data_3TQ5 # _model_server_result.job_id kBnIhJgGe7bB9yjRh21UvQ _model_server_result.datetime_utc '2024-11-16 19:39:10' _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 3tq5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":777}' # _entry.id 3TQ5 # _exptl.entry_id 3TQ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 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 120 _cell.entry_id 3TQ5 _cell.length_a 60.714 _cell.length_b 60.714 _cell.length_c 63.775 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TQ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.714 105.159733 0 3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.714 105.159733 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 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 377 n n N1 C6 UMP sing 378 n n N1 C1' UMP sing 379 n n C2 N3 UMP sing 380 n n C2 O2 UMP doub 381 n n N3 C4 UMP sing 382 n n N3 HN3 UMP sing 383 n n C4 C5 UMP sing 384 n n C4 O4 UMP doub 385 n n C5 C6 UMP doub 386 n n C5 H5 UMP sing 387 n n C6 H6 UMP sing 388 n n C1' C2' UMP sing 389 n n C1' O4' UMP sing 390 n n C1' H1' UMP sing 391 n n C2' C3' UMP sing 392 n n C2' H2' UMP sing 393 n n C2' "H2''" UMP sing 394 n n C3' C4' UMP sing 395 n n C3' O3' UMP sing 396 n n C3' H3' UMP sing 397 n n C4' O4' UMP sing 398 n n C4' C5' UMP sing 399 n n C4' H4' UMP sing 400 n n O3' HO3' UMP sing 401 n n C5' O5' UMP sing 402 n n C5' H5' UMP sing 403 n n C5' "H5''" UMP sing 404 n n O5' P UMP sing 405 n n P OP1 UMP doub 406 n n P OP2 UMP sing 407 n n P OP3 UMP sing 408 n n OP2 HOP2 UMP sing 409 n n OP3 HOP3 UMP sing 410 n n # _atom_sites.entry_id 3TQ5 _atom_sites.fract_transf_matrix[1][1] 0.016471 _atom_sites.fract_transf_matrix[1][2] 0.009509 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019019 _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] 0.01568 _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 UMP A 1 777 777 UMP UMP . C 3 TRS A 1 153 1 TRS TRS . D 4 HOH A 1 154 1 HOH HOH . D 4 HOH A 2 155 2 HOH HOH . D 4 HOH A 3 156 3 HOH HOH . D 4 HOH A 4 157 4 HOH HOH . D 4 HOH A 5 158 5 HOH HOH . D 4 HOH A 6 159 6 HOH HOH . D 4 HOH A 7 160 7 HOH HOH . D 4 HOH A 8 161 9 HOH HOH . D 4 HOH A 9 162 10 HOH HOH . D 4 HOH A 10 163 11 HOH HOH . D 4 HOH A 11 164 12 HOH HOH . D 4 HOH A 12 165 13 HOH HOH . D 4 HOH A 13 166 15 HOH HOH . D 4 HOH A 14 167 16 HOH HOH . D 4 HOH A 15 168 17 HOH HOH . D 4 HOH A 16 169 18 HOH HOH . D 4 HOH A 17 170 19 HOH HOH . D 4 HOH A 18 171 20 HOH HOH . D 4 HOH A 19 172 21 HOH HOH . D 4 HOH A 20 173 22 HOH HOH . D 4 HOH A 21 174 23 HOH HOH . D 4 HOH A 22 175 24 HOH HOH . D 4 HOH A 23 176 25 HOH HOH . D 4 HOH A 24 177 26 HOH HOH . D 4 HOH A 25 178 27 HOH HOH . D 4 HOH A 26 179 28 HOH HOH . D 4 HOH A 27 180 29 HOH HOH . D 4 HOH A 28 181 30 HOH HOH . D 4 HOH A 29 182 31 HOH HOH . D 4 HOH A 30 183 32 HOH HOH . D 4 HOH A 31 184 33 HOH HOH . D 4 HOH A 32 185 34 HOH HOH . D 4 HOH A 33 186 35 HOH HOH . D 4 HOH A 34 187 36 HOH HOH . D 4 HOH A 35 188 37 HOH HOH . D 4 HOH A 36 189 38 HOH HOH . D 4 HOH A 37 190 39 HOH HOH . D 4 HOH A 38 191 40 HOH HOH . D 4 HOH A 39 192 41 HOH HOH . D 4 HOH A 40 193 42 HOH HOH . D 4 HOH A 41 194 43 HOH HOH . D 4 HOH A 42 195 44 HOH HOH . D 4 HOH A 43 196 45 HOH HOH . D 4 HOH A 44 197 46 HOH HOH . D 4 HOH A 45 198 47 HOH HOH . D 4 HOH A 46 199 48 HOH HOH . D 4 HOH A 47 200 49 HOH HOH . D 4 HOH A 48 201 50 HOH HOH . D 4 HOH A 49 202 51 HOH HOH . D 4 HOH A 50 203 52 HOH HOH . D 4 HOH A 51 204 53 HOH HOH . D 4 HOH A 52 205 54 HOH HOH . D 4 HOH A 53 206 55 HOH HOH . D 4 HOH A 54 207 56 HOH HOH . D 4 HOH A 55 208 57 HOH HOH . D 4 HOH A 56 209 58 HOH HOH . D 4 HOH A 57 210 59 HOH HOH . D 4 HOH A 58 211 60 HOH HOH . D 4 HOH A 59 212 61 HOH HOH . D 4 HOH A 60 213 62 HOH HOH . D 4 HOH A 61 214 63 HOH HOH . D 4 HOH A 62 215 64 HOH HOH . D 4 HOH A 63 216 65 HOH HOH . D 4 HOH A 64 217 66 HOH HOH . D 4 HOH A 65 218 67 HOH HOH . D 4 HOH A 66 219 68 HOH HOH . D 4 HOH A 67 220 69 HOH HOH . D 4 HOH A 68 221 70 HOH HOH . D 4 HOH A 69 222 71 HOH HOH . D 4 HOH A 70 223 72 HOH HOH . D 4 HOH A 71 224 73 HOH HOH . D 4 HOH A 72 225 74 HOH HOH . D 4 HOH A 73 226 75 HOH HOH . D 4 HOH A 74 227 76 HOH HOH . D 4 HOH A 75 228 77 HOH HOH . D 4 HOH A 76 229 78 HOH HOH . D 4 HOH A 77 230 79 HOH HOH . D 4 HOH A 78 231 80 HOH HOH . D 4 HOH A 79 232 81 HOH HOH . D 4 HOH A 80 233 82 HOH HOH . D 4 HOH A 81 234 83 HOH HOH . D 4 HOH A 82 235 84 HOH HOH . D 4 HOH A 83 236 85 HOH HOH . D 4 HOH A 84 237 88 HOH HOH . D 4 HOH A 85 238 89 HOH HOH . D 4 HOH A 86 239 90 HOH HOH . D 4 HOH A 87 240 91 HOH HOH . D 4 HOH A 88 241 92 HOH HOH . D 4 HOH A 89 242 93 HOH HOH . D 4 HOH A 90 243 94 HOH HOH . D 4 HOH A 91 244 95 HOH HOH . D 4 HOH A 92 245 96 HOH HOH . D 4 HOH A 93 246 97 HOH HOH . D 4 HOH A 94 247 98 HOH HOH . D 4 HOH A 95 248 99 HOH HOH . D 4 HOH A 96 249 100 HOH HOH . D 4 HOH A 97 250 101 HOH HOH . D 4 HOH A 98 251 102 HOH HOH . D 4 HOH A 99 252 103 HOH HOH . D 4 HOH A 100 253 104 HOH HOH . D 4 HOH A 101 254 105 HOH HOH . D 4 HOH A 102 255 106 HOH HOH . D 4 HOH A 103 256 107 HOH HOH . D 4 HOH A 104 257 108 HOH HOH . D 4 HOH A 105 258 109 HOH HOH . D 4 HOH A 106 259 110 HOH HOH . D 4 HOH A 107 260 111 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 UMP . . . B 2 -4.901 57.377 30.619 1 13.8 ? N1 UMP 777 A 1 HETATM 2 C C2 UMP . . . B 2 -3.709 56.903 30.153 1 14 ? C2 UMP 777 A 1 HETATM 3 N N3 UMP . . . B 2 -2.808 57.736 29.534 1 12.37 ? N3 UMP 777 A 1 HETATM 4 C C4 UMP . . . B 2 -3.115 59.09 29.365 1 13.91 ? C4 UMP 777 A 1 HETATM 5 C C5 UMP . . . B 2 -4.34 59.589 29.829 1 12.82 ? C5 UMP 777 A 1 HETATM 6 C C6 UMP . . . B 2 -5.233 58.74 30.489 1 13.44 ? C6 UMP 777 A 1 HETATM 7 O O2 UMP . . . B 2 -3.327 55.697 30.248 1 16.15 ? O2 UMP 777 A 1 HETATM 8 O O4 UMP . . . B 2 -2.27 59.782 28.811 1 14.81 ? O4 UMP 777 A 1 HETATM 9 C C1' UMP . . . B 2 -5.813 56.433 31.303 1 15.88 ? C1' UMP 777 A 1 HETATM 10 C C2' UMP . . . B 2 -5.723 56.811 32.814 1 15.54 ? C2' UMP 777 A 1 HETATM 11 C C3' UMP . . . B 2 -6.989 57.629 33.096 1 16.58 ? C3' UMP 777 A 1 HETATM 12 C C4' UMP . . . B 2 -7.929 57.035 32.065 1 13.48 ? C4' UMP 777 A 1 HETATM 13 O O3' UMP . . . B 2 -7.436 57.423 34.444 1 17.48 ? O3' UMP 777 A 1 HETATM 14 O O4' UMP . . . B 2 -7.15 56.699 30.927 1 16.16 ? O4' UMP 777 A 1 HETATM 15 C C5' UMP . . . B 2 -9.083 57.953 31.673 1 16.53 ? C5' UMP 777 A 1 HETATM 16 O O5' UMP . . . B 2 -8.44 59.075 31.07 1 16.13 ? O5' UMP 777 A 1 HETATM 17 P P UMP . . . B 2 -9.048 60.549 31.369 1 14.71 ? P UMP 777 A 1 HETATM 18 O OP1 UMP . . . B 2 -10.445 60.492 31.289 1 16.67 ? OP1 UMP 777 A 1 HETATM 19 O OP2 UMP . . . B 2 -8.527 60.888 32.86 1 18.89 ? OP2 UMP 777 A 1 HETATM 20 O OP3 UMP . . . B 2 -8.321 61.481 30.497 1 15.73 ? OP3 UMP 777 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #