data_3DDY # _model_server_result.job_id TAHoKwstrHIlf1UVABI7Aw _model_server_result.datetime_utc '2024-11-17 12:25:16' _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 3ddy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":187}' # _entry.id 3DDY # _exptl.entry_id 3DDY _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 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 120 _cell.entry_id 3DDY _cell.length_a 79.188 _cell.length_b 79.188 _cell.length_c 67.62 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 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 3DDY _atom_sites.fract_transf_matrix[1][1] 0.012628 _atom_sites.fract_transf_matrix[1][2] 0.007291 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014582 _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] 0.014789 _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 RBF A 1 187 1 RBF RBF . C 3 HOH A 1 188 1 HOH TIP . C 3 HOH A 2 189 2 HOH TIP . C 3 HOH A 3 190 3 HOH TIP . C 3 HOH A 4 191 4 HOH TIP . C 3 HOH A 5 192 5 HOH TIP . C 3 HOH A 6 193 6 HOH TIP . C 3 HOH A 7 194 7 HOH TIP . C 3 HOH A 8 195 8 HOH TIP . C 3 HOH A 9 196 9 HOH TIP . C 3 HOH A 10 197 10 HOH TIP . C 3 HOH A 11 198 11 HOH TIP . C 3 HOH A 12 199 12 HOH TIP . C 3 HOH A 13 200 13 HOH TIP . C 3 HOH A 14 201 14 HOH TIP . C 3 HOH A 15 202 16 HOH TIP . C 3 HOH A 16 203 17 HOH TIP . C 3 HOH A 17 204 18 HOH TIP . C 3 HOH A 18 205 19 HOH TIP . C 3 HOH A 19 206 20 HOH TIP . C 3 HOH A 20 207 21 HOH TIP . C 3 HOH A 21 208 22 HOH TIP . C 3 HOH A 22 209 23 HOH TIP . C 3 HOH A 23 210 24 HOH TIP . C 3 HOH A 24 211 25 HOH TIP . C 3 HOH A 25 212 26 HOH TIP . C 3 HOH A 26 213 27 HOH TIP . C 3 HOH A 27 214 28 HOH TIP . C 3 HOH A 28 215 29 HOH TIP . C 3 HOH A 29 216 30 HOH TIP . C 3 HOH A 30 217 31 HOH TIP . C 3 HOH A 31 218 32 HOH TIP . C 3 HOH A 32 219 33 HOH TIP . C 3 HOH A 33 220 34 HOH TIP . C 3 HOH A 34 221 35 HOH TIP . C 3 HOH A 35 222 36 HOH TIP . C 3 HOH A 36 223 37 HOH TIP . C 3 HOH A 37 224 38 HOH TIP . C 3 HOH A 38 225 39 HOH TIP . C 3 HOH A 39 226 40 HOH TIP . C 3 HOH A 40 227 41 HOH TIP . C 3 HOH A 41 228 42 HOH TIP . C 3 HOH A 42 229 43 HOH TIP . C 3 HOH A 43 230 44 HOH TIP . C 3 HOH A 44 231 45 HOH TIP . C 3 HOH A 45 232 46 HOH TIP . C 3 HOH A 46 233 47 HOH TIP . C 3 HOH A 47 234 48 HOH TIP . C 3 HOH A 48 235 49 HOH TIP . C 3 HOH A 49 236 50 HOH TIP . C 3 HOH A 50 237 51 HOH TIP . C 3 HOH A 51 238 52 HOH TIP . C 3 HOH A 52 239 53 HOH TIP . C 3 HOH A 53 240 54 HOH TIP . C 3 HOH A 54 241 55 HOH TIP . C 3 HOH A 55 242 56 HOH TIP . C 3 HOH A 56 243 57 HOH TIP . C 3 HOH A 57 244 58 HOH TIP . C 3 HOH A 58 245 59 HOH TIP . C 3 HOH A 59 246 60 HOH TIP . C 3 HOH A 60 247 61 HOH TIP . C 3 HOH A 61 248 62 HOH TIP . C 3 HOH A 62 249 63 HOH TIP . C 3 HOH A 63 250 64 HOH TIP . C 3 HOH A 64 251 65 HOH TIP . C 3 HOH A 65 252 66 HOH TIP . C 3 HOH A 66 253 67 HOH TIP . C 3 HOH A 67 254 68 HOH TIP . C 3 HOH A 68 255 69 HOH TIP . C 3 HOH A 69 256 70 HOH TIP . C 3 HOH A 70 257 71 HOH TIP . C 3 HOH A 71 258 72 HOH TIP . C 3 HOH A 72 259 73 HOH TIP . C 3 HOH A 73 260 74 HOH TIP . C 3 HOH A 74 261 75 HOH TIP . C 3 HOH A 75 262 76 HOH TIP . C 3 HOH A 76 263 77 HOH TIP . C 3 HOH A 77 264 78 HOH TIP . C 3 HOH A 78 265 79 HOH TIP . C 3 HOH A 79 266 80 HOH TIP . C 3 HOH A 80 267 81 HOH TIP . C 3 HOH A 81 268 82 HOH TIP . C 3 HOH A 82 269 83 HOH TIP . C 3 HOH A 83 270 84 HOH TIP . C 3 HOH A 84 271 85 HOH TIP . C 3 HOH A 85 272 86 HOH TIP . C 3 HOH A 86 273 87 HOH TIP . C 3 HOH A 87 274 88 HOH TIP . C 3 HOH A 88 275 89 HOH TIP . C 3 HOH A 89 276 90 HOH TIP . C 3 HOH A 90 277 91 HOH TIP . C 3 HOH A 91 278 92 HOH TIP . C 3 HOH A 92 279 93 HOH TIP . C 3 HOH A 93 280 94 HOH TIP . C 3 HOH A 94 281 95 HOH TIP . C 3 HOH A 95 282 96 HOH TIP . C 3 HOH A 96 283 97 HOH TIP . C 3 HOH A 97 284 98 HOH TIP . C 3 HOH A 98 285 99 HOH TIP . C 3 HOH A 99 286 100 HOH TIP . C 3 HOH A 100 287 101 HOH TIP . C 3 HOH A 101 288 102 HOH TIP . C 3 HOH A 102 289 103 HOH TIP . C 3 HOH A 103 290 104 HOH TIP . C 3 HOH A 104 291 105 HOH TIP . C 3 HOH A 105 292 106 HOH TIP . C 3 HOH A 106 293 107 HOH TIP . C 3 HOH A 107 294 108 HOH TIP . C 3 HOH A 108 295 109 HOH TIP . C 3 HOH A 109 296 110 HOH TIP . C 3 HOH A 110 297 111 HOH TIP . C 3 HOH A 111 298 112 HOH TIP . C 3 HOH A 112 299 113 HOH TIP . C 3 HOH A 113 300 114 HOH TIP . C 3 HOH A 114 301 115 HOH TIP . C 3 HOH A 115 302 116 HOH TIP . C 3 HOH A 116 303 117 HOH TIP . C 3 HOH A 117 304 118 HOH TIP . C 3 HOH A 118 305 119 HOH TIP . C 3 HOH A 119 306 120 HOH TIP . C 3 HOH A 120 307 121 HOH TIP . C 3 HOH A 121 308 122 HOH TIP . C 3 HOH A 122 309 123 HOH TIP . C 3 HOH A 123 310 124 HOH TIP . C 3 HOH A 124 311 125 HOH TIP . C 3 HOH A 125 312 126 HOH TIP . C 3 HOH A 126 313 127 HOH TIP . C 3 HOH A 127 314 128 HOH TIP . C 3 HOH A 128 315 129 HOH TIP . C 3 HOH A 129 316 130 HOH TIP . C 3 HOH A 130 317 131 HOH TIP . C 3 HOH A 131 318 132 HOH TIP . C 3 HOH A 132 319 133 HOH TIP . C 3 HOH A 133 320 134 HOH TIP . C 3 HOH A 134 321 135 HOH TIP . C 3 HOH A 135 322 136 HOH TIP . C 3 HOH A 136 323 137 HOH TIP . C 3 HOH A 137 324 138 HOH TIP . C 3 HOH A 138 325 139 HOH TIP . C 3 HOH A 139 326 140 HOH TIP . C 3 HOH A 140 327 141 HOH TIP . C 3 HOH A 141 328 142 HOH TIP . C 3 HOH A 142 329 143 HOH TIP . C 3 HOH A 143 330 144 HOH TIP . C 3 HOH A 144 331 145 HOH TIP . C 3 HOH A 145 332 146 HOH TIP . C 3 HOH A 146 333 147 HOH TIP . C 3 HOH A 147 334 148 HOH TIP . C 3 HOH A 148 335 149 HOH TIP . C 3 HOH A 149 336 150 HOH TIP . C 3 HOH A 150 337 151 HOH TIP . C 3 HOH A 151 338 152 HOH TIP . C 3 HOH A 152 339 153 HOH TIP . C 3 HOH A 153 340 154 HOH TIP . C 3 HOH A 154 341 155 HOH TIP . C 3 HOH A 155 342 156 HOH TIP . C 3 HOH A 156 343 157 HOH TIP . C 3 HOH A 157 344 158 HOH TIP . C 3 HOH A 158 345 159 HOH TIP . C 3 HOH A 159 346 160 HOH TIP . C 3 HOH A 160 347 161 HOH TIP . C 3 HOH A 161 348 162 HOH TIP . C 3 HOH A 162 349 163 HOH TIP . C 3 HOH A 163 350 164 HOH TIP . C 3 HOH A 164 351 165 HOH TIP . C 3 HOH A 165 352 166 HOH TIP . C 3 HOH A 166 353 167 HOH TIP . C 3 HOH A 167 354 168 HOH TIP . C 3 HOH A 168 355 169 HOH TIP . C 3 HOH A 169 356 170 HOH TIP . C 3 HOH A 170 357 171 HOH TIP . C 3 HOH A 171 358 172 HOH TIP . C 3 HOH A 172 359 173 HOH TIP . C 3 HOH A 173 360 174 HOH TIP . C 3 HOH A 174 361 175 HOH TIP . C 3 HOH A 175 362 176 HOH TIP . C 3 HOH A 176 363 177 HOH TIP . C 3 HOH A 177 364 178 HOH TIP . C 3 HOH A 178 365 179 HOH TIP . C 3 HOH A 179 366 180 HOH TIP . C 3 HOH A 180 367 181 HOH TIP . C 3 HOH A 181 368 182 HOH TIP . C 3 HOH A 182 369 183 HOH TIP . C 3 HOH A 183 370 184 HOH TIP . C 3 HOH A 184 371 185 HOH TIP . C 3 HOH A 185 372 186 HOH TIP . C 3 HOH A 186 373 187 HOH TIP . C 3 HOH A 187 374 189 HOH TIP . C 3 HOH A 188 375 190 HOH TIP . C 3 HOH A 189 376 191 HOH TIP . C 3 HOH A 190 377 192 HOH TIP . C 3 HOH A 191 378 193 HOH TIP . C 3 HOH A 192 379 194 HOH TIP . C 3 HOH A 193 380 195 HOH TIP . C 3 HOH A 194 381 196 HOH TIP . C 3 HOH A 195 382 197 HOH TIP . C 3 HOH A 196 383 198 HOH TIP . C 3 HOH A 197 384 199 HOH TIP . C 3 HOH A 198 385 200 HOH TIP . C 3 HOH A 199 386 201 HOH TIP . C 3 HOH A 200 387 202 HOH TIP . C 3 HOH A 201 388 203 HOH TIP . C 3 HOH A 202 389 204 HOH TIP . C 3 HOH A 203 390 205 HOH TIP . C 3 HOH A 204 391 206 HOH TIP . C 3 HOH A 205 392 207 HOH TIP . C 3 HOH A 206 393 208 HOH TIP . C 3 HOH A 207 394 209 HOH TIP . C 3 HOH A 208 395 210 HOH TIP . C 3 HOH A 209 396 211 HOH TIP . C 3 HOH A 210 397 212 HOH TIP . C 3 HOH A 211 398 213 HOH TIP . C 3 HOH A 212 399 214 HOH TIP . C 3 HOH A 213 400 215 HOH TIP . # 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 . . . B 2 32.966 -26.956 -12.873 1 24.93 ? N1 RBF 187 A 1 HETATM 2 C C2 RBF . . . B 2 31.936 -26.093 -13.167 1 23.68 ? C2 RBF 187 A 1 HETATM 3 O O2 RBF . . . B 2 30.803 -26.591 -13.311 1 23.95 ? O2 RBF 187 A 1 HETATM 4 N N3 RBF . . . B 2 32.13 -24.756 -13.284 1 23.34 ? N3 RBF 187 A 1 HETATM 5 C C4 RBF . . . B 2 33.323 -24.161 -13.157 1 26.22 ? C4 RBF 187 A 1 HETATM 6 O O4 RBF . . . B 2 33.467 -22.935 -13.268 1 26.83 ? O4 RBF 187 A 1 HETATM 7 C C4A RBF . . . B 2 34.505 -25.02 -12.84 1 25.76 ? C4A RBF 187 A 1 HETATM 8 N N5 RBF . . . B 2 35.745 -24.492 -12.699 1 27.84 ? N5 RBF 187 A 1 HETATM 9 C C5A RBF . . . B 2 36.831 -25.294 -12.413 1 25.9 ? C5A RBF 187 A 1 HETATM 10 C C6 RBF . . . B 2 38.09 -24.7 -12.275 1 25.95 ? C6 RBF 187 A 1 HETATM 11 C C7 RBF . . . B 2 39.239 -25.494 -11.976 1 25.66 ? C7 RBF 187 A 1 HETATM 12 C C7M RBF . . . B 2 40.589 -24.804 -11.838 1 27.41 ? C7M RBF 187 A 1 HETATM 13 C C8 RBF . . . B 2 39.078 -26.987 -11.825 1 25.85 ? C8 RBF 187 A 1 HETATM 14 C C8M RBF . . . B 2 40.29 -27.858 -11.515 1 23.82 ? C8M RBF 187 A 1 HETATM 15 C C9 RBF . . . B 2 37.806 -27.602 -11.957 1 24.79 ? C9 RBF 187 A 1 HETATM 16 C C9A RBF . . . B 2 36.662 -26.791 -12.248 1 26.03 ? C9A RBF 187 A 1 HETATM 17 N N10 RBF . . . B 2 35.338 -27.381 -12.408 1 25.46 ? N10 RBF 187 A 1 HETATM 18 C C10 RBF . . . B 2 34.237 -26.489 -12.708 1 24.61 ? C10 RBF 187 A 1 HETATM 19 C C1' RBF . . . B 2 35.076 -28.844 -12.215 1 24.88 ? C1' RBF 187 A 1 HETATM 20 C C2' RBF . . . B 2 34.435 -29.085 -10.81 1 27.66 ? C2' RBF 187 A 1 HETATM 21 O O2' RBF . . . B 2 35.04 -28.116 -9.989 1 26.4 ? O2' RBF 187 A 1 HETATM 22 C C3' RBF . . . B 2 34.686 -30.465 -10.146 1 32.6 ? C3' RBF 187 A 1 HETATM 23 O O3' RBF . . . B 2 36.084 -30.666 -9.897 1 30.66 ? O3' RBF 187 A 1 HETATM 24 C C4' RBF . . . B 2 34.039 -31.634 -10.958 1 35.34 ? C4' RBF 187 A 1 HETATM 25 O O4' RBF . . . B 2 33.22 -31.138 -12.026 1 36.85 ? O4' RBF 187 A 1 HETATM 26 C C5' RBF . . . B 2 33.178 -32.539 -10.083 1 36.45 ? C5' RBF 187 A 1 HETATM 27 O O5' RBF . . . B 2 32.608 -33.596 -10.851 1 36.51 ? O5' RBF 187 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #