data_3TRL # _model_server_result.job_id jw6bbwpVt217noU5-JjCaA _model_server_result.datetime_utc '2024-11-23 10:40:21' _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 3trl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":777}' # _entry.id 3TRL # _exptl.entry_id 3TRL _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 3TRL _cell.length_a 60.827 _cell.length_b 60.827 _cell.length_c 63.999 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TRL _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 _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 60.827 105.355454 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 -60.827 105.355454 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 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 3TRL _atom_sites.fract_transf_matrix[1][1] 0.01644 _atom_sites.fract_transf_matrix[1][2] 0.009492 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018983 _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] 0.015625 _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 HOH A 1 153 1 HOH HOH . C 3 HOH A 2 154 2 HOH HOH . C 3 HOH A 3 155 3 HOH HOH . C 3 HOH A 4 156 4 HOH HOH . C 3 HOH A 5 157 5 HOH HOH . C 3 HOH A 6 158 6 HOH HOH . C 3 HOH A 7 159 7 HOH HOH . C 3 HOH A 8 160 8 HOH HOH . C 3 HOH A 9 161 9 HOH HOH . C 3 HOH A 10 162 10 HOH HOH . C 3 HOH A 11 163 11 HOH HOH . C 3 HOH A 12 164 12 HOH HOH . C 3 HOH A 13 165 13 HOH HOH . C 3 HOH A 14 166 14 HOH HOH . C 3 HOH A 15 167 15 HOH HOH . C 3 HOH A 16 168 16 HOH HOH . C 3 HOH A 17 169 17 HOH HOH . C 3 HOH A 18 170 18 HOH HOH . C 3 HOH A 19 171 19 HOH HOH . C 3 HOH A 20 172 20 HOH HOH . C 3 HOH A 21 173 21 HOH HOH . C 3 HOH A 22 174 22 HOH HOH . C 3 HOH A 23 175 23 HOH HOH . C 3 HOH A 24 176 24 HOH HOH . C 3 HOH A 25 177 25 HOH HOH . C 3 HOH A 26 178 26 HOH HOH . C 3 HOH A 27 179 27 HOH HOH . C 3 HOH A 28 180 28 HOH HOH . C 3 HOH A 29 181 29 HOH HOH . C 3 HOH A 30 182 30 HOH HOH . C 3 HOH A 31 183 31 HOH HOH . C 3 HOH A 32 184 32 HOH HOH . C 3 HOH A 33 185 33 HOH HOH . C 3 HOH A 34 186 34 HOH HOH . C 3 HOH A 35 187 35 HOH HOH . C 3 HOH A 36 188 36 HOH HOH . C 3 HOH A 37 189 37 HOH HOH . C 3 HOH A 38 190 38 HOH HOH . C 3 HOH A 39 191 40 HOH HOH . C 3 HOH A 40 192 41 HOH HOH . C 3 HOH A 41 193 42 HOH HOH . C 3 HOH A 42 194 43 HOH HOH . C 3 HOH A 43 195 44 HOH HOH . C 3 HOH A 44 196 45 HOH HOH . C 3 HOH A 45 197 46 HOH HOH . C 3 HOH A 46 198 47 HOH HOH . C 3 HOH A 47 199 48 HOH HOH . C 3 HOH A 48 200 49 HOH HOH . C 3 HOH A 49 201 50 HOH HOH . C 3 HOH A 50 202 51 HOH HOH . C 3 HOH A 51 203 52 HOH HOH . C 3 HOH A 52 204 53 HOH HOH . C 3 HOH A 53 205 54 HOH HOH . C 3 HOH A 54 206 55 HOH HOH . C 3 HOH A 55 207 56 HOH HOH . C 3 HOH A 56 208 57 HOH HOH . C 3 HOH A 57 209 58 HOH HOH . C 3 HOH A 58 210 59 HOH HOH . C 3 HOH A 59 211 60 HOH HOH . C 3 HOH A 60 212 61 HOH HOH . C 3 HOH A 61 213 62 HOH HOH . C 3 HOH A 62 214 63 HOH HOH . C 3 HOH A 63 215 64 HOH HOH . C 3 HOH A 64 216 65 HOH HOH . C 3 HOH A 65 217 66 HOH HOH . C 3 HOH A 66 218 67 HOH HOH . C 3 HOH A 67 219 68 HOH HOH . C 3 HOH A 68 220 69 HOH HOH . C 3 HOH A 69 221 70 HOH HOH . C 3 HOH A 70 222 71 HOH HOH . C 3 HOH A 71 223 72 HOH HOH . C 3 HOH A 72 224 73 HOH HOH . C 3 HOH A 73 225 74 HOH HOH . C 3 HOH A 74 226 75 HOH HOH . C 3 HOH A 75 227 76 HOH HOH . C 3 HOH A 76 228 77 HOH HOH . C 3 HOH A 77 229 78 HOH HOH . C 3 HOH A 78 230 79 HOH HOH . C 3 HOH A 79 231 80 HOH HOH . C 3 HOH A 80 232 81 HOH HOH . C 3 HOH A 81 233 82 HOH HOH . C 3 HOH A 82 234 83 HOH HOH . C 3 HOH A 83 235 85 HOH HOH . C 3 HOH A 84 236 86 HOH HOH . C 3 HOH A 85 237 87 HOH HOH . C 3 HOH A 86 238 88 HOH HOH . C 3 HOH A 87 239 90 HOH HOH . C 3 HOH A 88 240 92 HOH HOH . C 3 HOH A 89 241 94 HOH HOH . C 3 HOH A 90 242 95 HOH HOH . C 3 HOH A 91 243 96 HOH HOH . C 3 HOH A 92 244 98 HOH HOH . C 3 HOH A 93 245 99 HOH HOH . C 3 HOH A 94 246 100 HOH HOH . C 3 HOH A 95 247 101 HOH HOH . C 3 HOH A 96 248 102 HOH HOH . C 3 HOH A 97 249 103 HOH HOH . C 3 HOH A 98 250 104 HOH HOH . C 3 HOH A 99 251 105 HOH HOH . C 3 HOH A 100 252 106 HOH HOH . C 3 HOH A 101 253 107 HOH HOH . C 3 HOH A 102 254 108 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 -4.929 57.508 30.793 1 23.61 ? N1 UMP 777 A 1 HETATM 2 C C2 UMP . . . B 2 -3.712 57.046 30.327 1 22.59 ? C2 UMP 777 A 1 HETATM 3 N N3 UMP . . . B 2 -2.838 57.906 29.675 1 22.1 ? N3 UMP 777 A 1 HETATM 4 C C4 UMP . . . B 2 -3.158 59.253 29.534 1 23.6 ? C4 UMP 777 A 1 HETATM 5 C C5 UMP . . . B 2 -4.386 59.728 30.029 1 21.67 ? C5 UMP 777 A 1 HETATM 6 C C6 UMP . . . B 2 -5.308 58.855 30.62 1 21.69 ? C6 UMP 777 A 1 HETATM 7 O O2 UMP . . . B 2 -3.383 55.825 30.417 1 24.14 ? O2 UMP 777 A 1 HETATM 8 O O4 UMP . . . B 2 -2.308 59.969 28.964 1 23.61 ? O4 UMP 777 A 1 HETATM 9 C C1' UMP . . . B 2 -5.88 56.596 31.463 1 23.59 ? C1' UMP 777 A 1 HETATM 10 C C2' UMP . . . B 2 -5.812 56.88 32.982 1 23.24 ? C2' UMP 777 A 1 HETATM 11 C C3' UMP . . . B 2 -7.01 57.775 33.251 1 23.84 ? C3' UMP 777 A 1 HETATM 12 C C4' UMP . . . B 2 -7.995 57.182 32.26 1 23.3 ? C4' UMP 777 A 1 HETATM 13 O O3' UMP . . . B 2 -7.422 57.591 34.589 1 25.82 ? O3' UMP 777 A 1 HETATM 14 O O4' UMP . . . B 2 -7.253 56.833 31.12 1 24.58 ? O4' UMP 777 A 1 HETATM 15 C C5' UMP . . . B 2 -9.138 58.081 31.84 1 25.63 ? C5' UMP 777 A 1 HETATM 16 O O5' UMP . . . B 2 -8.526 59.208 31.184 1 27.39 ? O5' UMP 777 A 1 HETATM 17 P P UMP . . . B 2 -9.106 60.688 31.478 1 25.07 ? P UMP 777 A 1 HETATM 18 O OP1 UMP . . . B 2 -10.509 60.67 31.432 1 27.2 ? OP1 UMP 777 A 1 HETATM 19 O OP2 UMP . . . B 2 -8.611 60.931 32.925 1 30.5 ? OP2 UMP 777 A 1 HETATM 20 O OP3 UMP . . . B 2 -8.38 61.649 30.588 1 26.24 ? OP3 UMP 777 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #