data_3L0N # _model_server_result.job_id ie3Um4qgEF2nIgphZr8i1g _model_server_result.datetime_utc '2024-11-12 21:20:41' _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 3l0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":257}' # _entry.id 3L0N # _exptl.entry_id 3L0N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-sulfanyluridine-5'-phosphate" _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 113.99 _cell.angle_gamma 90 _cell.entry_id 3L0N _cell.length_a 69.644 _cell.length_b 62.165 _cell.length_c 69.935 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 'C9 H13 N2 O9 P S' _chem_comp.formula_weight 356.246 _chem_comp.id S5P _chem_comp.mon_nstd_flag . _chem_comp.name "6-sulfanyluridine-5'-phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "6-mercaptouridine-5'-monophosphate" # 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 O4 C4 S5P doub 277 n n C4 N3 S5P sing 278 n n C4 C5 S5P sing 279 n n C5 C6 S5P doub 280 n n C5 H5 S5P sing 281 n n C6 N1 S5P sing 282 n n C6 S22 S5P sing 283 n n S22 H12 S5P sing 284 n n N3 C2 S5P sing 285 n n N3 HN3 S5P sing 286 n n C2 O2 S5P doub 287 n n C2 N1 S5P sing 288 n n N1 C1' S5P sing 289 n n C1' C2' S5P sing 290 n n C1' O4' S5P sing 291 n n C1' H1' S5P sing 292 n n O4' C4' S5P sing 293 n n C2' C3' S5P sing 294 n n C2' H2' S5P sing 295 n n O2' C2' S5P sing 296 n n O2' HO2' S5P sing 297 n n C3' C4' S5P sing 298 n n C3' O3' S5P sing 299 n n C3' H3' S5P sing 300 n n O3' HO3' S5P sing 301 n n C4' H4' S5P sing 302 n n C5' C4' S5P sing 303 n n C5' O5' S5P sing 304 n n C5' H5' S5P sing 305 n n C5' "H5'A" S5P sing 306 n n O5' P S5P sing 307 n n P O2P S5P sing 308 n n P O3P S5P sing 309 n n O3P HO3P S5P sing 310 n n O1P P S5P doub 311 n n O2P HO2P S5P sing 312 n n # _atom_sites.entry_id 3L0N _atom_sites.fract_transf_matrix[1][1] 0.014359 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006389 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016086 _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] 0.015651 _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 S5P A 1 257 1 S5P S5P . D 2 S5P B 1 257 2 S5P S5P . E 3 HOH A 1 258 258 HOH HOH . E 3 HOH A 2 259 2 HOH HOH . E 3 HOH A 3 260 260 HOH HOH . E 3 HOH A 4 261 261 HOH HOH . E 3 HOH A 5 262 262 HOH HOH . E 3 HOH A 6 263 263 HOH HOH . E 3 HOH A 7 264 264 HOH HOH . E 3 HOH A 8 265 265 HOH HOH . E 3 HOH A 9 266 266 HOH HOH . E 3 HOH A 10 267 4 HOH HOH . E 3 HOH A 11 268 5 HOH HOH . E 3 HOH A 12 269 269 HOH HOH . E 3 HOH A 13 270 270 HOH HOH . E 3 HOH A 14 271 8 HOH HOH . E 3 HOH A 15 272 9 HOH HOH . E 3 HOH A 16 273 10 HOH HOH . E 3 HOH A 17 274 11 HOH HOH . E 3 HOH A 18 275 12 HOH HOH . E 3 HOH A 19 276 15 HOH HOH . E 3 HOH A 20 277 277 HOH HOH . E 3 HOH A 21 278 278 HOH HOH . E 3 HOH A 22 279 16 HOH HOH . E 3 HOH A 23 280 17 HOH HOH . E 3 HOH A 24 281 19 HOH HOH . E 3 HOH A 25 282 20 HOH HOH . E 3 HOH A 26 283 23 HOH HOH . E 3 HOH A 27 284 24 HOH HOH . E 3 HOH A 28 285 25 HOH HOH . E 3 HOH A 29 286 26 HOH HOH . E 3 HOH A 30 287 27 HOH HOH . E 3 HOH A 31 288 31 HOH HOH . E 3 HOH A 32 289 35 HOH HOH . E 3 HOH A 33 290 37 HOH HOH . E 3 HOH A 34 291 39 HOH HOH . E 3 HOH A 35 292 41 HOH HOH . E 3 HOH A 36 293 42 HOH HOH . E 3 HOH A 37 294 43 HOH HOH . E 3 HOH A 38 295 44 HOH HOH . E 3 HOH A 39 296 46 HOH HOH . E 3 HOH A 40 297 47 HOH HOH . E 3 HOH A 41 298 48 HOH HOH . E 3 HOH A 42 299 50 HOH HOH . E 3 HOH A 43 300 51 HOH HOH . E 3 HOH A 44 301 52 HOH HOH . E 3 HOH A 45 302 53 HOH HOH . E 3 HOH A 46 303 56 HOH HOH . E 3 HOH A 47 304 58 HOH HOH . E 3 HOH A 48 305 59 HOH HOH . E 3 HOH A 49 306 60 HOH HOH . E 3 HOH A 50 307 61 HOH HOH . E 3 HOH A 51 308 62 HOH HOH . E 3 HOH A 52 309 63 HOH HOH . E 3 HOH A 53 310 65 HOH HOH . E 3 HOH A 54 311 66 HOH HOH . E 3 HOH A 55 312 68 HOH HOH . E 3 HOH A 56 313 69 HOH HOH . E 3 HOH A 57 314 73 HOH HOH . E 3 HOH A 58 315 76 HOH HOH . E 3 HOH A 59 316 78 HOH HOH . E 3 HOH A 60 317 80 HOH HOH . E 3 HOH A 61 318 82 HOH HOH . E 3 HOH A 62 319 84 HOH HOH . E 3 HOH A 63 320 86 HOH HOH . E 3 HOH A 64 321 90 HOH HOH . E 3 HOH A 65 322 93 HOH HOH . E 3 HOH A 66 323 98 HOH HOH . E 3 HOH A 67 324 102 HOH HOH . E 3 HOH A 68 325 105 HOH HOH . E 3 HOH A 69 326 107 HOH HOH . E 3 HOH A 70 327 108 HOH HOH . E 3 HOH A 71 328 110 HOH HOH . E 3 HOH A 72 329 112 HOH HOH . E 3 HOH A 73 330 114 HOH HOH . E 3 HOH A 74 331 115 HOH HOH . E 3 HOH A 75 332 121 HOH HOH . E 3 HOH A 76 333 122 HOH HOH . E 3 HOH A 77 334 124 HOH HOH . E 3 HOH A 78 335 127 HOH HOH . E 3 HOH A 79 336 128 HOH HOH . E 3 HOH A 80 337 131 HOH HOH . E 3 HOH A 81 338 133 HOH HOH . E 3 HOH A 82 339 135 HOH HOH . E 3 HOH A 83 340 136 HOH HOH . E 3 HOH A 84 341 139 HOH HOH . E 3 HOH A 85 342 140 HOH HOH . E 3 HOH A 86 343 141 HOH HOH . E 3 HOH A 87 344 142 HOH HOH . E 3 HOH A 88 345 143 HOH HOH . E 3 HOH A 89 346 144 HOH HOH . E 3 HOH A 90 347 146 HOH HOH . E 3 HOH A 91 348 147 HOH HOH . E 3 HOH A 92 349 148 HOH HOH . E 3 HOH A 93 350 149 HOH HOH . E 3 HOH A 94 351 150 HOH HOH . E 3 HOH A 95 352 151 HOH HOH . E 3 HOH A 96 353 153 HOH HOH . E 3 HOH A 97 354 156 HOH HOH . E 3 HOH A 98 355 157 HOH HOH . E 3 HOH A 99 356 160 HOH HOH . E 3 HOH A 100 357 162 HOH HOH . E 3 HOH A 101 358 163 HOH HOH . E 3 HOH A 102 359 164 HOH HOH . E 3 HOH A 103 360 165 HOH HOH . E 3 HOH A 104 361 169 HOH HOH . E 3 HOH A 105 362 170 HOH HOH . E 3 HOH A 106 363 171 HOH HOH . E 3 HOH A 107 364 175 HOH HOH . E 3 HOH A 108 365 179 HOH HOH . E 3 HOH A 109 366 181 HOH HOH . E 3 HOH A 110 367 189 HOH HOH . E 3 HOH A 111 368 190 HOH HOH . E 3 HOH A 112 369 193 HOH HOH . E 3 HOH A 113 370 195 HOH HOH . E 3 HOH A 114 371 199 HOH HOH . E 3 HOH A 115 372 200 HOH HOH . E 3 HOH A 116 373 205 HOH HOH . E 3 HOH A 117 374 208 HOH HOH . E 3 HOH A 118 375 210 HOH HOH . E 3 HOH A 119 376 212 HOH HOH . E 3 HOH A 120 377 214 HOH HOH . E 3 HOH A 121 378 215 HOH HOH . E 3 HOH A 122 379 216 HOH HOH . E 3 HOH A 123 380 218 HOH HOH . E 3 HOH A 124 381 220 HOH HOH . E 3 HOH A 125 382 222 HOH HOH . E 3 HOH A 126 383 229 HOH HOH . E 3 HOH A 127 384 235 HOH HOH . E 3 HOH A 128 385 237 HOH HOH . E 3 HOH A 129 386 240 HOH HOH . E 3 HOH A 130 387 241 HOH HOH . E 3 HOH A 131 388 242 HOH HOH . E 3 HOH A 132 389 248 HOH HOH . E 3 HOH A 133 390 249 HOH HOH . E 3 HOH A 134 391 253 HOH HOH . E 3 HOH A 135 392 254 HOH HOH . E 3 HOH A 136 393 257 HOH HOH . F 3 HOH B 1 258 1 HOH HOH . F 3 HOH B 2 259 259 HOH HOH . F 3 HOH B 3 260 3 HOH HOH . F 3 HOH B 4 261 6 HOH HOH . F 3 HOH B 5 262 7 HOH HOH . F 3 HOH B 6 263 13 HOH HOH . F 3 HOH B 7 264 14 HOH HOH . F 3 HOH B 8 265 18 HOH HOH . F 3 HOH B 9 266 21 HOH HOH . F 3 HOH B 10 267 267 HOH HOH . F 3 HOH B 11 268 268 HOH HOH . F 3 HOH B 12 269 22 HOH HOH . F 3 HOH B 13 270 28 HOH HOH . F 3 HOH B 14 271 271 HOH HOH . F 3 HOH B 15 272 272 HOH HOH . F 3 HOH B 16 273 273 HOH HOH . F 3 HOH B 17 274 274 HOH HOH . F 3 HOH B 18 275 275 HOH HOH . F 3 HOH B 19 276 276 HOH HOH . F 3 HOH B 20 277 29 HOH HOH . F 3 HOH B 21 278 30 HOH HOH . F 3 HOH B 22 279 279 HOH HOH . F 3 HOH B 23 280 280 HOH HOH . F 3 HOH B 24 281 281 HOH HOH . F 3 HOH B 25 282 282 HOH HOH . F 3 HOH B 26 283 32 HOH HOH . F 3 HOH B 27 284 33 HOH HOH . F 3 HOH B 28 285 34 HOH HOH . F 3 HOH B 29 286 36 HOH HOH . F 3 HOH B 30 287 38 HOH HOH . F 3 HOH B 31 288 40 HOH HOH . F 3 HOH B 32 289 45 HOH HOH . F 3 HOH B 33 290 49 HOH HOH . F 3 HOH B 34 291 54 HOH HOH . F 3 HOH B 35 292 55 HOH HOH . F 3 HOH B 36 293 57 HOH HOH . F 3 HOH B 37 294 64 HOH HOH . F 3 HOH B 38 295 67 HOH HOH . F 3 HOH B 39 296 70 HOH HOH . F 3 HOH B 40 297 71 HOH HOH . F 3 HOH B 41 298 72 HOH HOH . F 3 HOH B 42 299 74 HOH HOH . F 3 HOH B 43 300 75 HOH HOH . F 3 HOH B 44 301 77 HOH HOH . F 3 HOH B 45 302 79 HOH HOH . F 3 HOH B 46 303 81 HOH HOH . F 3 HOH B 47 304 83 HOH HOH . F 3 HOH B 48 305 85 HOH HOH . F 3 HOH B 49 306 87 HOH HOH . F 3 HOH B 50 307 88 HOH HOH . F 3 HOH B 51 308 89 HOH HOH . F 3 HOH B 52 309 91 HOH HOH . F 3 HOH B 53 310 92 HOH HOH . F 3 HOH B 54 311 95 HOH HOH . F 3 HOH B 55 312 96 HOH HOH . F 3 HOH B 56 313 97 HOH HOH . F 3 HOH B 57 314 99 HOH HOH . F 3 HOH B 58 315 100 HOH HOH . F 3 HOH B 59 316 101 HOH HOH . F 3 HOH B 60 317 103 HOH HOH . F 3 HOH B 61 318 104 HOH HOH . F 3 HOH B 62 319 106 HOH HOH . F 3 HOH B 63 320 109 HOH HOH . F 3 HOH B 64 321 111 HOH HOH . F 3 HOH B 65 322 113 HOH HOH . F 3 HOH B 66 323 116 HOH HOH . F 3 HOH B 67 324 118 HOH HOH . F 3 HOH B 68 325 119 HOH HOH . F 3 HOH B 69 326 120 HOH HOH . F 3 HOH B 70 327 123 HOH HOH . F 3 HOH B 71 328 125 HOH HOH . F 3 HOH B 72 329 126 HOH HOH . F 3 HOH B 73 330 129 HOH HOH . F 3 HOH B 74 331 130 HOH HOH . F 3 HOH B 75 332 132 HOH HOH . F 3 HOH B 76 333 134 HOH HOH . F 3 HOH B 77 334 138 HOH HOH . F 3 HOH B 78 335 145 HOH HOH . F 3 HOH B 79 336 152 HOH HOH . F 3 HOH B 80 337 154 HOH HOH . F 3 HOH B 81 338 158 HOH HOH . F 3 HOH B 82 339 159 HOH HOH . F 3 HOH B 83 340 161 HOH HOH . F 3 HOH B 84 341 166 HOH HOH . F 3 HOH B 85 342 167 HOH HOH . F 3 HOH B 86 343 168 HOH HOH . F 3 HOH B 87 344 172 HOH HOH . F 3 HOH B 88 345 174 HOH HOH . F 3 HOH B 89 346 177 HOH HOH . F 3 HOH B 90 347 178 HOH HOH . F 3 HOH B 91 348 180 HOH HOH . F 3 HOH B 92 349 182 HOH HOH . F 3 HOH B 93 350 183 HOH HOH . F 3 HOH B 94 351 184 HOH HOH . F 3 HOH B 95 352 185 HOH HOH . F 3 HOH B 96 353 186 HOH HOH . F 3 HOH B 97 354 187 HOH HOH . F 3 HOH B 98 355 188 HOH HOH . F 3 HOH B 99 356 196 HOH HOH . F 3 HOH B 100 357 197 HOH HOH . F 3 HOH B 101 358 198 HOH HOH . F 3 HOH B 102 359 201 HOH HOH . F 3 HOH B 103 360 202 HOH HOH . F 3 HOH B 104 361 203 HOH HOH . F 3 HOH B 105 362 204 HOH HOH . F 3 HOH B 106 363 206 HOH HOH . F 3 HOH B 107 364 207 HOH HOH . F 3 HOH B 108 365 209 HOH HOH . F 3 HOH B 109 366 211 HOH HOH . F 3 HOH B 110 367 217 HOH HOH . F 3 HOH B 111 368 219 HOH HOH . F 3 HOH B 112 369 221 HOH HOH . F 3 HOH B 113 370 225 HOH HOH . F 3 HOH B 114 371 226 HOH HOH . F 3 HOH B 115 372 227 HOH HOH . F 3 HOH B 116 373 230 HOH HOH . F 3 HOH B 117 374 232 HOH HOH . F 3 HOH B 118 375 233 HOH HOH . F 3 HOH B 119 376 234 HOH HOH . F 3 HOH B 120 377 236 HOH HOH . F 3 HOH B 121 378 238 HOH HOH . F 3 HOH B 122 379 239 HOH HOH . F 3 HOH B 123 381 250 HOH HOH . F 3 HOH B 124 382 251 HOH HOH . F 3 HOH B 125 383 255 HOH HOH . F 3 HOH B 126 384 256 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 O O4 S5P . . . C 2 2.707 7.603 21.607 1 20.95 ? O4 S5P 257 A 1 HETATM 2 C C4 S5P . . . C 2 3.171 7.711 22.866 1 20.13 ? C4 S5P 257 A 1 HETATM 3 C C5 S5P . . . C 2 3.472 6.594 23.631 1 21.28 ? C5 S5P 257 A 1 HETATM 4 C C6 S5P . . . C 2 3.896 6.775 24.969 1 20.92 ? C6 S5P 257 A 1 HETATM 5 S S22 S5P . . . C 2 4.093 5.35 25.928 1 23.96 ? S22 S5P 257 A 1 HETATM 6 N N3 S5P . . . C 2 3.28 8.927 23.391 1 19.78 ? N3 S5P 257 A 1 HETATM 7 C C2 S5P . . . C 2 3.685 9.092 24.673 1 20.48 ? C2 S5P 257 A 1 HETATM 8 O O2 S5P . . . C 2 3.775 10.33 25.131 1 20.84 ? O2 S5P 257 A 1 HETATM 9 N N1 S5P . . . C 2 4.055 8.025 25.48 1 21.34 ? N1 S5P 257 A 1 HETATM 10 C C1' S5P . . . C 2 4.578 8.225 26.86 1 21.01 ? C1' S5P 257 A 1 HETATM 11 O O4' S5P . . . C 2 3.605 8.706 27.746 1 20.21 ? O4' S5P 257 A 1 HETATM 12 C C2' S5P . . . C 2 5.721 9.263 26.873 1 21.18 ? C2' S5P 257 A 1 HETATM 13 O O2' S5P . . . C 2 7.087 8.833 26.71 1 21.17 ? O2' S5P 257 A 1 HETATM 14 C C3' S5P . . . C 2 5.595 9.876 28.242 1 21.51 ? C3' S5P 257 A 1 HETATM 15 O O3' S5P . . . C 2 6.42 9.154 29.155 1 22.02 ? O3' S5P 257 A 1 HETATM 16 C C4' S5P . . . C 2 4.117 9.718 28.563 1 21.33 ? C4' S5P 257 A 1 HETATM 17 C C5' S5P . . . C 2 3.368 10.99 28.173 1 20.63 ? C5' S5P 257 A 1 HETATM 18 O O5' S5P . . . C 2 3.658 11.975 29.166 1 22 ? O5' S5P 257 A 1 HETATM 19 P P S5P . . . C 2 2.82 13.335 29.227 1 22.24 ? P S5P 257 A 1 HETATM 20 O O3P S5P . . . C 2 3.648 14.065 30.212 1 21.42 ? O3P S5P 257 A 1 HETATM 21 O O1P S5P . . . C 2 2.806 14.057 27.88 1 21.42 ? O1P S5P 257 A 1 HETATM 22 O O2P S5P . . . C 2 1.472 13.008 29.739 1 20.56 ? O2P S5P 257 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #