data_3FCW # _model_server_result.job_id tsd8tU1No0Hnt10_PZnNmw _model_server_result.datetime_utc '2025-07-23 04:21:50' _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 3fcw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":138}' # _entry.id 3FCW # _exptl.entry_id 3FCW _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 6 _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 3FCW _cell.length_a 80.994 _cell.length_b 152.812 _cell.length_c 186.554 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FCW _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,K,L,O,P,S,U,W 1 1,2 B,D,F,I,J,M,N,Q,R,T,V,X 2 1,3 # 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_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 161.988 0 93.277 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N 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 H O3B UDP . A UDP 138 1_555 G MG MG . A MG 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 L O1A UDP . C UDP 138 1_555 K MG MG . C MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc3 K MG MG . C MG 162 1_555 U O HOH . C HOH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 N O1A UDP . D UDP 138 1_555 M MG MG . D MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? # _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 3FCW _atom_sites.fract_transf_matrix[1][1] 0.012347 _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] 0.006544 _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] 0.00536 _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 G 2 MG A 1 160 160 MG MG . H 3 UDP A 1 138 160 UDP UDP . I 2 MG B 1 161 161 MG MG . J 3 UDP B 1 138 161 UDP UDP . K 2 MG C 1 162 162 MG MG . L 3 UDP C 1 138 162 UDP UDP . M 2 MG D 1 163 163 MG MG . N 3 UDP D 1 138 163 UDP UDP . O 2 MG E 1 164 164 MG MG . P 3 UDP E 1 138 164 UDP UDP . Q 2 MG F 1 165 165 MG MG . R 3 UDP F 1 138 165 UDP UDP . S 4 HOH A 1 139 3 HOH HOH . S 4 HOH A 2 140 5 HOH HOH . S 4 HOH A 3 141 7 HOH HOH . S 4 HOH A 4 142 16 HOH HOH . S 4 HOH A 5 143 25 HOH HOH . S 4 HOH A 6 144 28 HOH HOH . S 4 HOH A 7 145 29 HOH HOH . S 4 HOH A 8 146 33 HOH HOH . S 4 HOH A 9 147 36 HOH HOH . S 4 HOH A 10 148 39 HOH HOH . S 4 HOH A 11 149 60 HOH HOH . S 4 HOH A 12 150 125 HOH HOH . S 4 HOH A 13 151 127 HOH HOH . S 4 HOH A 14 155 155 HOH HOH . S 4 HOH A 15 163 163 HOH HOH . S 4 HOH A 16 186 186 HOH HOH . S 4 HOH A 17 188 188 HOH HOH . S 4 HOH A 18 190 190 HOH HOH . S 4 HOH A 19 204 204 HOH HOH . S 4 HOH A 20 220 220 HOH HOH . S 4 HOH A 21 222 222 HOH HOH . S 4 HOH A 22 226 226 HOH HOH . S 4 HOH A 23 227 227 HOH HOH . S 4 HOH A 24 232 232 HOH HOH . S 4 HOH A 25 238 238 HOH HOH . S 4 HOH A 26 256 256 HOH HOH . S 4 HOH A 27 268 268 HOH HOH . S 4 HOH A 28 272 272 HOH HOH . S 4 HOH A 29 276 276 HOH HOH . S 4 HOH A 30 278 278 HOH HOH . S 4 HOH A 31 283 283 HOH HOH . S 4 HOH A 32 290 290 HOH HOH . S 4 HOH A 33 294 294 HOH HOH . S 4 HOH A 34 299 299 HOH HOH . S 4 HOH A 35 300 300 HOH HOH . T 4 HOH B 1 139 30 HOH HOH . T 4 HOH B 2 140 42 HOH HOH . T 4 HOH B 3 141 44 HOH HOH . T 4 HOH B 4 142 45 HOH HOH . T 4 HOH B 5 143 47 HOH HOH . T 4 HOH B 6 144 65 HOH HOH . T 4 HOH B 7 145 68 HOH HOH . T 4 HOH B 8 146 76 HOH HOH . T 4 HOH B 9 147 87 HOH HOH . T 4 HOH B 10 148 92 HOH HOH . T 4 HOH B 11 149 96 HOH HOH . T 4 HOH B 12 150 99 HOH HOH . T 4 HOH B 13 151 105 HOH HOH . T 4 HOH B 14 153 153 HOH HOH . T 4 HOH B 15 160 160 HOH HOH . T 4 HOH B 16 185 185 HOH HOH . T 4 HOH B 17 216 216 HOH HOH . T 4 HOH B 18 231 231 HOH HOH . T 4 HOH B 19 261 261 HOH HOH . T 4 HOH B 20 274 274 HOH HOH . T 4 HOH B 21 287 287 HOH HOH . T 4 HOH B 22 291 291 HOH HOH . T 4 HOH B 23 296 296 HOH HOH . T 4 HOH B 24 301 301 HOH HOH . U 4 HOH C 1 139 4 HOH HOH . U 4 HOH C 2 140 6 HOH HOH . U 4 HOH C 3 141 8 HOH HOH . U 4 HOH C 4 142 9 HOH HOH . U 4 HOH C 5 143 10 HOH HOH . U 4 HOH C 6 144 12 HOH HOH . U 4 HOH C 7 145 13 HOH HOH . U 4 HOH C 8 146 15 HOH HOH . U 4 HOH C 9 147 19 HOH HOH . U 4 HOH C 10 148 22 HOH HOH . U 4 HOH C 11 149 26 HOH HOH . U 4 HOH C 12 150 27 HOH HOH . U 4 HOH C 13 151 31 HOH HOH . U 4 HOH C 14 152 152 HOH HOH . U 4 HOH C 15 153 48 HOH HOH . U 4 HOH C 16 154 51 HOH HOH . U 4 HOH C 17 155 54 HOH HOH . U 4 HOH C 18 156 58 HOH HOH . U 4 HOH C 19 157 78 HOH HOH . U 4 HOH C 20 158 95 HOH HOH . U 4 HOH C 21 159 108 HOH HOH . U 4 HOH C 22 160 110 HOH HOH . U 4 HOH C 23 161 161 HOH HOH . U 4 HOH C 24 163 111 HOH HOH . U 4 HOH C 25 164 115 HOH HOH . U 4 HOH C 26 165 124 HOH HOH . U 4 HOH C 27 166 131 HOH HOH . U 4 HOH C 28 167 162 HOH HOH . U 4 HOH C 29 174 174 HOH HOH . U 4 HOH C 30 177 177 HOH HOH . U 4 HOH C 31 206 206 HOH HOH . U 4 HOH C 32 208 208 HOH HOH . U 4 HOH C 33 251 251 HOH HOH . U 4 HOH C 34 253 253 HOH HOH . U 4 HOH C 35 264 264 HOH HOH . U 4 HOH C 36 266 266 HOH HOH . U 4 HOH C 37 270 270 HOH HOH . U 4 HOH C 38 273 273 HOH HOH . U 4 HOH C 39 277 277 HOH HOH . U 4 HOH C 40 281 281 HOH HOH . U 4 HOH C 41 288 288 HOH HOH . U 4 HOH C 42 292 292 HOH HOH . V 4 HOH D 1 139 57 HOH HOH . V 4 HOH D 2 140 140 HOH HOH . V 4 HOH D 3 141 141 HOH HOH . V 4 HOH D 4 142 59 HOH HOH . V 4 HOH D 5 143 62 HOH HOH . V 4 HOH D 6 144 144 HOH HOH . V 4 HOH D 7 145 63 HOH HOH . V 4 HOH D 8 146 146 HOH HOH . V 4 HOH D 9 147 66 HOH HOH . V 4 HOH D 10 148 69 HOH HOH . V 4 HOH D 11 149 80 HOH HOH . V 4 HOH D 12 150 89 HOH HOH . V 4 HOH D 13 151 120 HOH HOH . V 4 HOH D 14 152 138 HOH HOH . V 4 HOH D 15 154 154 HOH HOH . V 4 HOH D 16 167 167 HOH HOH . V 4 HOH D 17 175 175 HOH HOH . V 4 HOH D 18 182 182 HOH HOH . V 4 HOH D 19 195 195 HOH HOH . V 4 HOH D 20 221 221 HOH HOH . V 4 HOH D 21 233 233 HOH HOH . V 4 HOH D 22 234 234 HOH HOH . V 4 HOH D 23 237 237 HOH HOH . V 4 HOH D 24 240 240 HOH HOH . V 4 HOH D 25 254 254 HOH HOH . V 4 HOH D 26 255 255 HOH HOH . V 4 HOH D 27 257 257 HOH HOH . V 4 HOH D 28 259 259 HOH HOH . V 4 HOH D 29 260 260 HOH HOH . V 4 HOH D 30 262 262 HOH HOH . V 4 HOH D 31 263 263 HOH HOH . V 4 HOH D 32 267 267 HOH HOH . V 4 HOH D 33 280 280 HOH HOH . V 4 HOH D 34 286 286 HOH HOH . V 4 HOH D 35 297 297 HOH HOH . V 4 HOH D 36 298 298 HOH HOH . W 4 HOH E 1 139 1 HOH HOH . W 4 HOH E 2 140 17 HOH HOH . W 4 HOH E 3 141 23 HOH HOH . W 4 HOH E 4 142 38 HOH HOH . W 4 HOH E 5 143 41 HOH HOH . W 4 HOH E 6 144 50 HOH HOH . W 4 HOH E 7 145 52 HOH HOH . W 4 HOH E 8 146 53 HOH HOH . W 4 HOH E 9 147 55 HOH HOH . W 4 HOH E 10 148 56 HOH HOH . W 4 HOH E 11 149 74 HOH HOH . W 4 HOH E 12 150 75 HOH HOH . W 4 HOH E 13 151 77 HOH HOH . W 4 HOH E 14 152 84 HOH HOH . W 4 HOH E 15 153 93 HOH HOH . W 4 HOH E 16 154 100 HOH HOH . W 4 HOH E 17 155 101 HOH HOH . W 4 HOH E 18 156 114 HOH HOH . W 4 HOH E 19 172 172 HOH HOH . W 4 HOH E 20 179 179 HOH HOH . W 4 HOH E 21 189 189 HOH HOH . W 4 HOH E 22 214 214 HOH HOH . W 4 HOH E 23 239 239 HOH HOH . W 4 HOH E 24 271 271 HOH HOH . W 4 HOH E 25 275 275 HOH HOH . W 4 HOH E 26 282 282 HOH HOH . W 4 HOH E 27 289 289 HOH HOH . W 4 HOH E 28 293 293 HOH HOH . W 4 HOH E 29 295 295 HOH HOH . W 4 HOH E 30 302 302 HOH HOH . X 4 HOH F 1 139 2 HOH HOH . X 4 HOH F 2 140 14 HOH HOH . X 4 HOH F 3 141 24 HOH HOH . X 4 HOH F 4 142 37 HOH HOH . X 4 HOH F 5 143 70 HOH HOH . X 4 HOH F 6 144 72 HOH HOH . X 4 HOH F 7 145 83 HOH HOH . X 4 HOH F 8 146 94 HOH HOH . X 4 HOH F 9 157 157 HOH HOH . X 4 HOH F 10 158 158 HOH HOH . X 4 HOH F 11 159 159 HOH HOH . X 4 HOH F 12 166 166 HOH HOH . X 4 HOH F 13 192 192 HOH HOH . X 4 HOH F 14 201 201 HOH HOH . X 4 HOH F 15 215 215 HOH HOH . X 4 HOH F 16 225 225 HOH HOH . X 4 HOH F 17 245 245 HOH HOH . X 4 HOH F 18 250 250 HOH HOH . X 4 HOH F 19 252 252 HOH HOH . X 4 HOH F 20 265 265 HOH HOH . X 4 HOH F 21 269 269 HOH HOH . X 4 HOH F 22 279 279 HOH HOH . X 4 HOH F 23 284 284 HOH HOH . X 4 HOH F 24 285 285 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 . . . R 3 51.535 52.062 43.514 1 74.33 ? N1 UDP 138 F 1 HETATM 2 C C2 UDP . . . R 3 51.266 53.289 42.931 1 74.94 ? C2 UDP 138 F 1 HETATM 3 N N3 UDP . . . R 3 50.561 54.255 43.628 1 75.44 ? N3 UDP 138 F 1 HETATM 4 C C4 UDP . . . R 3 50.119 53.993 44.912 1 81.1 ? C4 UDP 138 F 1 HETATM 5 C C5 UDP . . . R 3 50.393 52.75 45.484 1 78.09 ? C5 UDP 138 F 1 HETATM 6 C C6 UDP . . . R 3 50.933 51.737 44.699 1 75.57 ? C6 UDP 138 F 1 HETATM 7 O O2 UDP . . . R 3 51.659 53.519 41.789 1 72.31 ? O2 UDP 138 F 1 HETATM 8 O O4 UDP . . . R 3 49.491 54.846 45.548 1 75.84 ? O4 UDP 138 F 1 HETATM 9 C C1' UDP . . . R 3 52.28 51.037 42.756 1 70.39 ? C1' UDP 138 F 1 HETATM 10 C C2' UDP . . . R 3 53.694 50.836 43.287 1 71.27 ? C2' UDP 138 F 1 HETATM 11 O O2' UDP . . . R 3 54.565 50.588 42.208 1 66.36 ? O2' UDP 138 F 1 HETATM 12 C C3' UDP . . . R 3 53.598 49.587 44.135 1 69.63 ? C3' UDP 138 F 1 HETATM 13 C C4' UDP . . . R 3 52.48 48.821 43.446 1 73.64 ? C4' UDP 138 F 1 HETATM 14 O O4' UDP . . . R 3 51.617 49.795 42.891 1 73.6 ? O4' UDP 138 F 1 HETATM 15 O O3' UDP . . . R 3 54.798 48.843 44.116 1 63.27 ? O3' UDP 138 F 1 HETATM 16 C C5' UDP . . . R 3 51.71 47.877 44.37 1 75.79 ? C5' UDP 138 F 1 HETATM 17 O O5' UDP . . . R 3 51.114 48.575 45.442 1 76.67 ? O5' UDP 138 F 1 HETATM 18 P PA UDP . . . R 3 51.448 48.055 46.929 1 80.64 ? PA UDP 138 F 1 HETATM 19 O O1A UDP . . . R 3 51.024 46.636 47.069 1 75.54 ? O1A UDP 138 F 1 HETATM 20 O O2A UDP . . . R 3 50.829 48.963 47.925 1 74.62 ? O2A UDP 138 F 1 HETATM 21 O O3A UDP . . . R 3 53.057 48.168 46.94 1 79.99 ? O3A UDP 138 F 1 HETATM 22 P PB UDP . . . R 3 54.037 46.952 47.362 1 73.34 ? PB UDP 138 F 1 HETATM 23 O O1B UDP . . . R 3 54.834 47.402 48.519 1 69.62 ? O1B UDP 138 F 1 HETATM 24 O O2B UDP . . . R 3 54.916 46.619 46.208 1 68.38 ? O2B UDP 138 F 1 HETATM 25 O O3B UDP . . . R 3 53.237 45.765 47.754 1 68.83 ? O3B UDP 138 F 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #