data_3QVB # _model_server_result.job_id 0yFRRGh3FQz1tj7bFm1y-w _model_server_result.datetime_utc '2024-11-16 07:38:21' _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 3qvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":264}' # _entry.id 3QVB # _exptl.entry_id 3QVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 90 _cell.angle_gamma 90 _cell.entry_id 3QVB _cell.length_a 57.4 _cell.length_b 100.97 _cell.length_c 48.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _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,E,F,G,H,I _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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 57.4 0 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 103 A ASP 102 1_555 B MN MN . A MN 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc2 A OD1 ASP 105 A ASP 104 1_555 B MN MN . A MN 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc3 A NE2 HIS 213 A HIS 212 1_555 B MN MN . A MN 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc4 B MN MN . A MN 263 1_555 C O2B UDP . A UDP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc5 B MN MN . A MN 263 1_555 C O1A UDP . A UDP 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 367 n n N1 C6 UDP sing 368 n n N1 C1' UDP sing 369 n n C2 N3 UDP sing 370 n n C2 O2 UDP doub 371 n n N3 C4 UDP sing 372 n n N3 HN3 UDP sing 373 n n C4 C5 UDP sing 374 n n C4 O4 UDP doub 375 n n C5 C6 UDP doub 376 n n C5 H5 UDP sing 377 n n C6 H6 UDP sing 378 n n C1' C2' UDP sing 379 n n C1' O4' UDP sing 380 n n C1' H1' UDP sing 381 n n C2' O2' UDP sing 382 n n C2' C3' UDP sing 383 n n C2' H2' UDP sing 384 n n O2' HO2' UDP sing 385 n n C3' C4' UDP sing 386 n n C3' O3' UDP sing 387 n n C3' H3' UDP sing 388 n n C4' O4' UDP sing 389 n n C4' C5' UDP sing 390 n n C4' H4' UDP sing 391 n n O3' HO3' UDP sing 392 n n C5' O5' UDP sing 393 n n C5' "H5'1" UDP sing 394 n n C5' "H5'2" UDP sing 395 n n O5' PA UDP sing 396 n n PA O1A UDP doub 397 n n PA O2A UDP sing 398 n n PA O3A UDP sing 399 n n O2A HOA2 UDP sing 400 n n O3A PB UDP sing 401 n n PB O1B UDP doub 402 n n PB O2B UDP sing 403 n n PB O3B UDP sing 404 n n O2B HOB2 UDP sing 405 n n O3B HOB3 UDP sing 406 n n # _atom_sites.entry_id 3QVB _atom_sites.fract_transf_matrix[1][1] 0.017422 _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] 0.009904 _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] 0.020433 _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 MN A 1 263 1 MN MN . C 3 UDP A 1 264 1 UDP UDP . D 4 EDO A 1 265 1 EDO EDO . E 4 EDO A 1 266 2 EDO EDO . F 4 EDO A 1 267 3 EDO EDO . G 4 EDO A 1 268 4 EDO EDO . H 4 EDO A 1 269 5 EDO EDO . I 5 HOH A 1 270 2 HOH HOH . I 5 HOH A 2 271 3 HOH HOH . I 5 HOH A 3 272 5 HOH HOH . I 5 HOH A 4 273 7 HOH HOH . I 5 HOH A 5 274 8 HOH HOH . I 5 HOH A 6 275 9 HOH HOH . I 5 HOH A 7 276 11 HOH HOH . I 5 HOH A 8 277 12 HOH HOH . I 5 HOH A 9 278 13 HOH HOH . I 5 HOH A 10 279 15 HOH HOH . I 5 HOH A 11 280 16 HOH HOH . I 5 HOH A 12 281 17 HOH HOH . I 5 HOH A 13 282 18 HOH HOH . I 5 HOH A 14 283 19 HOH HOH . I 5 HOH A 15 284 21 HOH HOH . I 5 HOH A 16 285 23 HOH HOH . I 5 HOH A 17 286 24 HOH HOH . I 5 HOH A 18 287 25 HOH HOH . I 5 HOH A 19 288 27 HOH HOH . I 5 HOH A 20 289 28 HOH HOH . I 5 HOH A 21 290 29 HOH HOH . I 5 HOH A 22 291 30 HOH HOH . I 5 HOH A 23 292 31 HOH HOH . I 5 HOH A 24 293 32 HOH HOH . I 5 HOH A 25 294 33 HOH HOH . I 5 HOH A 26 295 34 HOH HOH . I 5 HOH A 27 296 35 HOH HOH . I 5 HOH A 28 297 36 HOH HOH . I 5 HOH A 29 298 38 HOH HOH . I 5 HOH A 30 299 39 HOH HOH . I 5 HOH A 31 300 41 HOH HOH . I 5 HOH A 32 301 42 HOH HOH . I 5 HOH A 33 302 43 HOH HOH . I 5 HOH A 34 303 44 HOH HOH . I 5 HOH A 35 304 45 HOH HOH . I 5 HOH A 36 305 46 HOH HOH . I 5 HOH A 37 306 48 HOH HOH . I 5 HOH A 38 307 49 HOH HOH . I 5 HOH A 39 308 50 HOH HOH . I 5 HOH A 40 309 51 HOH HOH . I 5 HOH A 41 310 54 HOH HOH . I 5 HOH A 42 311 55 HOH HOH . I 5 HOH A 43 312 56 HOH HOH . I 5 HOH A 44 313 57 HOH HOH . I 5 HOH A 45 314 58 HOH HOH . I 5 HOH A 46 315 59 HOH HOH . I 5 HOH A 47 316 60 HOH HOH . I 5 HOH A 48 317 61 HOH HOH . I 5 HOH A 49 318 63 HOH HOH . I 5 HOH A 50 319 64 HOH HOH . I 5 HOH A 51 320 66 HOH HOH . I 5 HOH A 52 321 67 HOH HOH . I 5 HOH A 53 322 68 HOH HOH . I 5 HOH A 54 323 69 HOH HOH . I 5 HOH A 55 324 71 HOH HOH . I 5 HOH A 56 325 72 HOH HOH . I 5 HOH A 57 326 73 HOH HOH . I 5 HOH A 58 327 74 HOH HOH . I 5 HOH A 59 328 75 HOH HOH . I 5 HOH A 60 329 76 HOH HOH . I 5 HOH A 61 330 77 HOH HOH . I 5 HOH A 62 331 78 HOH HOH . I 5 HOH A 63 332 79 HOH HOH . I 5 HOH A 64 333 80 HOH HOH . I 5 HOH A 65 334 81 HOH HOH . I 5 HOH A 66 335 82 HOH HOH . I 5 HOH A 67 336 83 HOH HOH . I 5 HOH A 68 337 84 HOH HOH . I 5 HOH A 69 338 85 HOH HOH . I 5 HOH A 70 339 86 HOH HOH . I 5 HOH A 71 340 87 HOH HOH . I 5 HOH A 72 341 88 HOH HOH . I 5 HOH A 73 342 89 HOH HOH . I 5 HOH A 74 343 90 HOH HOH . I 5 HOH A 75 344 91 HOH HOH . I 5 HOH A 76 345 92 HOH HOH . I 5 HOH A 77 346 93 HOH HOH . I 5 HOH A 78 347 94 HOH HOH . I 5 HOH A 79 348 95 HOH HOH . I 5 HOH A 80 349 96 HOH HOH . I 5 HOH A 81 350 97 HOH HOH . I 5 HOH A 82 351 98 HOH HOH . I 5 HOH A 83 352 102 HOH HOH . I 5 HOH A 84 353 103 HOH HOH . I 5 HOH A 85 354 105 HOH HOH . I 5 HOH A 86 355 106 HOH HOH . I 5 HOH A 87 356 107 HOH HOH . I 5 HOH A 88 357 108 HOH HOH . I 5 HOH A 89 358 110 HOH HOH . I 5 HOH A 90 359 111 HOH HOH . I 5 HOH A 91 360 113 HOH HOH . I 5 HOH A 92 361 114 HOH HOH . I 5 HOH A 93 362 115 HOH HOH . I 5 HOH A 94 363 116 HOH HOH . I 5 HOH A 95 364 117 HOH HOH . I 5 HOH A 96 365 118 HOH HOH . I 5 HOH A 97 366 119 HOH HOH . I 5 HOH A 98 367 120 HOH HOH . I 5 HOH A 99 368 121 HOH HOH . I 5 HOH A 100 369 122 HOH HOH . I 5 HOH A 101 370 123 HOH HOH . I 5 HOH A 102 371 124 HOH HOH . I 5 HOH A 103 372 125 HOH HOH . I 5 HOH A 104 373 127 HOH HOH . I 5 HOH A 105 374 128 HOH HOH . I 5 HOH A 106 375 129 HOH HOH . I 5 HOH A 107 376 130 HOH HOH . I 5 HOH A 108 377 131 HOH HOH . I 5 HOH A 109 378 132 HOH HOH . I 5 HOH A 110 379 133 HOH HOH . I 5 HOH A 111 380 134 HOH HOH . I 5 HOH A 112 381 135 HOH HOH . I 5 HOH A 113 382 138 HOH HOH . I 5 HOH A 114 383 139 HOH HOH . I 5 HOH A 115 384 140 HOH HOH . I 5 HOH A 116 385 141 HOH HOH . I 5 HOH A 117 386 142 HOH HOH . I 5 HOH A 118 387 144 HOH HOH . I 5 HOH A 119 388 145 HOH HOH . I 5 HOH A 120 389 146 HOH HOH . I 5 HOH A 121 390 147 HOH HOH . I 5 HOH A 122 391 148 HOH HOH . I 5 HOH A 123 392 149 HOH HOH . I 5 HOH A 124 393 150 HOH HOH . I 5 HOH A 125 394 151 HOH HOH . I 5 HOH A 126 395 152 HOH HOH . I 5 HOH A 127 396 153 HOH HOH . I 5 HOH A 128 397 154 HOH HOH . I 5 HOH A 129 398 155 HOH HOH . I 5 HOH A 130 399 156 HOH HOH . I 5 HOH A 131 400 157 HOH HOH . I 5 HOH A 132 401 158 HOH HOH . I 5 HOH A 133 402 159 HOH HOH . I 5 HOH A 134 403 160 HOH HOH . I 5 HOH A 135 404 161 HOH HOH . I 5 HOH A 136 405 162 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 N N1 UDP . . . C 3 19.175 19.57 3.993 0.7 34.78 ? N1 UDP 264 A 1 HETATM 2 C C2 UDP . . . C 3 18.263 20.383 3.327 0.7 37.04 ? C2 UDP 264 A 1 HETATM 3 N N3 UDP . . . C 3 18.637 20.89 2.082 0.7 37.75 ? N3 UDP 264 A 1 HETATM 4 C C4 UDP . . . C 3 19.879 20.61 1.513 0.7 36.33 ? C4 UDP 264 A 1 HETATM 5 C C5 UDP . . . C 3 20.779 19.804 2.179 0.7 36.23 ? C5 UDP 264 A 1 HETATM 6 C C6 UDP . . . C 3 20.339 19.173 3.342 0.7 36.04 ? C6 UDP 264 A 1 HETATM 7 O O2 UDP . . . C 3 17.129 20.648 3.803 0.7 34.51 ? O2 UDP 264 A 1 HETATM 8 O O4 UDP . . . C 3 20.182 21.062 0.416 0.7 35.55 ? O4 UDP 264 A 1 HETATM 9 C C1' UDP . . . C 3 18.849 19.017 5.345 0.7 32.42 ? C1' UDP 264 A 1 HETATM 10 C C2' UDP . . . C 3 17.794 17.925 5.288 0.7 30.21 ? C2' UDP 264 A 1 HETATM 11 O O2' UDP . . . C 3 16.974 17.848 6.449 0.7 17.97 ? O2' UDP 264 A 1 HETATM 12 C C3' UDP . . . C 3 18.665 16.705 5.135 0.7 32.81 ? C3' UDP 264 A 1 HETATM 13 C C4' UDP . . . C 3 19.869 17.042 6.031 0.7 36.07 ? C4' UDP 264 A 1 HETATM 14 O O4' UDP . . . C 3 20.018 18.452 5.962 0.7 34.74 ? O4' UDP 264 A 1 HETATM 15 O O3' UDP . . . C 3 17.955 15.534 5.5 0.7 31.83 ? O3' UDP 264 A 1 HETATM 16 C C5' UDP . . . C 3 21.183 16.313 5.7 0.7 37.09 ? C5' UDP 264 A 1 HETATM 17 O O5' UDP . . . C 3 21.39 16.259 4.308 0.7 39.79 ? O5' UDP 264 A 1 HETATM 18 P PA UDP . . . C 3 21.086 14.947 3.412 0.7 41.02 ? PA UDP 264 A 1 HETATM 19 O O1A UDP . . . C 3 19.966 14.211 4.04 0.7 40.24 ? O1A UDP 264 A 1 HETATM 20 O O2A UDP . . . C 3 20.708 15.334 2.022 0.7 41.5 ? O2A UDP 264 A 1 HETATM 21 O O3A UDP . . . C 3 22.489 14.099 3.423 0.7 38.44 ? O3A UDP 264 A 1 HETATM 22 P PB UDP . . . C 3 22.55 12.469 3.454 0.7 37.68 ? PB UDP 264 A 1 HETATM 23 O O1B UDP . . . C 3 22.138 11.959 2.117 0.7 33.7 ? O1B UDP 264 A 1 HETATM 24 O O2B UDP . . . C 3 21.588 12.027 4.527 0.7 34.27 ? O2B UDP 264 A 1 HETATM 25 O O3B UDP . . . C 3 23.924 11.924 3.692 0.7 35.09 ? O3B UDP 264 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #