data_9DA1 # _model_server_result.job_id M_R5BVgCbwdUXjDdUiqNGA _model_server_result.datetime_utc '2025-06-24 12:54:04' _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 9da1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 9DA1 # _exptl.entry_id 9DA1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 354.207 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-(hydroxymethyl)uridine 5'-(dihydrogen 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 90 _cell.angle_gamma 90 _cell.entry_id 9DA1 _cell.length_a 60.761 _cell.length_b 64.833 _cell.length_c 128.48 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DA1 _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 _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 'C10 H15 N2 O10 P' _chem_comp.formula_weight 354.207 _chem_comp.id A1BBB _chem_comp.mon_nstd_flag n _chem_comp.name "5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "5-(hydroxymethyl)uridine 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 O3' C3' A1BBB sing 1 n n O4' C4' A1BBB sing 2 n n O4' C1' A1BBB sing 3 n n O2' C2' A1BBB sing 4 n n C4' C3' A1BBB sing 5 n n C4' C5' A1BBB sing 6 n n C1' C2' A1BBB sing 7 n n C1' N1 A1BBB sing 8 n n OP1 P A1BBB doub 9 n n O5' C5' A1BBB sing 10 n n O5' P A1BBB sing 11 n n C3' C2' A1BBB sing 12 n n P OP2 A1BBB sing 13 n n P OP3 A1BBB sing 14 n n N1 C6 A1BBB sing 15 n n N1 C2 A1BBB sing 16 n n O2 C2 A1BBB doub 17 n n C6 C5 A1BBB doub 18 n n C2 N3 A1BBB sing 19 n n O5B C5A A1BBB sing 20 n n C5 C5A A1BBB sing 21 n n C5 C4 A1BBB sing 22 n n N3 C4 A1BBB sing 23 n n C4 O4 A1BBB doub 24 n n N3 H3 A1BBB sing 25 n n C6 H6 A1BBB sing 26 n n C1' H1' A1BBB sing 27 n n C2' H2' A1BBB sing 28 n n C3' H3' A1BBB sing 29 n n C4' H4' A1BBB sing 30 n n C5' "H5''" A1BBB sing 31 n n C5' H5' A1BBB sing 32 n n C5A H10 A1BBB sing 33 n n C5A H11 A1BBB sing 34 n n OP3 HOP3 A1BBB sing 35 n n O2' HO2' A1BBB sing 36 n n O3' HO3' A1BBB sing 37 n n O5B H12 A1BBB sing 38 n n OP2 HOP2 A1BBB sing 39 n n # _atom_sites.entry_id 9DA1 _atom_sites.fract_transf_matrix[1][1] 0.016458 _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] 0.015424 _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] 0.007783 _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 A1BBB A 1 201 201 A1BBB HMU . D 2 A1BBB B 1 201 201 A1BBB HMU . E 3 HOH A 1 301 94 HOH HOH . E 3 HOH A 2 302 63 HOH HOH . E 3 HOH A 3 303 79 HOH HOH . E 3 HOH A 4 304 134 HOH HOH . E 3 HOH A 5 305 188 HOH HOH . E 3 HOH A 6 306 6 HOH HOH . E 3 HOH A 7 307 34 HOH HOH . E 3 HOH A 8 308 73 HOH HOH . E 3 HOH A 9 309 196 HOH HOH . E 3 HOH A 10 310 82 HOH HOH . E 3 HOH A 11 311 126 HOH HOH . E 3 HOH A 12 312 129 HOH HOH . E 3 HOH A 13 313 157 HOH HOH . E 3 HOH A 14 314 86 HOH HOH . E 3 HOH A 15 315 13 HOH HOH . E 3 HOH A 16 316 41 HOH HOH . E 3 HOH A 17 317 118 HOH HOH . E 3 HOH A 18 318 155 HOH HOH . E 3 HOH A 19 319 43 HOH HOH . E 3 HOH A 20 320 164 HOH HOH . E 3 HOH A 21 321 96 HOH HOH . E 3 HOH A 22 322 178 HOH HOH . E 3 HOH A 23 323 69 HOH HOH . E 3 HOH A 24 324 184 HOH HOH . E 3 HOH A 25 325 22 HOH HOH . E 3 HOH A 26 326 141 HOH HOH . E 3 HOH A 27 327 54 HOH HOH . E 3 HOH A 28 328 151 HOH HOH . E 3 HOH A 29 329 50 HOH HOH . E 3 HOH A 30 330 3 HOH HOH . E 3 HOH A 31 331 33 HOH HOH . E 3 HOH A 32 332 116 HOH HOH . E 3 HOH A 33 333 194 HOH HOH . E 3 HOH A 34 334 9 HOH HOH . E 3 HOH A 35 335 175 HOH HOH . E 3 HOH A 36 336 17 HOH HOH . E 3 HOH A 37 337 14 HOH HOH . E 3 HOH A 38 338 38 HOH HOH . E 3 HOH A 39 339 182 HOH HOH . E 3 HOH A 40 340 185 HOH HOH . E 3 HOH A 41 341 59 HOH HOH . E 3 HOH A 42 342 121 HOH HOH . E 3 HOH A 43 343 42 HOH HOH . E 3 HOH A 44 344 103 HOH HOH . E 3 HOH A 45 345 40 HOH HOH . E 3 HOH A 46 346 203 HOH HOH . E 3 HOH A 47 347 119 HOH HOH . E 3 HOH A 48 348 124 HOH HOH . E 3 HOH A 49 349 1 HOH HOH . E 3 HOH A 50 350 57 HOH HOH . E 3 HOH A 51 351 28 HOH HOH . E 3 HOH A 52 352 154 HOH HOH . E 3 HOH A 53 353 200 HOH HOH . E 3 HOH A 54 354 132 HOH HOH . E 3 HOH A 55 355 2 HOH HOH . E 3 HOH A 56 356 199 HOH HOH . E 3 HOH A 57 357 168 HOH HOH . E 3 HOH A 58 358 70 HOH HOH . E 3 HOH A 59 359 190 HOH HOH . E 3 HOH A 60 360 110 HOH HOH . E 3 HOH A 61 361 55 HOH HOH . E 3 HOH A 62 362 127 HOH HOH . E 3 HOH A 63 363 76 HOH HOH . E 3 HOH A 64 364 90 HOH HOH . E 3 HOH A 65 365 53 HOH HOH . E 3 HOH A 66 366 99 HOH HOH . E 3 HOH A 67 367 7 HOH HOH . E 3 HOH A 68 368 32 HOH HOH . E 3 HOH A 69 369 161 HOH HOH . E 3 HOH A 70 370 98 HOH HOH . E 3 HOH A 71 371 187 HOH HOH . E 3 HOH A 72 372 46 HOH HOH . E 3 HOH A 73 373 80 HOH HOH . E 3 HOH A 74 374 95 HOH HOH . E 3 HOH A 75 375 209 HOH HOH . E 3 HOH A 76 376 204 HOH HOH . E 3 HOH A 77 377 142 HOH HOH . E 3 HOH A 78 378 89 HOH HOH . E 3 HOH A 79 379 193 HOH HOH . E 3 HOH A 80 380 202 HOH HOH . E 3 HOH A 81 381 19 HOH HOH . E 3 HOH A 82 382 140 HOH HOH . E 3 HOH A 83 383 27 HOH HOH . E 3 HOH A 84 384 174 HOH HOH . E 3 HOH A 85 385 201 HOH HOH . E 3 HOH A 86 386 123 HOH HOH . E 3 HOH A 87 387 165 HOH HOH . E 3 HOH A 88 388 37 HOH HOH . E 3 HOH A 89 389 101 HOH HOH . E 3 HOH A 90 390 148 HOH HOH . E 3 HOH A 91 391 20 HOH HOH . E 3 HOH A 92 392 149 HOH HOH . E 3 HOH A 93 393 78 HOH HOH . E 3 HOH A 94 394 215 HOH HOH . E 3 HOH A 95 395 64 HOH HOH . E 3 HOH A 96 396 111 HOH HOH . E 3 HOH A 97 397 213 HOH HOH . E 3 HOH A 98 398 31 HOH HOH . E 3 HOH A 99 399 216 HOH HOH . E 3 HOH A 100 400 181 HOH HOH . E 3 HOH A 101 401 88 HOH HOH . E 3 HOH A 102 402 173 HOH HOH . E 3 HOH A 103 403 147 HOH HOH . E 3 HOH A 104 404 160 HOH HOH . E 3 HOH A 105 405 138 HOH HOH . E 3 HOH A 106 406 205 HOH HOH . E 3 HOH A 107 407 105 HOH HOH . E 3 HOH A 108 408 112 HOH HOH . E 3 HOH A 109 409 58 HOH HOH . E 3 HOH A 110 410 211 HOH HOH . E 3 HOH A 111 411 143 HOH HOH . E 3 HOH A 112 412 131 HOH HOH . E 3 HOH A 113 413 144 HOH HOH . E 3 HOH A 114 414 97 HOH HOH . E 3 HOH A 115 415 113 HOH HOH . E 3 HOH A 116 416 217 HOH HOH . E 3 HOH A 117 417 206 HOH HOH . F 3 HOH B 1 301 146 HOH HOH . F 3 HOH B 2 302 137 HOH HOH . F 3 HOH B 3 303 83 HOH HOH . F 3 HOH B 4 304 197 HOH HOH . F 3 HOH B 5 305 207 HOH HOH . F 3 HOH B 6 306 56 HOH HOH . F 3 HOH B 7 307 214 HOH HOH . F 3 HOH B 8 308 15 HOH HOH . F 3 HOH B 9 309 100 HOH HOH . F 3 HOH B 10 310 67 HOH HOH . F 3 HOH B 11 311 8 HOH HOH . F 3 HOH B 12 312 60 HOH HOH . F 3 HOH B 13 313 136 HOH HOH . F 3 HOH B 14 314 18 HOH HOH . F 3 HOH B 15 315 163 HOH HOH . F 3 HOH B 16 316 71 HOH HOH . F 3 HOH B 17 317 24 HOH HOH . F 3 HOH B 18 318 77 HOH HOH . F 3 HOH B 19 319 23 HOH HOH . F 3 HOH B 20 320 87 HOH HOH . F 3 HOH B 21 321 189 HOH HOH . F 3 HOH B 22 322 180 HOH HOH . F 3 HOH B 23 323 49 HOH HOH . F 3 HOH B 24 324 72 HOH HOH . F 3 HOH B 25 325 74 HOH HOH . F 3 HOH B 26 326 36 HOH HOH . F 3 HOH B 27 327 25 HOH HOH . F 3 HOH B 28 328 52 HOH HOH . F 3 HOH B 29 329 158 HOH HOH . F 3 HOH B 30 330 107 HOH HOH . F 3 HOH B 31 331 150 HOH HOH . F 3 HOH B 32 332 125 HOH HOH . F 3 HOH B 33 333 170 HOH HOH . F 3 HOH B 34 334 75 HOH HOH . F 3 HOH B 35 335 30 HOH HOH . F 3 HOH B 36 336 12 HOH HOH . F 3 HOH B 37 337 208 HOH HOH . F 3 HOH B 38 338 102 HOH HOH . F 3 HOH B 39 339 93 HOH HOH . F 3 HOH B 40 340 169 HOH HOH . F 3 HOH B 41 341 66 HOH HOH . F 3 HOH B 42 342 122 HOH HOH . F 3 HOH B 43 343 45 HOH HOH . F 3 HOH B 44 344 109 HOH HOH . F 3 HOH B 45 345 179 HOH HOH . F 3 HOH B 46 346 198 HOH HOH . F 3 HOH B 47 347 117 HOH HOH . F 3 HOH B 48 348 191 HOH HOH . F 3 HOH B 49 349 51 HOH HOH . F 3 HOH B 50 350 153 HOH HOH . F 3 HOH B 51 351 16 HOH HOH . F 3 HOH B 52 352 183 HOH HOH . F 3 HOH B 53 353 166 HOH HOH . F 3 HOH B 54 354 106 HOH HOH . F 3 HOH B 55 355 167 HOH HOH . F 3 HOH B 56 356 4 HOH HOH . F 3 HOH B 57 357 48 HOH HOH . F 3 HOH B 58 358 159 HOH HOH . F 3 HOH B 59 359 176 HOH HOH . F 3 HOH B 60 360 152 HOH HOH . F 3 HOH B 61 361 156 HOH HOH . F 3 HOH B 62 362 10 HOH HOH . F 3 HOH B 63 363 5 HOH HOH . F 3 HOH B 64 364 21 HOH HOH . F 3 HOH B 65 365 11 HOH HOH . F 3 HOH B 66 366 135 HOH HOH . F 3 HOH B 67 367 35 HOH HOH . F 3 HOH B 68 368 47 HOH HOH . F 3 HOH B 69 369 91 HOH HOH . F 3 HOH B 70 370 84 HOH HOH . F 3 HOH B 71 371 108 HOH HOH . F 3 HOH B 72 372 62 HOH HOH . F 3 HOH B 73 373 29 HOH HOH . F 3 HOH B 74 374 192 HOH HOH . F 3 HOH B 75 375 65 HOH HOH . F 3 HOH B 76 376 26 HOH HOH . F 3 HOH B 77 377 68 HOH HOH . F 3 HOH B 78 378 210 HOH HOH . F 3 HOH B 79 379 114 HOH HOH . F 3 HOH B 80 380 39 HOH HOH . F 3 HOH B 81 381 44 HOH HOH . F 3 HOH B 82 382 92 HOH HOH . F 3 HOH B 83 383 195 HOH HOH . F 3 HOH B 84 384 130 HOH HOH . F 3 HOH B 85 385 61 HOH HOH . F 3 HOH B 86 386 85 HOH HOH . F 3 HOH B 87 387 172 HOH HOH . F 3 HOH B 88 388 81 HOH HOH . F 3 HOH B 89 389 145 HOH HOH . F 3 HOH B 90 390 177 HOH HOH . F 3 HOH B 91 391 139 HOH HOH . F 3 HOH B 92 392 212 HOH HOH . F 3 HOH B 93 393 171 HOH HOH . F 3 HOH B 94 394 162 HOH HOH . F 3 HOH B 95 395 133 HOH HOH . F 3 HOH B 96 396 128 HOH HOH . F 3 HOH B 97 397 104 HOH HOH . F 3 HOH B 98 398 120 HOH HOH . F 3 HOH B 99 399 115 HOH HOH . F 3 HOH B 100 400 186 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 A1BBB . . . D 2 -12.261 -23.581 -22.939 1 14.8 ? N1 A1BBB 201 B 1 HETATM 2 C C2 A1BBB . . . D 2 -11.537 -24.163 -24.032 1 16.25 ? C2 A1BBB 201 B 1 HETATM 3 O O2 A1BBB . . . D 2 -12.149 -24.739 -24.853 1 18.35 ? O2 A1BBB 201 B 1 HETATM 4 N N3 A1BBB . . . D 2 -10.128 -24.089 -24.059 1 18.42 ? N3 A1BBB 201 B 1 HETATM 5 C C4 A1BBB . . . D 2 -9.42 -23.405 -23.07 1 19.19 ? C4 A1BBB 201 B 1 HETATM 6 O O4 A1BBB . . . D 2 -8.22 -23.328 -23.086 1 20.72 ? O4 A1BBB 201 B 1 HETATM 7 C C5 A1BBB . . . D 2 -10.184 -22.736 -21.95 1 15.44 ? C5 A1BBB 201 B 1 HETATM 8 C C6 A1BBB . . . D 2 -11.531 -22.828 -21.912 1 15.38 ? C6 A1BBB 201 B 1 HETATM 9 C C1' A1BBB . . . D 2 -13.676 -23.768 -22.901 1 14.36 ? C1' A1BBB 201 B 1 HETATM 10 C C2' A1BBB . . . D 2 -14.013 -25.227 -22.681 1 17.32 ? C2' A1BBB 201 B 1 HETATM 11 C C3' A1BBB . . . D 2 -14.484 -25.448 -21.282 1 13.61 ? C3' A1BBB 201 B 1 HETATM 12 C C4' A1BBB . . . D 2 -14.581 -24.073 -20.653 1 11.66 ? C4' A1BBB 201 B 1 HETATM 13 C C5' A1BBB . . . D 2 -13.681 -23.914 -19.485 1 11.86 ? C5' A1BBB 201 B 1 HETATM 14 C C5A A1BBB . . . D 2 -9.435 -21.963 -20.887 1 17.89 ? C5A A1BBB 201 B 1 HETATM 15 O OP3 A1BBB . . . D 2 -11.29 -22.249 -18.424 1 13.4 ? OP3 A1BBB 201 B 1 HETATM 16 O O2' A1BBB . . . D 2 -15.007 -25.638 -23.632 1 18.03 ? O2' A1BBB 201 B 1 HETATM 17 O O3' A1BBB . . . D 2 -15.757 -26.121 -21.208 1 14.24 ? O3' A1BBB 201 B 1 HETATM 18 O O4' A1BBB . . . D 2 -14.228 -23.097 -21.704 1 13.84 ? O4' A1BBB 201 B 1 HETATM 19 O O5' A1BBB . . . D 2 -13.794 -22.604 -18.957 1 11.88 ? O5' A1BBB 201 B 1 HETATM 20 O O5B A1BBB . . . D 2 -10.25 -20.972 -20.326 1 15.26 ? O5B A1BBB 201 B 1 HETATM 21 O OP1 A1BBB . . . D 2 -13.205 -20.741 -17.464 1 11.49 ? OP1 A1BBB 201 B 1 HETATM 22 O OP2 A1BBB . . . D 2 -12.849 -23.048 -16.659 1 11.76 ? OP2 A1BBB 201 B 1 HETATM 23 P P A1BBB . . . D 2 -12.764 -22.124 -17.795 1 11.88 ? P A1BBB 201 B 1 HETATM 24 H H6 A1BBB . . . D 2 -12.001 -22.409 -21.227 1 18.49 ? H6 A1BBB 201 B 1 HETATM 25 H H1' A1BBB . . . D 2 -14.054 -23.432 -23.729 1 17.26 ? H1' A1BBB 201 B 1 HETATM 26 H H2' A1BBB . . . D 2 -13.204 -25.752 -22.793 1 20.82 ? H2' A1BBB 201 B 1 HETATM 27 H H3' A1BBB . . . D 2 -13.841 -26.011 -20.823 1 16.37 ? H3' A1BBB 201 B 1 HETATM 28 H H4' A1BBB . . . D 2 -15.488 -23.939 -20.338 1 14.03 ? H4' A1BBB 201 B 1 HETATM 29 H "H5''" A1BBB . . . D 2 -12.765 -24.07 -19.762 1 14.26 ? "H5''" A1BBB 201 B 1 HETATM 30 H H5' A1BBB . . . D 2 -13.926 -24.557 -18.801 1 14.26 ? H5' A1BBB 201 B 1 HETATM 31 H H10 A1BBB . . . D 2 -8.656 -21.546 -21.287 1 21.5 ? H10 A1BBB 201 B 1 HETATM 32 H H11 A1BBB . . . D 2 -9.152 -22.575 -20.189 1 21.5 ? H11 A1BBB 201 B 1 HETATM 33 H HOP3 A1BBB . . . D 2 -10.898 -21.517 -18.296 1 16.11 ? HOP3 A1BBB 201 B 1 HETATM 34 H HO2' A1BBB . . . D 2 -14.841 -26.434 -23.891 1 21.67 ? HO2' A1BBB 201 B 1 HETATM 35 H HO3' A1BBB . . . D 2 -16.259 -25.844 -21.832 1 17.12 ? HO3' A1BBB 201 B 1 HETATM 36 H H12 A1BBB . . . D 2 -9.819 -20.595 -19.703 1 18.34 ? H12 A1BBB 201 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 476 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #