data_6CI4 # _model_server_result.job_id quB0Vx9gdomP4oGXnCU81A _model_server_result.datetime_utc '2024-11-29 04:09:14' _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 6ci4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6CI4 # _exptl.entry_id 6CI4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 590.37 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R,3R,4S,5R,6S)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen 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 103.474 _cell.angle_gamma 90 _cell.entry_id 6CI4 _cell.length_a 96.425 _cell.length_b 73.78 _cell.length_c 41.805 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CI4 _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 ? _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H28 N4 O15 P2' _chem_comp.formula_weight 590.37 _chem_comp.id F5P _chem_comp.mon_nstd_flag . _chem_comp.name '(2R,3R,4S,5R,6S)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-4-amino-4,6-dideoxy-L-AltNAc # 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 O27 C16 F5P sing 70 n n O28 C15 F5P sing 71 n n C14 O26 F5P sing 72 n n C14 C15 F5P sing 73 n n C14 C13 F5P sing 74 n n C16 C17 F5P sing 75 n n C16 C15 F5P sing 76 n n O26 C17 F5P sing 77 n n C17 N18 F5P sing 78 n n C13 O12 F5P sing 79 n n O25 C19 F5P doub 80 n n N18 C19 F5P sing 81 n n N18 C23 F5P sing 82 n n C19 N20 F5P sing 83 n n O12 P11 F5P sing 84 n n C23 C22 F5P doub 85 n n O10 P11 F5P sing 86 n n O10 P08 F5P sing 87 n n O31 P08 F5P doub 88 n n O30 P11 F5P doub 89 n n N20 C21 F5P sing 90 n n P11 O29 F5P sing 91 n n P08 O09 F5P sing 92 n n P08 O07 F5P sing 93 n n C22 C21 F5P sing 94 n n C21 O24 F5P doub 95 n n O07 C06 F5P sing 96 n n C06 C32 F5P sing 97 n n C06 O05 F5P sing 98 n n C32 N33 F5P sing 99 n n C32 C37 F5P sing 100 n n O38 C37 F5P sing 101 n n O36 C34 F5P doub 102 n n O05 C03 F5P sing 103 n n N33 C34 F5P sing 104 n n C34 C35 F5P sing 105 n n C37 C02 F5P sing 106 n n C03 C02 F5P sing 107 n n C03 C04 F5P sing 108 n n C02 N01 F5P sing 109 n n C13 H132 F5P sing 110 n n C13 H131 F5P sing 111 n n C15 H151 F5P sing 112 n n C17 H171 F5P sing 113 n n C22 H221 F5P sing 114 n n C02 H021 F5P sing 115 n n C03 H031 F5P sing 116 n n C04 H043 F5P sing 117 n n C04 H042 F5P sing 118 n n C04 H041 F5P sing 119 n n C06 H061 F5P sing 120 n n C14 H141 F5P sing 121 n n C16 H161 F5P sing 122 n n C23 H231 F5P sing 123 n n C32 H321 F5P sing 124 n n C35 H352 F5P sing 125 n n C35 H353 F5P sing 126 n n C35 H351 F5P sing 127 n n C37 H371 F5P sing 128 n n N01 H1 F5P sing 129 n n N01 H012 F5P sing 130 n n N20 H201 F5P sing 131 n n N33 H331 F5P sing 132 n n O09 H2 F5P sing 133 n n O27 H271 F5P sing 134 n n O28 H281 F5P sing 135 n n O29 H3 F5P sing 136 n n O38 H381 F5P sing 137 n n # _atom_sites.entry_id 6CI4 _atom_sites.fract_transf_matrix[1][1] 0.010371 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002485 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013554 _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] 0.024598 _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 F5P A 1 301 216 F5P LIG . C 3 HOH A 1 401 230 HOH HOH . C 3 HOH A 2 402 322 HOH HOH . C 3 HOH A 3 403 313 HOH HOH . C 3 HOH A 4 404 259 HOH HOH . C 3 HOH A 5 405 281 HOH HOH . C 3 HOH A 6 406 231 HOH HOH . C 3 HOH A 7 407 265 HOH HOH . C 3 HOH A 8 408 246 HOH HOH . C 3 HOH A 9 409 323 HOH HOH . C 3 HOH A 10 410 252 HOH HOH . C 3 HOH A 11 411 319 HOH HOH . C 3 HOH A 12 412 280 HOH HOH . C 3 HOH A 13 413 304 HOH HOH . C 3 HOH A 14 414 218 HOH HOH . C 3 HOH A 15 415 257 HOH HOH . C 3 HOH A 16 416 267 HOH HOH . C 3 HOH A 17 417 273 HOH HOH . C 3 HOH A 18 418 298 HOH HOH . C 3 HOH A 19 419 331 HOH HOH . C 3 HOH A 20 420 309 HOH HOH . C 3 HOH A 21 421 277 HOH HOH . C 3 HOH A 22 422 225 HOH HOH . C 3 HOH A 23 423 241 HOH HOH . C 3 HOH A 24 424 266 HOH HOH . C 3 HOH A 25 425 268 HOH HOH . C 3 HOH A 26 426 290 HOH HOH . C 3 HOH A 27 427 256 HOH HOH . C 3 HOH A 28 428 229 HOH HOH . C 3 HOH A 29 429 301 HOH HOH . C 3 HOH A 30 430 276 HOH HOH . C 3 HOH A 31 431 221 HOH HOH . C 3 HOH A 32 432 306 HOH HOH . C 3 HOH A 33 433 236 HOH HOH . C 3 HOH A 34 434 243 HOH HOH . C 3 HOH A 35 435 217 HOH HOH . C 3 HOH A 36 436 269 HOH HOH . C 3 HOH A 37 437 291 HOH HOH . C 3 HOH A 38 438 263 HOH HOH . C 3 HOH A 39 439 244 HOH HOH . C 3 HOH A 40 440 242 HOH HOH . C 3 HOH A 41 441 222 HOH HOH . C 3 HOH A 42 442 219 HOH HOH . C 3 HOH A 43 443 224 HOH HOH . C 3 HOH A 44 444 248 HOH HOH . C 3 HOH A 45 445 227 HOH HOH . C 3 HOH A 46 446 284 HOH HOH . C 3 HOH A 47 447 228 HOH HOH . C 3 HOH A 48 448 282 HOH HOH . C 3 HOH A 49 449 271 HOH HOH . C 3 HOH A 50 450 260 HOH HOH . C 3 HOH A 51 451 258 HOH HOH . C 3 HOH A 52 452 261 HOH HOH . C 3 HOH A 53 453 289 HOH HOH . C 3 HOH A 54 454 278 HOH HOH . C 3 HOH A 55 455 250 HOH HOH . C 3 HOH A 56 456 240 HOH HOH . C 3 HOH A 57 457 255 HOH HOH . C 3 HOH A 58 458 305 HOH HOH . C 3 HOH A 59 459 253 HOH HOH . C 3 HOH A 60 460 307 HOH HOH . C 3 HOH A 61 461 220 HOH HOH . C 3 HOH A 62 462 238 HOH HOH . C 3 HOH A 63 463 327 HOH HOH . C 3 HOH A 64 464 254 HOH HOH . C 3 HOH A 65 465 285 HOH HOH . C 3 HOH A 66 466 328 HOH HOH . C 3 HOH A 67 467 295 HOH HOH . C 3 HOH A 68 468 249 HOH HOH . C 3 HOH A 69 469 299 HOH HOH . C 3 HOH A 70 470 333 HOH HOH . C 3 HOH A 71 471 286 HOH HOH . C 3 HOH A 72 472 262 HOH HOH . C 3 HOH A 73 473 310 HOH HOH . C 3 HOH A 74 474 326 HOH HOH . C 3 HOH A 75 475 321 HOH HOH . C 3 HOH A 76 476 226 HOH HOH . C 3 HOH A 77 477 330 HOH HOH . C 3 HOH A 78 478 293 HOH HOH . C 3 HOH A 79 479 294 HOH HOH . C 3 HOH A 80 480 237 HOH HOH . C 3 HOH A 81 481 311 HOH HOH . C 3 HOH A 82 482 274 HOH HOH . C 3 HOH A 83 483 275 HOH HOH . C 3 HOH A 84 484 335 HOH HOH . C 3 HOH A 85 485 297 HOH HOH . C 3 HOH A 86 486 317 HOH HOH . C 3 HOH A 87 487 324 HOH HOH . C 3 HOH A 88 488 334 HOH HOH . C 3 HOH A 89 489 272 HOH HOH . C 3 HOH A 90 490 308 HOH HOH . C 3 HOH A 91 491 329 HOH HOH . C 3 HOH A 92 492 332 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 C C13 F5P . . . B 2 32.314 28.294 -1.093 1 37.79 ? C13 F5P 301 A 1 HETATM 2 C C15 F5P . . . B 2 34.901 28.105 -1.44 1 38.23 ? C15 F5P 301 A 1 HETATM 3 C C17 F5P . . . B 2 35.224 30.329 -1.46 1 37.49 ? C17 F5P 301 A 1 HETATM 4 C C21 F5P . . . B 2 36.338 31.652 2.464 1 33.25 ? C21 F5P 301 A 1 HETATM 5 C C22 F5P . . . B 2 35.004 31.084 2.264 1 35.94 ? C22 F5P 301 A 1 HETATM 6 C C02 F5P . . . B 2 30.889 22.843 6.528 1 42.04 ? C02 F5P 301 A 1 HETATM 7 C C03 F5P . . . B 2 32.234 23.252 5.959 1 34.18 ? C03 F5P 301 A 1 HETATM 8 C C04 F5P . . . B 2 33.231 23.676 7.003 1 38.69 ? C04 F5P 301 A 1 HETATM 9 C C06 F5P . . . B 2 31.244 23.964 3.928 1 35.01 ? C06 F5P 301 A 1 HETATM 10 C C14 F5P . . . B 2 33.493 28.864 -1.861 1 36.78 ? C14 F5P 301 A 1 HETATM 11 C C16 F5P . . . B 2 35.835 28.908 -1.825 1 36.06 ? C16 F5P 301 A 1 HETATM 12 C C19 F5P . . . B 2 36.915 31.327 -0.027 1 35.8 ? C19 F5P 301 A 1 HETATM 13 C C23 F5P . . . B 2 34.63 30.604 0.941 1 34.56 ? C23 F5P 301 A 1 HETATM 14 C C32 F5P . . . B 2 29.854 23.531 4.403 1 36.98 ? C32 F5P 301 A 1 HETATM 15 C C34 F5P . . . B 2 27.811 24.827 5.286 1 43.33 ? C34 F5P 301 A 1 HETATM 16 C C35 F5P . . . B 2 27.286 26.084 5.994 1 46.55 ? C35 F5P 301 A 1 HETATM 17 C C37 F5P . . . B 2 29.932 22.506 5.46 1 39.83 ? C37 F5P 301 A 1 HETATM 18 N N01 F5P . . . B 2 31.246 21.661 7.326 1 47.68 ? N01 F5P 301 A 1 HETATM 19 N N18 F5P . . . B 2 35.552 30.725 -0.194 1 35.85 ? N18 F5P 301 A 1 HETATM 20 N N20 F5P . . . B 2 37.234 31.803 1.361 1 35.18 ? N20 F5P 301 A 1 HETATM 21 N N33 F5P . . . B 2 29.243 24.728 5.057 1 35.78 ? N33 F5P 301 A 1 HETATM 22 O O05 F5P . . . B 2 32.042 24.403 5.054 1 32.98 ? O05 F5P 301 A 1 HETATM 23 O O07 F5P . . . B 2 31.132 25.001 3.077 1 31.49 ? O07 F5P 301 A 1 HETATM 24 O O09 F5P . . . B 2 33.701 25.123 2.657 1 34 -1 O09 F5P 301 A 1 HETATM 25 O O10 F5P . . . B 2 32.114 26.301 1.023 1 34.46 ? O10 F5P 301 A 1 HETATM 26 O O12 F5P . . . B 2 32.557 28.521 0.322 1 35.5 ? O12 F5P 301 A 1 HETATM 27 O O24 F5P . . . B 2 36.706 32.034 3.52 1 31.83 ? O24 F5P 301 A 1 HETATM 28 O O25 F5P . . . B 2 37.664 31.423 -0.902 1 39.71 ? O25 F5P 301 A 1 HETATM 29 O O26 F5P . . . B 2 33.713 30.117 -1.58 1 38.26 ? O26 F5P 301 A 1 HETATM 30 O O27 F5P . . . B 2 36.125 28.784 -3.269 1 35.82 ? O27 F5P 301 A 1 HETATM 31 O O28 F5P . . . B 2 34.967 26.806 -2.083 1 37.2 ? O28 F5P 301 A 1 HETATM 32 O O29 F5P . . . B 2 32.308 28.152 2.869 1 35.63 -1 O29 F5P 301 A 1 HETATM 33 O O30 F5P . . . B 2 30.238 28.033 1.308 1 37.56 ? O30 F5P 301 A 1 HETATM 34 O O31 F5P . . . B 2 32.227 23.735 1.202 1 33.75 ? O31 F5P 301 A 1 HETATM 35 O O36 F5P . . . B 2 27.114 23.952 4.933 1 48.93 ? O36 F5P 301 A 1 HETATM 36 O O38 F5P . . . B 2 30.333 21.23 4.881 1 39.52 ? O38 F5P 301 A 1 HETATM 37 P P08 F5P . . . B 2 32.329 25.012 1.976 1 36.07 ? P08 F5P 301 A 1 HETATM 38 P P11 F5P . . . B 2 31.706 27.804 1.497 1 37.06 ? P11 F5P 301 A 1 HETATM 39 H H132 F5P . . . B 2 32.238 27.343 -1.264 1 44.21 ? H132 F5P 301 A 1 HETATM 40 H H131 F5P . . . B 2 31.498 28.744 -1.362 1 44.21 ? H131 F5P 301 A 1 HETATM 41 H H151 F5P . . . B 2 34.941 28.001 -0.477 1 45.57 ? H151 F5P 301 A 1 HETATM 42 H H171 F5P . . . B 2 35.517 30.991 -2.106 1 43.95 ? H171 F5P 301 A 1 HETATM 43 H H221 F5P . . . B 2 34.42 30.993 2.981 1 42.58 ? H221 F5P 301 A 1 HETATM 44 H H021 F5P . . . B 2 30.533 23.546 7.094 1 50.34 ? H021 F5P 301 A 1 HETATM 45 H H031 F5P . . . B 2 32.599 22.511 5.451 1 41.55 ? H031 F5P 301 A 1 HETATM 46 H H043 F5P . . . B 2 32.776 24.17 7.704 1 47.25 ? H043 F5P 301 A 1 HETATM 47 H H042 F5P . . . B 2 33.905 24.243 6.595 1 47.25 ? H042 F5P 301 A 1 HETATM 48 H H041 F5P . . . B 2 33.654 22.891 7.383 1 47.25 ? H041 F5P 301 A 1 HETATM 49 H H061 F5P . . . B 2 31.685 23.22 3.488 1 42.06 ? H061 F5P 301 A 1 HETATM 50 H H141 F5P . . . B 2 33.345 28.765 -2.814 1 43.03 ? H141 F5P 301 A 1 HETATM 51 H H161 F5P . . . B 2 36.64 28.752 -1.306 1 42.8 ? H161 F5P 301 A 1 HETATM 52 H H231 F5P . . . B 2 33.784 30.242 0.808 1 40.78 ? H231 F5P 301 A 1 HETATM 53 H H321 F5P . . . B 2 29.312 23.224 3.659 1 43.77 ? H321 F5P 301 A 1 HETATM 54 H H352 F5P . . . B 2 26.597 26.496 5.451 1 53.35 ? H352 F5P 301 A 1 HETATM 55 H H353 F5P . . . B 2 28.014 26.712 6.124 1 53.35 ? H353 F5P 301 A 1 HETATM 56 H H351 F5P . . . B 2 26.916 25.837 6.856 1 53.35 ? H351 F5P 301 A 1 HETATM 57 H H371 F5P . . . B 2 29.052 22.407 5.856 1 47.26 ? H371 F5P 301 A 1 HETATM 58 H H1 F5P . . . B 2 30.567 21.087 7.327 1 57.2 ? H1 F5P 301 A 1 HETATM 59 H H012 F5P . . . B 2 31.428 21.91 8.161 1 57.2 ? H012 F5P 301 A 1 HETATM 60 H H201 F5P . . . B 2 38.016 32.127 1.512 1 41.65 ? H201 F5P 301 A 1 HETATM 61 H H331 F5P . . . B 2 29.756 25.364 5.327 1 41.88 ? H331 F5P 301 A 1 HETATM 62 H H271 F5P . . . B 2 36.947 28.952 -3.408 1 42.14 ? H271 F5P 301 A 1 HETATM 63 H H281 F5P . . . B 2 35.206 26.221 -1.514 1 44.52 ? H281 F5P 301 A 1 HETATM 64 H H381 F5P . . . B 2 29.663 20.863 4.51 1 47.09 ? H381 F5P 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 64 #