data_5UMX # _model_server_result.job_id I4uD5SRPlNOOnaafzG3BXA _model_server_result.datetime_utc '2025-07-04 23:11:12' _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 5umx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5UMX # _exptl.entry_id 5UMX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 90 _cell.angle_gamma 90 _cell.entry_id 5UMX _cell.length_a 45.059 _cell.length_b 60.915 _cell.length_c 85.659 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 C N N ? 2 D N N # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 RBF sing 277 n n N1 C10 RBF doub 278 n n C2 O2 RBF doub 279 n n C2 N3 RBF sing 280 n n N3 C4 RBF sing 281 n n N3 HN3 RBF sing 282 n n C4 O4 RBF doub 283 n n C4 C4A RBF sing 284 n n C4A N5 RBF doub 285 n n C4A C10 RBF sing 286 n n N5 C5A RBF sing 287 n n C5A C6 RBF doub 288 n y C5A C9A RBF sing 289 n y C6 C7 RBF sing 290 n y C6 HC6 RBF sing 291 n n C7 C7M RBF sing 292 n n C7 C8 RBF doub 293 n y C7M HC71 RBF sing 294 n n C7M HC72 RBF sing 295 n n C7M HC73 RBF sing 296 n n C8 C8M RBF sing 297 n n C8 C9 RBF sing 298 n y C8M HC81 RBF sing 299 n n C8M HC82 RBF sing 300 n n C8M HC83 RBF sing 301 n n C9 C9A RBF doub 302 n y C9 HC9 RBF sing 303 n n C9A N10 RBF sing 304 n n N10 C10 RBF sing 305 n n N10 C1' RBF sing 306 n n C1' C2' RBF sing 307 n n C1' HC11 RBF sing 308 n n C1' HC12 RBF sing 309 n n C2' O2' RBF sing 310 n n C2' C3' RBF sing 311 n n C2' HC2' RBF sing 312 n n O2' HO2' RBF sing 313 n n C3' O3' RBF sing 314 n n C3' C4' RBF sing 315 n n C3' HC3' RBF sing 316 n n O3' HO3' RBF sing 317 n n C4' O4' RBF sing 318 n n C4' C5' RBF sing 319 n n C4' HC4' RBF sing 320 n n O4' HO4' RBF sing 321 n n C5' O5' RBF sing 322 n n C5' HC51 RBF sing 323 n n C5' HC52 RBF sing 324 n n O5' HO5' RBF sing 325 n n # _atom_sites.entry_id 5UMX _atom_sites.fract_transf_matrix[1][1] 0.022193 _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] 0.016416 _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] 0.011674 _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 C 2 RBF B 1 201 1 RBF RBF . D 2 RBF B 1 202 2 RBF RBF . E 3 HOH A 1 201 224 HOH HOH . E 3 HOH A 2 202 92 HOH HOH . E 3 HOH A 3 203 117 HOH HOH . E 3 HOH A 4 204 42 HOH HOH . E 3 HOH A 5 205 164 HOH HOH . E 3 HOH A 6 206 28 HOH HOH . E 3 HOH A 7 207 184 HOH HOH . E 3 HOH A 8 208 67 HOH HOH . E 3 HOH A 9 209 205 HOH HOH . E 3 HOH A 10 210 154 HOH HOH . E 3 HOH A 11 211 226 HOH HOH . E 3 HOH A 12 212 148 HOH HOH . E 3 HOH A 13 213 90 HOH HOH . E 3 HOH A 14 214 132 HOH HOH . E 3 HOH A 15 215 41 HOH HOH . E 3 HOH A 16 216 24 HOH HOH . E 3 HOH A 17 217 115 HOH HOH . E 3 HOH A 18 218 3 HOH HOH . E 3 HOH A 19 219 58 HOH HOH . E 3 HOH A 20 220 73 HOH HOH . E 3 HOH A 21 221 223 HOH HOH . E 3 HOH A 22 222 155 HOH HOH . E 3 HOH A 23 223 39 HOH HOH . E 3 HOH A 24 224 169 HOH HOH . E 3 HOH A 25 225 159 HOH HOH . E 3 HOH A 26 226 11 HOH HOH . E 3 HOH A 27 227 219 HOH HOH . E 3 HOH A 28 228 84 HOH HOH . E 3 HOH A 29 229 60 HOH HOH . E 3 HOH A 30 230 172 HOH HOH . E 3 HOH A 31 231 14 HOH HOH . E 3 HOH A 32 232 48 HOH HOH . E 3 HOH A 33 233 106 HOH HOH . E 3 HOH A 34 234 12 HOH HOH . E 3 HOH A 35 235 38 HOH HOH . E 3 HOH A 36 236 105 HOH HOH . E 3 HOH A 37 237 216 HOH HOH . E 3 HOH A 38 238 32 HOH HOH . E 3 HOH A 39 239 207 HOH HOH . E 3 HOH A 40 240 174 HOH HOH . E 3 HOH A 41 241 102 HOH HOH . E 3 HOH A 42 242 121 HOH HOH . E 3 HOH A 43 243 141 HOH HOH . E 3 HOH A 44 244 94 HOH HOH . E 3 HOH A 45 245 127 HOH HOH . E 3 HOH A 46 246 17 HOH HOH . E 3 HOH A 47 247 19 HOH HOH . E 3 HOH A 48 248 29 HOH HOH . E 3 HOH A 49 249 34 HOH HOH . E 3 HOH A 50 250 99 HOH HOH . E 3 HOH A 51 251 118 HOH HOH . E 3 HOH A 52 252 5 HOH HOH . E 3 HOH A 53 253 43 HOH HOH . E 3 HOH A 54 254 71 HOH HOH . E 3 HOH A 55 255 220 HOH HOH . E 3 HOH A 56 256 162 HOH HOH . E 3 HOH A 57 257 143 HOH HOH . E 3 HOH A 58 258 144 HOH HOH . E 3 HOH A 59 259 91 HOH HOH . E 3 HOH A 60 260 81 HOH HOH . E 3 HOH A 61 261 228 HOH HOH . E 3 HOH A 62 262 158 HOH HOH . E 3 HOH A 63 263 171 HOH HOH . E 3 HOH A 64 264 173 HOH HOH . E 3 HOH A 65 265 160 HOH HOH . E 3 HOH A 66 266 150 HOH HOH . E 3 HOH A 67 267 134 HOH HOH . E 3 HOH A 68 268 70 HOH HOH . E 3 HOH A 69 269 80 HOH HOH . E 3 HOH A 70 270 167 HOH HOH . E 3 HOH A 71 271 72 HOH HOH . E 3 HOH A 72 272 13 HOH HOH . E 3 HOH A 73 273 206 HOH HOH . E 3 HOH A 74 274 63 HOH HOH . E 3 HOH A 75 275 59 HOH HOH . E 3 HOH A 76 276 77 HOH HOH . E 3 HOH A 77 277 133 HOH HOH . E 3 HOH A 78 278 89 HOH HOH . E 3 HOH A 79 279 47 HOH HOH . E 3 HOH A 80 280 27 HOH HOH . E 3 HOH A 81 281 57 HOH HOH . E 3 HOH A 82 282 15 HOH HOH . E 3 HOH A 83 283 119 HOH HOH . E 3 HOH A 84 284 22 HOH HOH . E 3 HOH A 85 285 161 HOH HOH . E 3 HOH A 86 286 241 HOH HOH . E 3 HOH A 87 287 33 HOH HOH . E 3 HOH A 88 288 125 HOH HOH . E 3 HOH A 89 289 217 HOH HOH . E 3 HOH A 90 290 166 HOH HOH . E 3 HOH A 91 291 6 HOH HOH . E 3 HOH A 92 292 200 HOH HOH . E 3 HOH A 93 293 131 HOH HOH . E 3 HOH A 94 294 142 HOH HOH . E 3 HOH A 95 295 175 HOH HOH . E 3 HOH A 96 296 78 HOH HOH . E 3 HOH A 97 297 177 HOH HOH . E 3 HOH A 98 298 152 HOH HOH . E 3 HOH A 99 299 1 HOH HOH . E 3 HOH A 100 300 209 HOH HOH . E 3 HOH A 101 301 229 HOH HOH . E 3 HOH A 102 302 126 HOH HOH . E 3 HOH A 103 303 227 HOH HOH . E 3 HOH A 104 304 230 HOH HOH . E 3 HOH A 105 305 95 HOH HOH . E 3 HOH A 106 306 151 HOH HOH . E 3 HOH A 107 307 170 HOH HOH . E 3 HOH A 108 308 176 HOH HOH . E 3 HOH A 109 309 49 HOH HOH . E 3 HOH A 110 310 116 HOH HOH . E 3 HOH A 111 311 153 HOH HOH . E 3 HOH A 112 312 213 HOH HOH . E 3 HOH A 113 313 168 HOH HOH . E 3 HOH A 114 314 83 HOH HOH . E 3 HOH A 115 315 214 HOH HOH . E 3 HOH A 116 316 201 HOH HOH . E 3 HOH A 117 317 149 HOH HOH . E 3 HOH A 118 318 215 HOH HOH . E 3 HOH A 119 319 114 HOH HOH . E 3 HOH A 120 320 124 HOH HOH . E 3 HOH A 121 321 238 HOH HOH . E 3 HOH A 122 322 183 HOH HOH . E 3 HOH A 123 323 203 HOH HOH . E 3 HOH A 124 324 156 HOH HOH . E 3 HOH A 125 325 208 HOH HOH . E 3 HOH A 126 326 135 HOH HOH . E 3 HOH A 127 327 222 HOH HOH . E 3 HOH A 128 328 66 HOH HOH . E 3 HOH A 129 329 157 HOH HOH . F 3 HOH B 1 301 202 HOH HOH . F 3 HOH B 2 302 185 HOH HOH . F 3 HOH B 3 303 179 HOH HOH . F 3 HOH B 4 304 182 HOH HOH . F 3 HOH B 5 305 74 HOH HOH . F 3 HOH B 6 306 18 HOH HOH . F 3 HOH B 7 307 243 HOH HOH . F 3 HOH B 8 308 199 HOH HOH . F 3 HOH B 9 309 232 HOH HOH . F 3 HOH B 10 310 108 HOH HOH . F 3 HOH B 11 311 122 HOH HOH . F 3 HOH B 12 312 51 HOH HOH . F 3 HOH B 13 313 65 HOH HOH . F 3 HOH B 14 314 165 HOH HOH . F 3 HOH B 15 315 46 HOH HOH . F 3 HOH B 16 316 9 HOH HOH . F 3 HOH B 17 317 191 HOH HOH . F 3 HOH B 18 318 93 HOH HOH . F 3 HOH B 19 319 21 HOH HOH . F 3 HOH B 20 320 130 HOH HOH . F 3 HOH B 21 321 76 HOH HOH . F 3 HOH B 22 322 10 HOH HOH . F 3 HOH B 23 323 103 HOH HOH . F 3 HOH B 24 324 79 HOH HOH . F 3 HOH B 25 325 197 HOH HOH . F 3 HOH B 26 326 4 HOH HOH . F 3 HOH B 27 327 16 HOH HOH . F 3 HOH B 28 328 239 HOH HOH . F 3 HOH B 29 329 50 HOH HOH . F 3 HOH B 30 330 7 HOH HOH . F 3 HOH B 31 331 234 HOH HOH . F 3 HOH B 32 332 100 HOH HOH . F 3 HOH B 33 333 52 HOH HOH . F 3 HOH B 34 334 109 HOH HOH . F 3 HOH B 35 335 187 HOH HOH . F 3 HOH B 36 336 30 HOH HOH . F 3 HOH B 37 337 129 HOH HOH . F 3 HOH B 38 338 8 HOH HOH . F 3 HOH B 39 339 35 HOH HOH . F 3 HOH B 40 340 123 HOH HOH . F 3 HOH B 41 341 145 HOH HOH . F 3 HOH B 42 342 120 HOH HOH . F 3 HOH B 43 343 61 HOH HOH . F 3 HOH B 44 344 55 HOH HOH . F 3 HOH B 45 345 44 HOH HOH . F 3 HOH B 46 346 64 HOH HOH . F 3 HOH B 47 347 56 HOH HOH . F 3 HOH B 48 348 45 HOH HOH . F 3 HOH B 49 349 2 HOH HOH . F 3 HOH B 50 350 85 HOH HOH . F 3 HOH B 51 351 140 HOH HOH . F 3 HOH B 52 352 69 HOH HOH . F 3 HOH B 53 353 36 HOH HOH . F 3 HOH B 54 354 242 HOH HOH . F 3 HOH B 55 355 87 HOH HOH . F 3 HOH B 56 356 88 HOH HOH . F 3 HOH B 57 357 101 HOH HOH . F 3 HOH B 58 358 189 HOH HOH . F 3 HOH B 59 359 136 HOH HOH . F 3 HOH B 60 360 138 HOH HOH . F 3 HOH B 61 361 104 HOH HOH . F 3 HOH B 62 362 37 HOH HOH . F 3 HOH B 63 363 40 HOH HOH . F 3 HOH B 64 364 23 HOH HOH . F 3 HOH B 65 365 178 HOH HOH . F 3 HOH B 66 366 62 HOH HOH . F 3 HOH B 67 367 25 HOH HOH . F 3 HOH B 68 368 240 HOH HOH . F 3 HOH B 69 369 244 HOH HOH . F 3 HOH B 70 370 221 HOH HOH . F 3 HOH B 71 371 31 HOH HOH . F 3 HOH B 72 372 192 HOH HOH . F 3 HOH B 73 373 86 HOH HOH . F 3 HOH B 74 374 53 HOH HOH . F 3 HOH B 75 375 54 HOH HOH . F 3 HOH B 76 376 96 HOH HOH . F 3 HOH B 77 377 196 HOH HOH . F 3 HOH B 78 378 212 HOH HOH . F 3 HOH B 79 379 128 HOH HOH . F 3 HOH B 80 380 188 HOH HOH . F 3 HOH B 81 381 26 HOH HOH . F 3 HOH B 82 382 225 HOH HOH . F 3 HOH B 83 383 211 HOH HOH . F 3 HOH B 84 384 181 HOH HOH . F 3 HOH B 85 385 198 HOH HOH . F 3 HOH B 86 386 233 HOH HOH . F 3 HOH B 87 387 112 HOH HOH . F 3 HOH B 88 388 247 HOH HOH . F 3 HOH B 89 389 20 HOH HOH . F 3 HOH B 90 390 235 HOH HOH . F 3 HOH B 91 391 97 HOH HOH . F 3 HOH B 92 392 139 HOH HOH . F 3 HOH B 93 393 110 HOH HOH . F 3 HOH B 94 394 186 HOH HOH . F 3 HOH B 95 395 194 HOH HOH . F 3 HOH B 96 396 204 HOH HOH . F 3 HOH B 97 397 195 HOH HOH . F 3 HOH B 98 398 237 HOH HOH . F 3 HOH B 99 399 111 HOH HOH . F 3 HOH B 100 400 82 HOH HOH . F 3 HOH B 101 401 113 HOH HOH . F 3 HOH B 102 402 180 HOH HOH . F 3 HOH B 103 403 245 HOH HOH . F 3 HOH B 104 404 231 HOH HOH . F 3 HOH B 105 405 68 HOH HOH . F 3 HOH B 106 406 246 HOH HOH . F 3 HOH B 107 407 193 HOH HOH . F 3 HOH B 108 408 210 HOH HOH . F 3 HOH B 109 409 163 HOH HOH . F 3 HOH B 110 410 190 HOH HOH . F 3 HOH B 111 411 236 HOH HOH . F 3 HOH B 112 412 137 HOH HOH . F 3 HOH B 113 413 98 HOH HOH . F 3 HOH B 114 414 75 HOH HOH . F 3 HOH B 115 415 147 HOH HOH . F 3 HOH B 116 416 146 HOH HOH . F 3 HOH B 117 417 107 HOH HOH . F 3 HOH B 118 418 218 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 RBF . . . C 2 10.679 -4.951 7.963 1 21.92 ? N1 RBF 201 B 1 HETATM 2 C C2 RBF . . . C 2 11.445 -4.754 9.074 1 23.94 ? C2 RBF 201 B 1 HETATM 3 O O2 RBF . . . C 2 12.252 -5.661 9.441 1 25.77 ? O2 RBF 201 B 1 HETATM 4 N N3 RBF . . . C 2 11.364 -3.624 9.813 1 22.26 ? N3 RBF 201 B 1 HETATM 5 C C4 RBF . . . C 2 10.523 -2.622 9.509 1 21.78 ? C4 RBF 201 B 1 HETATM 6 O O4 RBF . . . C 2 10.464 -1.594 10.233 1 21.46 ? O4 RBF 201 B 1 HETATM 7 C C4A RBF . . . C 2 9.663 -2.758 8.297 1 21.36 ? C4A RBF 201 B 1 HETATM 8 N N5 RBF . . . C 2 8.798 -1.777 7.94 1 21.11 ? N5 RBF 201 B 1 HETATM 9 C C5A RBF . . . C 2 8.03 -1.955 6.834 1 22.04 ? C5A RBF 201 B 1 HETATM 10 C C6 RBF . . . C 2 7.167 -0.925 6.497 1 22.9 ? C6 RBF 201 B 1 HETATM 11 C C7 RBF . . . C 2 6.358 -1.028 5.379 1 23.44 ? C7 RBF 201 B 1 HETATM 12 C C7M RBF . . . C 2 5.409 0.099 5.033 1 24.41 ? C7M RBF 201 B 1 HETATM 13 C C8 RBF . . . C 2 6.413 -2.269 4.565 1 23.53 ? C8 RBF 201 B 1 HETATM 14 C C8M RBF . . . C 2 5.521 -2.418 3.368 1 23.79 ? C8M RBF 201 B 1 HETATM 15 C C9 RBF . . . C 2 7.271 -3.306 4.896 1 22.08 ? C9 RBF 201 B 1 HETATM 16 C C9A RBF . . . C 2 8.105 -3.213 6.012 1 23.06 ? C9A RBF 201 B 1 HETATM 17 N N10 RBF . . . C 2 8.994 -4.262 6.382 1 24.64 ? N10 RBF 201 B 1 HETATM 18 C C10 RBF . . . C 2 9.781 -4.033 7.533 1 22.39 ? C10 RBF 201 B 1 HETATM 19 C C1' RBF . . . C 2 9.118 -5.558 5.638 1 30.45 ? C1' RBF 201 B 1 HETATM 20 C C2' RBF . . . C 2 9.757 -5.521 4.233 1 34.45 ? C2' RBF 201 B 1 HETATM 21 O O2' RBF . . . C 2 8.767 -5.245 3.245 1 37.8 ? O2' RBF 201 B 1 HETATM 22 C C3' RBF . . . C 2 10.368 -6.805 3.68 1 39.1 ? C3' RBF 201 B 1 HETATM 23 O O3' RBF . . . C 2 10.851 -7.638 4.74 1 40.14 ? O3' RBF 201 B 1 HETATM 24 C C4' RBF . . . C 2 11.473 -6.472 2.644 1 42.27 ? C4' RBF 201 B 1 HETATM 25 O O4' RBF . . . C 2 11.065 -5.427 1.729 1 43.29 ? O4' RBF 201 B 1 HETATM 26 C C5' RBF . . . C 2 11.925 -7.69 1.827 1 42.83 ? C5' RBF 201 B 1 HETATM 27 O O5' RBF . . . C 2 13.154 -8.229 2.335 1 42.65 ? O5' RBF 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #