data_9DA6 # _model_server_result.job_id drkzyUJawl3gB-ZrLtzSHw _model_server_result.datetime_utc '2025-03-10 17:34:59' _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 9da6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 9DA6 # _exptl.entry_id 9DA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 198.134 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium _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 9DA6 _cell.length_a 62.749 _cell.length_b 63.925 _cell.length_c 127.407 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DA6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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,G _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 E N N # _chem_comp.formula 'C5 H13 N O5 P 1' _chem_comp.formula_weight 198.134 _chem_comp.id NR1 _chem_comp.mon_nstd_flag . _chem_comp.name (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium _chem_comp.type 'dna 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' NR1 sing 246 n n N1' C6' NR1 sing 247 n n C2' C3' NR1 sing 248 n n C6' C4' NR1 sing 249 n n O3' C3' NR1 sing 250 n n C3' C4' NR1 sing 251 n n C4' C5' NR1 sing 252 n n OP2 P NR1 doub 253 n n O5' C5' NR1 sing 254 n n O5' P NR1 sing 255 n n P OP1 NR1 sing 256 n n P O1 NR1 sing 257 n n OP1 H1 NR1 sing 258 n n C2' "H2''" NR1 sing 259 n n C2' H2' NR1 sing 260 n n C5' H5' NR1 sing 261 n n C5' "H5''" NR1 sing 262 n n C4' H4' NR1 sing 263 n n C3' H3' NR1 sing 264 n n C6' "H6'1" NR1 sing 265 n n C6' "H6'2" NR1 sing 266 n n N1' "H1'2" NR1 sing 267 n n O3' H2 NR1 sing 268 n n O1 H3 NR1 sing 269 n n N1' "H1'1" NR1 sing 270 n n # _atom_sites.entry_id 9DA6 _atom_sites.fract_transf_matrix[1][1] 0.015937 _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] 0.015643 _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] 0.007849 _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 NR1 A 1 201 201 NR1 E70 . D 3 EDO A 1 202 202 EDO EDO . E 2 NR1 B 1 201 201 NR1 E70 . F 4 HOH A 1 301 218 HOH HOH . F 4 HOH A 2 302 96 HOH HOH . F 4 HOH A 3 303 29 HOH HOH . F 4 HOH A 4 304 66 HOH HOH . F 4 HOH A 5 305 118 HOH HOH . F 4 HOH A 6 306 14 HOH HOH . F 4 HOH A 7 307 135 HOH HOH . F 4 HOH A 8 308 98 HOH HOH . F 4 HOH A 9 309 11 HOH HOH . F 4 HOH A 10 310 92 HOH HOH . F 4 HOH A 11 311 170 HOH HOH . F 4 HOH A 12 312 137 HOH HOH . F 4 HOH A 13 313 54 HOH HOH . F 4 HOH A 14 314 90 HOH HOH . F 4 HOH A 15 315 89 HOH HOH . F 4 HOH A 16 316 116 HOH HOH . F 4 HOH A 17 317 216 HOH HOH . F 4 HOH A 18 318 33 HOH HOH . F 4 HOH A 19 319 81 HOH HOH . F 4 HOH A 20 320 131 HOH HOH . F 4 HOH A 21 321 243 HOH HOH . F 4 HOH A 22 322 240 HOH HOH . F 4 HOH A 23 323 228 HOH HOH . F 4 HOH A 24 324 100 HOH HOH . F 4 HOH A 25 325 121 HOH HOH . F 4 HOH A 26 326 165 HOH HOH . F 4 HOH A 27 327 17 HOH HOH . F 4 HOH A 28 328 2 HOH HOH . F 4 HOH A 29 329 60 HOH HOH . F 4 HOH A 30 330 51 HOH HOH . F 4 HOH A 31 331 9 HOH HOH . F 4 HOH A 32 332 7 HOH HOH . F 4 HOH A 33 333 12 HOH HOH . F 4 HOH A 34 334 152 HOH HOH . F 4 HOH A 35 335 91 HOH HOH . F 4 HOH A 36 336 4 HOH HOH . F 4 HOH A 37 337 73 HOH HOH . F 4 HOH A 38 338 101 HOH HOH . F 4 HOH A 39 339 6 HOH HOH . F 4 HOH A 40 340 21 HOH HOH . F 4 HOH A 41 341 31 HOH HOH . F 4 HOH A 42 342 179 HOH HOH . F 4 HOH A 43 343 63 HOH HOH . F 4 HOH A 44 344 132 HOH HOH . F 4 HOH A 45 345 111 HOH HOH . F 4 HOH A 46 346 205 HOH HOH . F 4 HOH A 47 347 210 HOH HOH . F 4 HOH A 48 348 208 HOH HOH . F 4 HOH A 49 349 177 HOH HOH . F 4 HOH A 50 350 160 HOH HOH . F 4 HOH A 51 351 26 HOH HOH . F 4 HOH A 52 352 172 HOH HOH . F 4 HOH A 53 353 1 HOH HOH . F 4 HOH A 54 354 55 HOH HOH . F 4 HOH A 55 355 185 HOH HOH . F 4 HOH A 56 356 13 HOH HOH . F 4 HOH A 57 357 35 HOH HOH . F 4 HOH A 58 358 77 HOH HOH . F 4 HOH A 59 359 27 HOH HOH . F 4 HOH A 60 360 10 HOH HOH . F 4 HOH A 61 361 8 HOH HOH . F 4 HOH A 62 362 69 HOH HOH . F 4 HOH A 63 363 142 HOH HOH . F 4 HOH A 64 364 23 HOH HOH . F 4 HOH A 65 365 86 HOH HOH . F 4 HOH A 66 366 151 HOH HOH . F 4 HOH A 67 367 99 HOH HOH . F 4 HOH A 68 368 157 HOH HOH . F 4 HOH A 69 369 34 HOH HOH . F 4 HOH A 70 370 217 HOH HOH . F 4 HOH A 71 371 24 HOH HOH . F 4 HOH A 72 372 19 HOH HOH . F 4 HOH A 73 373 84 HOH HOH . F 4 HOH A 74 374 78 HOH HOH . F 4 HOH A 75 375 127 HOH HOH . F 4 HOH A 76 376 88 HOH HOH . F 4 HOH A 77 377 183 HOH HOH . F 4 HOH A 78 378 155 HOH HOH . F 4 HOH A 79 379 38 HOH HOH . F 4 HOH A 80 380 221 HOH HOH . F 4 HOH A 81 381 79 HOH HOH . F 4 HOH A 82 382 56 HOH HOH . F 4 HOH A 83 383 87 HOH HOH . F 4 HOH A 84 384 168 HOH HOH . F 4 HOH A 85 385 169 HOH HOH . F 4 HOH A 86 386 148 HOH HOH . F 4 HOH A 87 387 206 HOH HOH . F 4 HOH A 88 388 133 HOH HOH . F 4 HOH A 89 389 18 HOH HOH . F 4 HOH A 90 390 126 HOH HOH . F 4 HOH A 91 391 50 HOH HOH . F 4 HOH A 92 392 58 HOH HOH . F 4 HOH A 93 393 48 HOH HOH . F 4 HOH A 94 394 74 HOH HOH . F 4 HOH A 95 395 52 HOH HOH . F 4 HOH A 96 396 114 HOH HOH . F 4 HOH A 97 397 239 HOH HOH . F 4 HOH A 98 398 242 HOH HOH . F 4 HOH A 99 399 94 HOH HOH . F 4 HOH A 100 400 164 HOH HOH . F 4 HOH A 101 401 42 HOH HOH . F 4 HOH A 102 402 85 HOH HOH . F 4 HOH A 103 403 175 HOH HOH . F 4 HOH A 104 404 196 HOH HOH . F 4 HOH A 105 405 233 HOH HOH . F 4 HOH A 106 406 80 HOH HOH . F 4 HOH A 107 407 178 HOH HOH . F 4 HOH A 108 408 181 HOH HOH . F 4 HOH A 109 409 70 HOH HOH . F 4 HOH A 110 410 241 HOH HOH . F 4 HOH A 111 411 171 HOH HOH . F 4 HOH A 112 412 173 HOH HOH . F 4 HOH A 113 413 176 HOH HOH . F 4 HOH A 114 414 82 HOH HOH . F 4 HOH A 115 415 44 HOH HOH . F 4 HOH A 116 416 199 HOH HOH . F 4 HOH A 117 417 244 HOH HOH . F 4 HOH A 118 418 227 HOH HOH . F 4 HOH A 119 419 122 HOH HOH . F 4 HOH A 120 420 162 HOH HOH . F 4 HOH A 121 421 158 HOH HOH . F 4 HOH A 122 422 167 HOH HOH . F 4 HOH A 123 423 201 HOH HOH . F 4 HOH A 124 424 198 HOH HOH . F 4 HOH A 125 425 143 HOH HOH . F 4 HOH A 126 426 184 HOH HOH . F 4 HOH A 127 427 230 HOH HOH . F 4 HOH A 128 428 224 HOH HOH . F 4 HOH A 129 429 53 HOH HOH . F 4 HOH A 130 430 202 HOH HOH . F 4 HOH A 131 431 187 HOH HOH . F 4 HOH A 132 432 120 HOH HOH . F 4 HOH A 133 433 174 HOH HOH . F 4 HOH A 134 434 223 HOH HOH . F 4 HOH A 135 435 211 HOH HOH . F 4 HOH A 136 436 200 HOH HOH . F 4 HOH A 137 437 64 HOH HOH . F 4 HOH A 138 438 229 HOH HOH . F 4 HOH A 139 439 194 HOH HOH . F 4 HOH A 140 440 204 HOH HOH . F 4 HOH A 141 441 161 HOH HOH . G 4 HOH B 1 301 76 HOH HOH . G 4 HOH B 2 302 237 HOH HOH . G 4 HOH B 3 303 139 HOH HOH . G 4 HOH B 4 304 214 HOH HOH . G 4 HOH B 5 305 39 HOH HOH . G 4 HOH B 6 306 213 HOH HOH . G 4 HOH B 7 307 25 HOH HOH . G 4 HOH B 8 308 220 HOH HOH . G 4 HOH B 9 309 47 HOH HOH . G 4 HOH B 10 310 43 HOH HOH . G 4 HOH B 11 311 144 HOH HOH . G 4 HOH B 12 312 65 HOH HOH . G 4 HOH B 13 313 150 HOH HOH . G 4 HOH B 14 314 22 HOH HOH . G 4 HOH B 15 315 147 HOH HOH . G 4 HOH B 16 316 207 HOH HOH . G 4 HOH B 17 317 103 HOH HOH . G 4 HOH B 18 318 225 HOH HOH . G 4 HOH B 19 319 109 HOH HOH . G 4 HOH B 20 320 130 HOH HOH . G 4 HOH B 21 321 104 HOH HOH . G 4 HOH B 22 322 49 HOH HOH . G 4 HOH B 23 323 128 HOH HOH . G 4 HOH B 24 324 159 HOH HOH . G 4 HOH B 25 325 40 HOH HOH . G 4 HOH B 26 326 45 HOH HOH . G 4 HOH B 27 327 163 HOH HOH . G 4 HOH B 28 328 117 HOH HOH . G 4 HOH B 29 329 119 HOH HOH . G 4 HOH B 30 330 16 HOH HOH . G 4 HOH B 31 331 166 HOH HOH . G 4 HOH B 32 332 102 HOH HOH . G 4 HOH B 33 333 46 HOH HOH . G 4 HOH B 34 334 107 HOH HOH . G 4 HOH B 35 335 20 HOH HOH . G 4 HOH B 36 336 108 HOH HOH . G 4 HOH B 37 337 75 HOH HOH . G 4 HOH B 38 338 193 HOH HOH . G 4 HOH B 39 339 37 HOH HOH . G 4 HOH B 40 340 106 HOH HOH . G 4 HOH B 41 341 145 HOH HOH . G 4 HOH B 42 342 189 HOH HOH . G 4 HOH B 43 343 5 HOH HOH . G 4 HOH B 44 344 71 HOH HOH . G 4 HOH B 45 345 110 HOH HOH . G 4 HOH B 46 346 112 HOH HOH . G 4 HOH B 47 347 105 HOH HOH . G 4 HOH B 48 348 32 HOH HOH . G 4 HOH B 49 349 83 HOH HOH . G 4 HOH B 50 350 191 HOH HOH . G 4 HOH B 51 351 28 HOH HOH . G 4 HOH B 52 352 36 HOH HOH . G 4 HOH B 53 353 97 HOH HOH . G 4 HOH B 54 354 62 HOH HOH . G 4 HOH B 55 355 186 HOH HOH . G 4 HOH B 56 356 222 HOH HOH . G 4 HOH B 57 357 195 HOH HOH . G 4 HOH B 58 358 67 HOH HOH . G 4 HOH B 59 359 146 HOH HOH . G 4 HOH B 60 360 156 HOH HOH . G 4 HOH B 61 361 30 HOH HOH . G 4 HOH B 62 362 136 HOH HOH . G 4 HOH B 63 363 41 HOH HOH . G 4 HOH B 64 364 125 HOH HOH . G 4 HOH B 65 365 59 HOH HOH . G 4 HOH B 66 366 72 HOH HOH . G 4 HOH B 67 367 93 HOH HOH . G 4 HOH B 68 368 141 HOH HOH . G 4 HOH B 69 369 182 HOH HOH . G 4 HOH B 70 370 3 HOH HOH . G 4 HOH B 71 371 209 HOH HOH . G 4 HOH B 72 372 232 HOH HOH . G 4 HOH B 73 373 212 HOH HOH . G 4 HOH B 74 374 180 HOH HOH . G 4 HOH B 75 375 15 HOH HOH . G 4 HOH B 76 376 149 HOH HOH . G 4 HOH B 77 377 129 HOH HOH . G 4 HOH B 78 378 219 HOH HOH . G 4 HOH B 79 379 113 HOH HOH . G 4 HOH B 80 380 234 HOH HOH . G 4 HOH B 81 381 61 HOH HOH . G 4 HOH B 82 382 215 HOH HOH . G 4 HOH B 83 383 235 HOH HOH . G 4 HOH B 84 384 123 HOH HOH . G 4 HOH B 85 385 95 HOH HOH . G 4 HOH B 86 386 68 HOH HOH . G 4 HOH B 87 387 190 HOH HOH . G 4 HOH B 88 388 138 HOH HOH . G 4 HOH B 89 389 226 HOH HOH . G 4 HOH B 90 390 134 HOH HOH . G 4 HOH B 91 391 238 HOH HOH . G 4 HOH B 92 392 188 HOH HOH . G 4 HOH B 93 393 124 HOH HOH . G 4 HOH B 94 394 140 HOH HOH . G 4 HOH B 95 395 153 HOH HOH . G 4 HOH B 96 396 197 HOH HOH . G 4 HOH B 97 397 115 HOH HOH . G 4 HOH B 98 398 203 HOH HOH . G 4 HOH B 99 399 154 HOH HOH . G 4 HOH B 100 400 57 HOH HOH . G 4 HOH B 101 401 192 HOH HOH . G 4 HOH B 102 402 236 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 P P NR1 . . . E 2 -8.137 -14.118 -8.45 1 14.79 ? P NR1 201 B 1 HETATM 2 O OP1 NR1 . . . E 2 -8.072 -12.983 -9.414 1 15.09 ? OP1 NR1 201 B 1 HETATM 3 O OP2 NR1 . . . E 2 -7.27 -14.008 -7.251 1 16.16 ? OP2 NR1 201 B 1 HETATM 4 O O5' NR1 . . . E 2 -7.6 -15.369 -9.329 1 15.15 ? O5' NR1 201 B 1 HETATM 5 C C2' NR1 . . . E 2 -5.218 -18.894 -9.049 1 16.42 ? C2' NR1 201 B 1 HETATM 6 C C5' NR1 . . . E 2 -7.38 -16.626 -8.686 1 14.71 ? C5' NR1 201 B 1 HETATM 7 C C4' NR1 . . . E 2 -7.092 -17.658 -9.787 1 15.73 ? C4' NR1 201 B 1 HETATM 8 C C3' NR1 . . . E 2 -6.724 -18.978 -9.199 1 15.64 ? C3' NR1 201 B 1 HETATM 9 C C6' NR1 . . . E 2 -5.909 -17.201 -10.626 1 16.54 ? C6' NR1 201 B 1 HETATM 10 N N1' NR1 . . . E 2 -4.721 -17.955 -10.108 1 18.12 ? N1' NR1 201 B 1 HETATM 11 O O3' NR1 . . . E 2 -7.089 -20.044 -10.068 1 17.2 ? O3' NR1 201 B 1 HETATM 12 O O1 NR1 . . . E 2 -9.506 -14.41 -8.017 1 14.41 ? O1 NR1 201 B 1 HETATM 13 H "H2''" NR1 . . . E 2 -4.824 -19.772 -9.175 1 19.69 ? "H2''" NR1 201 B 1 HETATM 14 H H2' NR1 . . . E 2 -4.993 -18.55 -8.171 1 19.69 ? H2' NR1 201 B 1 HETATM 15 H H5' NR1 . . . E 2 -6.623 -16.563 -8.084 1 17.64 ? H5' NR1 201 B 1 HETATM 16 H "H5''" NR1 . . . E 2 -8.17 -16.885 -8.186 1 17.64 ? "H5''" NR1 201 B 1 HETATM 17 H H4' NR1 . . . E 2 -7.888 -17.753 -10.333 1 18.87 ? H4' NR1 201 B 1 HETATM 18 H H3' NR1 . . . E 2 -7.172 -19.141 -8.354 1 18.75 ? H3' NR1 201 B 1 HETATM 19 H "H6'1" NR1 . . . E 2 -6.059 -17.416 -11.56 1 19.83 ? "H6'1" NR1 201 B 1 HETATM 20 H "H6'2" NR1 . . . E 2 -5.772 -16.247 -10.519 1 19.83 ? "H6'2" NR1 201 B 1 HETATM 21 H H2 NR1 . . . E 2 -6.728 -20.755 -9.785 1 20.63 ? H2 NR1 201 B 1 HETATM 22 H "H1'1" NR1 . . . E 2 -4.338 -18.414 -10.768 1 21.73 ? "H1'1" NR1 201 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #