data_8RPS # _model_server_result.job_id g7gqt9-mzVOLi_qnPiz2Og _model_server_result.datetime_utc '2025-06-26 09:49:23' _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 8rps # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 8RPS # _exptl.entry_id 8RPS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 338.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE" _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 106.45 _cell.angle_gamma 90 _cell.entry_id 8RPS _cell.length_a 74.879 _cell.length_b 56.828 _cell.length_c 88.543 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RPS _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,F 1 1,2 B,C,E,G,H 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -25.073475 0 84.918689 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N # _chem_comp.formula 'C10 H15 N2 O9 P' _chem_comp.formula_weight 338.208 _chem_comp.id 5HU _chem_comp.mon_nstd_flag n _chem_comp.name "5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE" _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 P OP1 5HU doub 1 n n P OP2 5HU sing 2 n n P OP3 5HU sing 3 n n P O5' 5HU sing 4 n n OP2 HO2P 5HU sing 5 n n OP3 HO3P 5HU sing 6 n n O5' C5' 5HU sing 7 n n C5' C4' 5HU sing 8 n n C5' H5' 5HU sing 9 n n C5' "H5''" 5HU sing 10 n n C4' O4' 5HU sing 11 n n C4' C3' 5HU sing 12 n n C4' HC4' 5HU sing 13 n n O4' C1' 5HU sing 14 n n C3' O3' 5HU sing 15 n n C3' C2' 5HU sing 16 n n C3' HC3' 5HU sing 17 n n O3' HO3' 5HU sing 18 n n C2' C1' 5HU sing 19 n n C2' H2' 5HU sing 20 n n C2' "H2''" 5HU sing 21 n n C1' N1 5HU sing 22 n n C1' HC1' 5HU sing 23 n n N1 C2 5HU sing 24 n n N1 C6 5HU sing 25 n n C2 O2 5HU doub 26 n n C2 N3 5HU sing 27 n n N3 C4 5HU sing 28 n n N3 HN3 5HU sing 29 n n C4 O4 5HU doub 30 n n C4 C5 5HU sing 31 n n C5 C5A 5HU sing 32 n n C5 C6 5HU doub 33 n n C5A O5B 5HU sing 34 n n C5A H5A1 5HU sing 35 n n C5A H5A2 5HU sing 36 n n C6 HC6 5HU sing 37 n n O5B HO5B 5HU sing 38 n n # _atom_sites.entry_id 8RPS _atom_sites.fract_transf_matrix[1][1] 0.013355 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003943 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017597 _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] 0.011776 _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 D 2 5HU C 1 201 1 5HU 5HU . E 2 5HU A 1 201 2 5HU 5HU . F 3 HOH C 1 301 28 HOH HOH . F 3 HOH C 2 302 180 HOH HOH . F 3 HOH C 3 303 15 HOH HOH . F 3 HOH C 4 304 133 HOH HOH . F 3 HOH C 5 305 146 HOH HOH . F 3 HOH C 6 306 186 HOH HOH . F 3 HOH C 7 307 115 HOH HOH . F 3 HOH C 8 308 18 HOH HOH . F 3 HOH C 9 309 38 HOH HOH . F 3 HOH C 10 310 189 HOH HOH . F 3 HOH C 11 311 134 HOH HOH . F 3 HOH C 12 312 198 HOH HOH . F 3 HOH C 13 313 170 HOH HOH . F 3 HOH C 14 314 46 HOH HOH . F 3 HOH C 15 315 31 HOH HOH . F 3 HOH C 16 316 185 HOH HOH . F 3 HOH C 17 317 54 HOH HOH . F 3 HOH C 18 318 119 HOH HOH . F 3 HOH C 19 319 132 HOH HOH . F 3 HOH C 20 320 171 HOH HOH . F 3 HOH C 21 321 20 HOH HOH . F 3 HOH C 22 322 50 HOH HOH . F 3 HOH C 23 323 9 HOH HOH . F 3 HOH C 24 324 143 HOH HOH . F 3 HOH C 25 325 76 HOH HOH . F 3 HOH C 26 326 43 HOH HOH . F 3 HOH C 27 327 56 HOH HOH . F 3 HOH C 28 328 87 HOH HOH . F 3 HOH C 29 329 182 HOH HOH . F 3 HOH C 30 330 5 HOH HOH . F 3 HOH C 31 331 17 HOH HOH . F 3 HOH C 32 332 106 HOH HOH . F 3 HOH C 33 333 184 HOH HOH . F 3 HOH C 34 334 47 HOH HOH . F 3 HOH C 35 335 90 HOH HOH . F 3 HOH C 36 336 197 HOH HOH . F 3 HOH C 37 337 42 HOH HOH . F 3 HOH C 38 338 109 HOH HOH . F 3 HOH C 39 339 72 HOH HOH . F 3 HOH C 40 340 179 HOH HOH . F 3 HOH C 41 341 67 HOH HOH . F 3 HOH C 42 342 172 HOH HOH . F 3 HOH C 43 343 138 HOH HOH . F 3 HOH C 44 344 84 HOH HOH . F 3 HOH C 45 345 125 HOH HOH . F 3 HOH C 46 346 58 HOH HOH . F 3 HOH C 47 347 80 HOH HOH . F 3 HOH C 48 348 11 HOH HOH . F 3 HOH C 49 349 153 HOH HOH . F 3 HOH C 50 350 32 HOH HOH . F 3 HOH C 51 351 97 HOH HOH . F 3 HOH C 52 352 64 HOH HOH . F 3 HOH C 53 353 156 HOH HOH . F 3 HOH C 54 354 86 HOH HOH . F 3 HOH C 55 355 114 HOH HOH . F 3 HOH C 56 356 187 HOH HOH . F 3 HOH C 57 357 135 HOH HOH . F 3 HOH C 58 358 12 HOH HOH . F 3 HOH C 59 359 66 HOH HOH . F 3 HOH C 60 360 98 HOH HOH . F 3 HOH C 61 361 63 HOH HOH . F 3 HOH C 62 362 53 HOH HOH . F 3 HOH C 63 363 108 HOH HOH . F 3 HOH C 64 364 103 HOH HOH . F 3 HOH C 65 365 164 HOH HOH . F 3 HOH C 66 366 169 HOH HOH . F 3 HOH C 67 367 49 HOH HOH . F 3 HOH C 68 368 110 HOH HOH . F 3 HOH C 69 369 95 HOH HOH . F 3 HOH C 70 370 70 HOH HOH . F 3 HOH C 71 371 158 HOH HOH . F 3 HOH C 72 372 141 HOH HOH . F 3 HOH C 73 373 165 HOH HOH . F 3 HOH C 74 374 104 HOH HOH . F 3 HOH C 75 375 160 HOH HOH . F 3 HOH C 76 376 168 HOH HOH . F 3 HOH C 77 377 193 HOH HOH . F 3 HOH C 78 378 48 HOH HOH . F 3 HOH C 79 379 102 HOH HOH . F 3 HOH C 80 380 116 HOH HOH . F 3 HOH C 81 381 161 HOH HOH . F 3 HOH C 82 382 78 HOH HOH . F 3 HOH C 83 383 128 HOH HOH . F 3 HOH C 84 384 194 HOH HOH . F 3 HOH C 85 385 117 HOH HOH . G 3 HOH A 1 301 75 HOH HOH . G 3 HOH A 2 302 173 HOH HOH . G 3 HOH A 3 303 3 HOH HOH . G 3 HOH A 4 304 151 HOH HOH . G 3 HOH A 5 305 68 HOH HOH . G 3 HOH A 6 306 105 HOH HOH . G 3 HOH A 7 307 100 HOH HOH . G 3 HOH A 8 308 107 HOH HOH . G 3 HOH A 9 309 6 HOH HOH . G 3 HOH A 10 310 26 HOH HOH . G 3 HOH A 11 311 89 HOH HOH . G 3 HOH A 12 312 65 HOH HOH . G 3 HOH A 13 313 166 HOH HOH . G 3 HOH A 14 314 2 HOH HOH . G 3 HOH A 15 315 157 HOH HOH . G 3 HOH A 16 316 22 HOH HOH . G 3 HOH A 17 317 79 HOH HOH . G 3 HOH A 18 318 30 HOH HOH . G 3 HOH A 19 319 14 HOH HOH . G 3 HOH A 20 320 118 HOH HOH . G 3 HOH A 21 321 93 HOH HOH . G 3 HOH A 22 322 122 HOH HOH . G 3 HOH A 23 323 36 HOH HOH . G 3 HOH A 24 324 69 HOH HOH . G 3 HOH A 25 325 94 HOH HOH . G 3 HOH A 26 326 27 HOH HOH . G 3 HOH A 27 327 142 HOH HOH . G 3 HOH A 28 328 59 HOH HOH . G 3 HOH A 29 329 40 HOH HOH . G 3 HOH A 30 330 35 HOH HOH . G 3 HOH A 31 331 159 HOH HOH . G 3 HOH A 32 332 101 HOH HOH . G 3 HOH A 33 333 82 HOH HOH . G 3 HOH A 34 334 113 HOH HOH . G 3 HOH A 35 335 4 HOH HOH . G 3 HOH A 36 336 129 HOH HOH . G 3 HOH A 37 337 121 HOH HOH . G 3 HOH A 38 338 120 HOH HOH . G 3 HOH A 39 339 13 HOH HOH . G 3 HOH A 40 340 34 HOH HOH . G 3 HOH A 41 341 149 HOH HOH . G 3 HOH A 42 342 136 HOH HOH . G 3 HOH A 43 343 10 HOH HOH . G 3 HOH A 44 344 88 HOH HOH . G 3 HOH A 45 345 45 HOH HOH . G 3 HOH A 46 346 130 HOH HOH . G 3 HOH A 47 347 144 HOH HOH . G 3 HOH A 48 348 73 HOH HOH . G 3 HOH A 49 349 139 HOH HOH . G 3 HOH A 50 350 178 HOH HOH . G 3 HOH A 51 351 196 HOH HOH . G 3 HOH A 52 352 57 HOH HOH . G 3 HOH A 53 353 71 HOH HOH . G 3 HOH A 54 354 148 HOH HOH . G 3 HOH A 55 355 147 HOH HOH . G 3 HOH A 56 356 177 HOH HOH . G 3 HOH A 57 357 155 HOH HOH . G 3 HOH A 58 358 154 HOH HOH . G 3 HOH A 59 359 163 HOH HOH . H 3 HOH B 1 201 191 HOH HOH . H 3 HOH B 2 202 192 HOH HOH . H 3 HOH B 3 203 190 HOH HOH . H 3 HOH B 4 204 1 HOH HOH . H 3 HOH B 5 205 85 HOH HOH . H 3 HOH B 6 206 83 HOH HOH . H 3 HOH B 7 207 137 HOH HOH . H 3 HOH B 8 208 188 HOH HOH . H 3 HOH B 9 209 21 HOH HOH . H 3 HOH B 10 210 61 HOH HOH . H 3 HOH B 11 211 195 HOH HOH . H 3 HOH B 12 212 81 HOH HOH . H 3 HOH B 13 213 140 HOH HOH . H 3 HOH B 14 214 33 HOH HOH . H 3 HOH B 15 215 92 HOH HOH . H 3 HOH B 16 216 39 HOH HOH . H 3 HOH B 17 217 16 HOH HOH . H 3 HOH B 18 218 37 HOH HOH . H 3 HOH B 19 219 23 HOH HOH . H 3 HOH B 20 220 62 HOH HOH . H 3 HOH B 21 221 77 HOH HOH . H 3 HOH B 22 222 51 HOH HOH . H 3 HOH B 23 223 183 HOH HOH . H 3 HOH B 24 224 29 HOH HOH . H 3 HOH B 25 225 145 HOH HOH . H 3 HOH B 26 226 174 HOH HOH . H 3 HOH B 27 227 60 HOH HOH . H 3 HOH B 28 228 111 HOH HOH . H 3 HOH B 29 229 176 HOH HOH . H 3 HOH B 30 230 44 HOH HOH . H 3 HOH B 31 231 96 HOH HOH . H 3 HOH B 32 232 41 HOH HOH . H 3 HOH B 33 233 19 HOH HOH . H 3 HOH B 34 234 24 HOH HOH . H 3 HOH B 35 235 55 HOH HOH . H 3 HOH B 36 236 8 HOH HOH . H 3 HOH B 37 237 25 HOH HOH . H 3 HOH B 38 238 7 HOH HOH . H 3 HOH B 39 239 126 HOH HOH . H 3 HOH B 40 240 112 HOH HOH . H 3 HOH B 41 241 131 HOH HOH . H 3 HOH B 42 242 99 HOH HOH . H 3 HOH B 43 243 74 HOH HOH . H 3 HOH B 44 244 52 HOH HOH . H 3 HOH B 45 245 162 HOH HOH . H 3 HOH B 46 246 175 HOH HOH . H 3 HOH B 47 247 123 HOH HOH . H 3 HOH B 48 248 167 HOH HOH . H 3 HOH B 49 249 150 HOH HOH . H 3 HOH B 50 250 181 HOH HOH . H 3 HOH B 51 251 152 HOH HOH . H 3 HOH B 52 252 124 HOH HOH . H 3 HOH B 53 253 127 HOH HOH . H 3 HOH B 54 254 91 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 5HU . . . D 2 -14.532 -3.56 35.698 1 17.05 ? P 5HU 201 C 1 HETATM 2 O OP1 5HU . . . D 2 -15.211 -4.621 36.495 1 17.1 ? OP1 5HU 201 C 1 HETATM 3 O OP2 5HU . . . D 2 -13.195 -3.244 36.278 1 17.23 ? OP2 5HU 201 C 1 HETATM 4 O OP3 5HU . . . D 2 -14.373 -3.98 34.283 1 18.82 ? OP3 5HU 201 C 1 HETATM 5 O O5' 5HU . . . D 2 -15.434 -2.199 35.724 1 17.2 ? O5' 5HU 201 C 1 HETATM 6 C C5' 5HU . . . D 2 -16.766 -2.256 35.359 1 19.86 ? C5' 5HU 201 C 1 HETATM 7 C C4' 5HU . . . D 2 -17.289 -0.819 35.199 1 20.26 ? C4' 5HU 201 C 1 HETATM 8 O O4' 5HU . . . D 2 -16.294 -0.031 34.277 1 20.39 ? O4' 5HU 201 C 1 HETATM 9 C C3' 5HU . . . D 2 -18.429 -0.82 34.601 1 23.19 ? C3' 5HU 201 C 1 HETATM 10 O O3' 5HU . . . D 2 -19.46 -0.381 35.514 1 21.96 ? O3' 5HU 201 C 1 HETATM 11 C C2' 5HU . . . D 2 -18.349 0.271 33.404 1 20.12 ? C2' 5HU 201 C 1 HETATM 12 C C1' 5HU . . . D 2 -17.089 0.388 33.042 1 19.92 ? C1' 5HU 201 C 1 HETATM 13 N N1 5HU . . . D 2 -16.779 -0.51 31.926 1 20.32 ? N1 5HU 201 C 1 HETATM 14 C C2 5HU . . . D 2 -17.501 -0.392 30.648 1 20.9 ? C2 5HU 201 C 1 HETATM 15 O O2 5HU . . . D 2 -18.309 0.436 30.488 1 21.97 ? O2 5HU 201 C 1 HETATM 16 N N3 5HU . . . D 2 -17.176 -1.305 29.538 1 19.58 ? N3 5HU 201 C 1 HETATM 17 C C4 5HU . . . D 2 -16.166 -2.319 29.682 1 21.07 ? C4 5HU 201 C 1 HETATM 18 O O4 5HU . . . D 2 -15.92 -3.042 28.797 1 22.88 ? O4 5HU 201 C 1 HETATM 19 C C5 5HU . . . D 2 -15.439 -2.434 30.966 1 19.66 ? C5 5HU 201 C 1 HETATM 20 C C5A 5HU . . . D 2 -14.369 -3.49 31.13 1 18.98 ? C5A 5HU 201 C 1 HETATM 21 C C6 5HU . . . D 2 -15.754 -1.516 32.081 1 18.27 ? C6 5HU 201 C 1 HETATM 22 O O5B 5HU . . . D 2 -13.386 -3 31.984 1 19.21 ? O5B 5HU 201 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #