data_1STO # _model_server_result.job_id 8ykKKeSaQMDg7C4_N-Yhdw _model_server_result.datetime_utc '2024-11-25 05:10:28' _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 1sto # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":216}' # _entry.id 1STO # _exptl.entry_id 1STO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 368.191 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "OROTIDINE-5'-MONOPHOSPHATE" _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 90 _cell.entry_id 1STO _cell.length_a 47.2 _cell.length_b 47.2 _cell.length_c 216.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1STO _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 'C10 H13 N2 O11 P' _chem_comp.formula_weight 368.191 _chem_comp.id OMP _chem_comp.mon_nstd_flag . _chem_comp.name "OROTIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 O1P OMP doub 237 n n P O2P OMP sing 238 n n P O3P OMP sing 239 n n P O5' OMP sing 240 n n O2P HOP2 OMP sing 241 n n O3P HOP3 OMP sing 242 n n O5' C5' OMP sing 243 n n C5' C4' OMP sing 244 n n C5' "H5'1" OMP sing 245 n n C5' "H5'2" OMP sing 246 n n C4' O4' OMP sing 247 n n C4' C3' OMP sing 248 n n C4' H4' OMP sing 249 n n O4' C1' OMP sing 250 n n C3' C2' OMP sing 251 n n C3' O3' OMP sing 252 n n C3' H3' OMP sing 253 n n O3' HO3' OMP sing 254 n n C2' C1' OMP sing 255 n n C2' O2' OMP sing 256 n n C2' H2' OMP sing 257 n n O2' HO2' OMP sing 258 n n C1' N1 OMP sing 259 n n C1' H1' OMP sing 260 n n N1 C2 OMP sing 261 n n N1 C6 OMP sing 262 n n C2 N3 OMP sing 263 n n C2 O2 OMP doub 264 n n N3 C4 OMP sing 265 n n N3 HN3 OMP sing 266 n n C4 C5 OMP sing 267 n n C4 O4 OMP doub 268 n n C5 C6 OMP doub 269 n n C5 H5 OMP sing 270 n n C6 C7 OMP sing 271 n n C7 O71 OMP doub 272 n n C7 O72 OMP sing 273 n n O72 HO7 OMP sing 274 n n # _atom_sites.entry_id 1STO _atom_sites.fract_transf_matrix[1][1] 0.021186 _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] 0.021186 _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] 0.004615 _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 OMP A 1 216 216 OMP OMP . C 3 HOH A 1 301 301 HOH HOH . C 3 HOH A 2 302 302 HOH HOH . C 3 HOH A 3 303 303 HOH HOH . C 3 HOH A 4 304 304 HOH HOH . C 3 HOH A 5 305 305 HOH HOH . C 3 HOH A 6 306 306 HOH HOH . C 3 HOH A 7 307 307 HOH HOH . C 3 HOH A 8 308 308 HOH HOH . C 3 HOH A 9 309 309 HOH HOH . C 3 HOH A 10 310 310 HOH HOH . C 3 HOH A 11 311 311 HOH HOH . C 3 HOH A 12 312 312 HOH HOH . C 3 HOH A 13 313 313 HOH HOH . C 3 HOH A 14 314 314 HOH HOH . C 3 HOH A 15 315 315 HOH HOH . C 3 HOH A 16 316 316 HOH HOH . C 3 HOH A 17 317 317 HOH HOH . C 3 HOH A 18 318 318 HOH HOH . C 3 HOH A 19 319 319 HOH HOH . C 3 HOH A 20 321 321 HOH HOH . C 3 HOH A 21 322 322 HOH HOH . C 3 HOH A 22 323 323 HOH HOH . C 3 HOH A 23 324 324 HOH HOH . C 3 HOH A 24 325 325 HOH HOH . C 3 HOH A 25 326 326 HOH HOH . C 3 HOH A 26 327 327 HOH HOH . C 3 HOH A 27 328 328 HOH HOH . C 3 HOH A 28 329 329 HOH HOH . C 3 HOH A 29 330 330 HOH HOH . C 3 HOH A 30 331 331 HOH HOH . C 3 HOH A 31 332 332 HOH HOH . C 3 HOH A 32 333 333 HOH HOH . C 3 HOH A 33 334 334 HOH HOH . C 3 HOH A 34 336 336 HOH HOH . C 3 HOH A 35 337 337 HOH HOH . C 3 HOH A 36 338 338 HOH HOH . C 3 HOH A 37 339 339 HOH HOH . C 3 HOH A 38 340 340 HOH HOH . C 3 HOH A 39 341 341 HOH HOH . C 3 HOH A 40 342 342 HOH HOH . C 3 HOH A 41 343 343 HOH HOH . C 3 HOH A 42 344 344 HOH HOH . C 3 HOH A 43 345 345 HOH HOH . C 3 HOH A 44 346 346 HOH HOH . C 3 HOH A 45 347 347 HOH HOH . C 3 HOH A 46 348 348 HOH HOH . C 3 HOH A 47 349 349 HOH HOH . C 3 HOH A 48 350 350 HOH HOH . C 3 HOH A 49 351 351 HOH HOH . C 3 HOH A 50 352 352 HOH HOH . C 3 HOH A 51 354 354 HOH HOH . C 3 HOH A 52 355 355 HOH HOH . C 3 HOH A 53 356 356 HOH HOH . C 3 HOH A 54 357 357 HOH HOH . C 3 HOH A 55 358 358 HOH HOH . C 3 HOH A 56 359 359 HOH HOH . C 3 HOH A 57 360 360 HOH HOH . C 3 HOH A 58 361 361 HOH HOH . C 3 HOH A 59 362 362 HOH HOH . C 3 HOH A 60 363 363 HOH HOH . C 3 HOH A 61 364 364 HOH HOH . C 3 HOH A 62 365 365 HOH HOH . C 3 HOH A 63 366 366 HOH HOH . C 3 HOH A 64 367 367 HOH HOH . C 3 HOH A 65 368 368 HOH HOH . C 3 HOH A 66 369 369 HOH HOH . C 3 HOH A 67 370 370 HOH HOH . C 3 HOH A 68 371 371 HOH HOH . C 3 HOH A 69 372 372 HOH HOH . C 3 HOH A 70 373 373 HOH HOH . C 3 HOH A 71 374 374 HOH HOH . C 3 HOH A 72 375 375 HOH HOH . C 3 HOH A 73 376 376 HOH HOH . C 3 HOH A 74 377 377 HOH HOH . C 3 HOH A 75 378 378 HOH HOH . C 3 HOH A 76 379 379 HOH HOH . C 3 HOH A 77 380 380 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 OMP . . . B 2 19.716 26.724 15.9 1 53.92 ? P OMP 216 A 1 HETATM 2 O O1P OMP . . . B 2 18.46 26.167 16.51 1 53.05 ? O1P OMP 216 A 1 HETATM 3 O O2P OMP . . . B 2 20.987 26.528 16.671 1 55.66 ? O2P OMP 216 A 1 HETATM 4 O O3P OMP . . . B 2 19.676 26.256 14.48 1 56.16 ? O3P OMP 216 A 1 HETATM 5 O O5' OMP . . . B 2 19.706 28.329 15.372 1 50.56 ? O5' OMP 216 A 1 HETATM 6 C C5' OMP . . . B 2 19.119 29.242 14.421 1 45.64 ? C5' OMP 216 A 1 HETATM 7 C C4' OMP . . . B 2 17.863 29.992 14.931 1 39.67 ? C4' OMP 216 A 1 HETATM 8 O O4' OMP . . . B 2 18.093 30.678 16.16 1 34.79 ? O4' OMP 216 A 1 HETATM 9 C C3' OMP . . . B 2 16.863 30.76 14.39 1 39.25 ? C3' OMP 216 A 1 HETATM 10 O O3' OMP . . . B 2 15.683 30.371 13.672 1 42.02 ? O3' OMP 216 A 1 HETATM 11 C C2' OMP . . . B 2 16.915 32.246 14.866 1 35.41 ? C2' OMP 216 A 1 HETATM 12 O O2' OMP . . . B 2 15.89 32.998 14.597 1 34.05 ? O2' OMP 216 A 1 HETATM 13 C C1' OMP . . . B 2 17.111 31.747 16.309 1 32.89 ? C1' OMP 216 A 1 HETATM 14 N N1 OMP . . . B 2 17.557 32.834 17.167 1 29.78 ? N1 OMP 216 A 1 HETATM 15 C C2 OMP . . . B 2 18.402 33.558 16.631 1 26.28 ? C2 OMP 216 A 1 HETATM 16 O O2 OMP . . . B 2 18.953 33.479 15.422 1 25.77 ? O2 OMP 216 A 1 HETATM 17 N N3 OMP . . . B 2 18.987 34.555 17.32 1 24.97 ? N3 OMP 216 A 1 HETATM 18 C C4 OMP . . . B 2 18.664 34.755 18.596 1 23.04 ? C4 OMP 216 A 1 HETATM 19 O O4 OMP . . . B 2 19.244 35.608 19.347 1 19.44 ? O4 OMP 216 A 1 HETATM 20 C C5 OMP . . . B 2 17.739 33.969 19.248 1 26.57 ? C5 OMP 216 A 1 HETATM 21 C C6 OMP . . . B 2 17.063 32.988 18.508 1 29.43 ? C6 OMP 216 A 1 HETATM 22 C C7 OMP . . . B 2 16.127 32.301 19.316 1 31.01 ? C7 OMP 216 A 1 HETATM 23 O O71 OMP . . . B 2 14.935 32.057 19.005 1 31.72 ? O71 OMP 216 A 1 HETATM 24 O O72 OMP . . . B 2 16.563 31.464 20.13 1 30.48 ? O72 OMP 216 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 24 #