C C5 UPG . . . C 3 42.459 11.197 94.926 1 31.12 ? C5 UPG 343 A 1 HETATM 6 C C6 UPG . . . C 3 41.304 10.875 94.286 1 31.14 ? C6 UPG 343 A 1 HETATM 7 O O2 UPG . . . C 3 39.01 13.213 95.579 1 27.1 ? O2 UPG 343 A 1 HETATM 8 O O4 UPG . . . C 3 43.417 12.701 96.524 1 33.79 ? O4 UPG 343 A 1 HETATM 9 C C1C UPG . . . C 3 38.906 11.125 93.771 1 29.59 ? C1C UPG 343 A 1 HETATM 10 C C2C UPG . . . C 3 39.055 11.052 92.273 1 30.61 ? C2C UPG 343 A 1 HETATM 11 O O2C UPG . . . C 3 38.789 12.323 91.685 1 30.65 ? O2C UPG 343 A 1 HETATM 12 C C3C UPG . . . C 3 38.061 10.035 91.849 1 31.36 ? C3C UPG 343 A 1 HETATM 13 C C4C UPG . . . C 3 37.888 9.16 93.071 1 32.13 ? C4C UPG 343 A 1 HETATM 14 O O4C UPG . . . C 3 38.475 9.836 94.191 1 29.49 ? O4C UPG 343 A 1 HETATM 15 O O3C UPG . . . C 3 36.813 10.673 91.592 1 29.45 ? O3C UPG 343 A 1 HETATM 16 C C5C UPG . . . C 3 38.588 7.827 92.886 1 31.25 ? C5C UPG 343 A 1 HETATM 17 O O5C UPG . . . C 3 39.963 8.074 92.655 1 35.48 ? O5C UPG 343 A 1 HETATM 18 P PA UPG . . . C 3 40.82 6.899 91.948 1 33.61 ? PA UPG 343 A 1 HETATM 19 O O1A UPG . . . C 3 42.094 7.414 91.104 1 37.58 ? O1A UPG 343 A 1 HETATM 20 O O2A UPG . . . C 3 41.175 5.877 93.14 1 34.68 ? O2A UPG 343 A 1 HETATM 21 O O3A UPG . . . C 3 39.727 6.11 91.084 1 38.9 ? O3A UPG 343 A 1 HETATM 22 P PB UPG . . . C 3 39.511 6.088 89.507 1 38.18 ? PB UPG 343 A 1 HETATM 23 O O1B UPG . . . C 3 39.596 7.533 88.795 1 41.26 ? O1B UPG 343 A 1 HETATM 24 O O2B UPG . . . C 3 38.103 5.323 89.322 1 39.08 ? O2B UPG 343 A 1 HETATM 25 O O3B UPG . . . C 3 40.639 5.04 89.017 1 41.7 ? O3B UPG 343 A 1 HETATM 26 C C1' UPG . . . C 3 40.536 3.707 89.494 0 40.95 ? C1' UPG 343 A 1 HETATM 27 C C2' UPG . . . C 3 41.913 3.175 89.87 0 41.23 ? C2' UPG 343 A 1 HETATM 28 C C3' UPG . . . C 3 42.844 3.135 88.661 0 41.2 ? C3' UPG 343 A 1 HETATM 29 C C4' UPG . . . C 3 42.163 2.515 87.448 0 41.24 ? C4' UPG 343 A 1 HETATM 30 C C5' UPG . . . C 3 40.818 3.199 87.206 0 41.22 ? C5' UPG 343 A 1 HETATM 31 C C6' UPG . . . C 3 40.106 2.606 86.01 0 41.26 ? C6' UPG 343 A 1 HETATM 32 O O2' UPG . . . C 3 42.48 4.042 90.844 0 41.16 ? O2' UPG 343 A 1 HETATM 33 O O3' UPG . . . C 3 43.971 2.338 88.995 0 41.22 ? O3' UPG 343 A 1 HETATM 34 O O4' UPG . . . C 3 42.999 2.78 86.33 0 41.23 ? O4' UPG 343 A 1 HETATM 35 O O5' UPG . . . C 3 39.988 3.03 88.364 0 41.25 ? O5' UPG 343 A 1 HETATM 36 O O6' UPG . . . C 3 39.228 1.579 86.462 0 41.27 ? O6' UPG 343 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #