data_11BA # _model_server_result.job_id azKVLxFmr9H8QguhXKWbXQ _model_server_result.datetime_utc '2024-11-21 14:31:13' _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 11ba # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":125}' # _entry.id 11BA # _exptl.entry_id 11BA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 573.407 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDYLYL-2'-5'-PHOSPHO-ADENOSINE" _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 117.35 _cell.angle_gamma 90 _cell.entry_id 11BA _cell.length_a 49.45 _cell.length_b 60.64 _cell.length_c 50.75 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 11BA _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D,E,F,G,H,I _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 ? 3 D N N ? 3 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 A SG CYS 31 A CYS 31 1_555 B SG CYS 32 B CYS 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? disulf ? disulf3 A SG CYS 32 A CYS 32 1_555 B SG CYS 31 B CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf5 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf6 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? disulf ? disulf7 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf8 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf9 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? disulf ? disulf10 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? # _chem_comp.formula 'C19 H24 N7 O12 P' _chem_comp.formula_weight 573.407 _chem_comp.id UPA _chem_comp.mon_nstd_flag . _chem_comp.name "URIDYLYL-2'-5'-PHOSPHO-ADENOSINE" _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 N1U C2U UPA sing 334 n n N1U C6U UPA sing 335 n n N1U C1D UPA sing 336 n n C2U O2U UPA doub 337 n n C2U N3U UPA sing 338 n n N3U C4U UPA sing 339 n n N3U H3U UPA sing 340 n n O4U C4U UPA doub 341 n n C4U C5U UPA sing 342 n n C5U C6U UPA doub 343 n n C5U H5U UPA sing 344 n n C6U H6U UPA sing 345 n n C5D O5D UPA sing 346 n n C5D C4D UPA sing 347 n n C5D H5U1 UPA sing 348 n n C5D H5U2 UPA sing 349 n n O5D HOU5 UPA sing 350 n n C4D O4D UPA sing 351 n n C4D C3D UPA sing 352 n n C4D H4U' UPA sing 353 n n O4D C1D UPA sing 354 n n C3D O3D UPA sing 355 n n C3D C2D UPA sing 356 n n C3D H3U' UPA sing 357 n n O3D HOU3 UPA sing 358 n n C2D O2D UPA sing 359 n n C2D C1D UPA sing 360 n n C2D H2U' UPA sing 361 n n O2D P UPA sing 362 n n C1D H1U' UPA sing 363 n n P O1P UPA doub 364 n n P O2P UPA sing 365 n n P O5B UPA sing 366 n n O2P HOP2 UPA sing 367 n n O5B C5B UPA sing 368 n n C5B C4B UPA sing 369 n n C5B H5A1 UPA sing 370 n n C5B H5A2 UPA sing 371 n n C4B O4B UPA sing 372 n n C4B C3B UPA sing 373 n n C4B H4A' UPA sing 374 n n O4B C1B UPA sing 375 n n C3B O3B UPA sing 376 n n C3B C2B UPA sing 377 n n C3B H3A' UPA sing 378 n n O3B HOA3 UPA sing 379 n n C2B O2B UPA sing 380 n n C2B C1B UPA sing 381 n n C2B H2A' UPA sing 382 n n O2B HOA2 UPA sing 383 n n C1B N9A UPA sing 384 n n C1B H1A' UPA sing 385 n n N9A C8A UPA sing 386 n y N9A C4A UPA sing 387 n y C8A N7A UPA doub 388 n y C8A H8A UPA sing 389 n n N7A C5A UPA sing 390 n y C6A N6A UPA sing 391 n n C6A C5A UPA sing 392 n y C6A N1A UPA doub 393 n y N6A H6A1 UPA sing 394 n n N6A H6A2 UPA sing 395 n n C5A C4A UPA doub 396 n y C4A N3A UPA sing 397 n y N3A C2A UPA doub 398 n y C2A N1A UPA sing 399 n y C2A H2A UPA sing 400 n n # _atom_sites.entry_id 11BA _atom_sites.fract_transf_matrix[1][1] 0.020222 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.01046 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016491 _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] 0.022184 _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 SO4 A 1 127 127 SO4 SO4 . D 3 UPA A 1 125 125 UPA UPA . E 2 SO4 B 1 128 128 SO4 SO4 . F 2 SO4 B 1 129 129 SO4 SO4 . G 3 UPA B 1 126 126 UPA UPA . H 4 HOH A 1 130 130 HOH HOH . H 4 HOH A 2 132 132 HOH HOH . H 4 HOH A 3 134 134 HOH HOH . H 4 HOH A 4 135 135 HOH HOH . H 4 HOH A 5 136 136 HOH HOH . H 4 HOH A 6 137 137 HOH HOH . H 4 HOH A 7 140 140 HOH HOH . H 4 HOH A 8 142 142 HOH HOH . H 4 HOH A 9 143 143 HOH HOH . H 4 HOH A 10 144 144 HOH HOH . H 4 HOH A 11 145 145 HOH HOH . H 4 HOH A 12 146 146 HOH HOH . H 4 HOH A 13 147 147 HOH HOH . H 4 HOH A 14 148 148 HOH HOH . H 4 HOH A 15 150 150 HOH HOH . H 4 HOH A 16 151 151 HOH HOH . H 4 HOH A 17 152 152 HOH HOH . H 4 HOH A 18 153 153 HOH HOH . H 4 HOH A 19 154 154 HOH HOH . H 4 HOH A 20 155 155 HOH HOH . H 4 HOH A 21 156 156 HOH HOH . H 4 HOH A 22 157 157 HOH HOH . H 4 HOH A 23 158 158 HOH HOH . H 4 HOH A 24 159 159 HOH HOH . H 4 HOH A 25 160 160 HOH HOH . H 4 HOH A 26 161 161 HOH HOH . H 4 HOH A 27 162 162 HOH HOH . H 4 HOH A 28 164 164 HOH HOH . H 4 HOH A 29 165 165 HOH HOH . H 4 HOH A 30 166 166 HOH HOH . H 4 HOH A 31 167 167 HOH HOH . H 4 HOH A 32 168 168 HOH HOH . H 4 HOH A 33 169 169 HOH HOH . H 4 HOH A 34 170 170 HOH HOH . H 4 HOH A 35 171 171 HOH HOH . H 4 HOH A 36 172 172 HOH HOH . H 4 HOH A 37 173 173 HOH HOH . H 4 HOH A 38 174 174 HOH HOH . H 4 HOH A 39 175 175 HOH HOH . H 4 HOH A 40 176 176 HOH HOH . H 4 HOH A 41 177 177 HOH HOH . H 4 HOH A 42 178 178 HOH HOH . H 4 HOH A 43 179 179 HOH HOH . H 4 HOH A 44 180 180 HOH HOH . H 4 HOH A 45 181 181 HOH HOH . H 4 HOH A 46 184 184 HOH HOH . H 4 HOH A 47 196 196 HOH HOH . H 4 HOH A 48 225 225 HOH HOH . H 4 HOH A 49 226 226 HOH HOH . H 4 HOH A 50 228 228 HOH HOH . H 4 HOH A 51 231 231 HOH HOH . H 4 HOH A 52 233 233 HOH HOH . H 4 HOH A 53 234 234 HOH HOH . H 4 HOH A 54 238 238 HOH HOH . I 4 HOH B 1 131 131 HOH HOH . I 4 HOH B 2 133 133 HOH HOH . I 4 HOH B 3 138 138 HOH HOH . I 4 HOH B 4 139 139 HOH HOH . I 4 HOH B 5 141 141 HOH HOH . I 4 HOH B 6 149 149 HOH HOH . I 4 HOH B 7 163 163 HOH HOH . I 4 HOH B 8 182 182 HOH HOH . I 4 HOH B 9 183 183 HOH HOH . I 4 HOH B 10 185 185 HOH HOH . I 4 HOH B 11 186 186 HOH HOH . I 4 HOH B 12 187 187 HOH HOH . I 4 HOH B 13 188 188 HOH HOH . I 4 HOH B 14 189 189 HOH HOH . I 4 HOH B 15 190 190 HOH HOH . I 4 HOH B 16 191 191 HOH HOH . I 4 HOH B 17 192 192 HOH HOH . I 4 HOH B 18 193 193 HOH HOH . I 4 HOH B 19 194 194 HOH HOH . I 4 HOH B 20 195 195 HOH HOH . I 4 HOH B 21 197 197 HOH HOH . I 4 HOH B 22 198 198 HOH HOH . I 4 HOH B 23 199 199 HOH HOH . I 4 HOH B 24 200 200 HOH HOH . I 4 HOH B 25 201 201 HOH HOH . I 4 HOH B 26 202 202 HOH HOH . I 4 HOH B 27 203 203 HOH HOH . I 4 HOH B 28 204 204 HOH HOH . I 4 HOH B 29 205 205 HOH HOH . I 4 HOH B 30 206 206 HOH HOH . I 4 HOH B 31 208 208 HOH HOH . I 4 HOH B 32 209 209 HOH HOH . I 4 HOH B 33 210 210 HOH HOH . I 4 HOH B 34 211 211 HOH HOH . I 4 HOH B 35 212 212 HOH HOH . I 4 HOH B 36 213 213 HOH HOH . I 4 HOH B 37 214 214 HOH HOH . I 4 HOH B 38 215 215 HOH HOH . I 4 HOH B 39 216 216 HOH HOH . I 4 HOH B 40 217 217 HOH HOH . I 4 HOH B 41 218 218 HOH HOH . I 4 HOH B 42 219 219 HOH HOH . I 4 HOH B 43 220 220 HOH HOH . I 4 HOH B 44 221 221 HOH HOH . I 4 HOH B 45 222 222 HOH HOH . I 4 HOH B 46 223 223 HOH HOH . I 4 HOH B 47 224 224 HOH HOH . I 4 HOH B 48 227 227 HOH HOH . I 4 HOH B 49 229 229 HOH HOH . I 4 HOH B 50 230 230 HOH HOH . I 4 HOH B 51 232 232 HOH HOH . I 4 HOH B 52 235 235 HOH HOH . I 4 HOH B 53 236 236 HOH HOH . I 4 HOH B 54 237 237 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 N1U UPA . . . D 3 -14.054 14.986 5.129 1 13.32 ? N1U UPA 125 A 1 HETATM 2 C C2U UPA . . . D 3 -14.5 14.015 5.984 1 12.96 ? C2U UPA 125 A 1 HETATM 3 O O2U UPA . . . D 3 -14.277 12.811 5.845 1 12.3 ? O2U UPA 125 A 1 HETATM 4 N N3U UPA . . . D 3 -15.248 14.467 7.031 1 12.72 ? N3U UPA 125 A 1 HETATM 5 O O4U UPA . . . D 3 -16.359 16.008 8.264 1 13.1 ? O4U UPA 125 A 1 HETATM 6 C C4U UPA . . . D 3 -15.672 15.747 7.265 1 12.8 ? C4U UPA 125 A 1 HETATM 7 C C5U UPA . . . D 3 -15.151 16.686 6.324 1 12.74 ? C5U UPA 125 A 1 HETATM 8 C C6U UPA . . . D 3 -14.406 16.288 5.3 1 12.45 ? C6U UPA 125 A 1 HETATM 9 C C5D UPA . . . D 3 -11.902 17.713 2.417 1 14.83 ? C5D UPA 125 A 1 HETATM 10 O O5D UPA . . . D 3 -12.695 18.487 3.349 1 17.51 ? O5D UPA 125 A 1 HETATM 11 C C4D UPA . . . D 3 -12.184 16.229 2.537 1 14.8 ? C4D UPA 125 A 1 HETATM 12 O O4D UPA . . . D 3 -12.232 15.735 3.893 1 14.63 ? O4D UPA 125 A 1 HETATM 13 C C3D UPA . . . D 3 -13.531 15.877 1.999 1 14.3 ? C3D UPA 125 A 1 HETATM 14 O O3D UPA . . . D 3 -13.443 15.758 0.581 1 14.39 ? O3D UPA 125 A 1 HETATM 15 C C2D UPA . . . D 3 -13.703 14.508 2.621 1 14.56 ? C2D UPA 125 A 1 HETATM 16 O O2D UPA . . . D 3 -13.003 13.557 1.912 1 15.77 ? O2D UPA 125 A 1 HETATM 17 C C1D UPA . . . D 3 -13.135 14.586 4.012 1 13.79 ? C1D UPA 125 A 1 HETATM 18 P P UPA . . . D 3 -13.538 12.474 0.945 1 17.01 ? P UPA 125 A 1 HETATM 19 O O1P UPA . . . D 3 -13.016 11.141 1.381 1 17.07 ? O1P UPA 125 A 1 HETATM 20 O O2P UPA . . . D 3 -15.026 12.671 0.98 1 17.97 ? O2P UPA 125 A 1 HETATM 21 O O5B UPA . . . D 3 -13.094 12.982 -0.445 1 16.46 ? O5B UPA 125 A 1 HETATM 22 C C5B UPA . . . D 3 -13.084 12.206 -1.611 1 16.53 ? C5B UPA 125 A 1 HETATM 23 C C4B UPA . . . D 3 -13.237 13.069 -2.778 1 16.93 ? C4B UPA 125 A 1 HETATM 24 O O4B UPA . . . D 3 -14.6 13.551 -2.885 1 17.52 ? O4B UPA 125 A 1 HETATM 25 C C3B UPA . . . D 3 -12.339 14.344 -2.707 1 17.48 ? C3B UPA 125 A 1 HETATM 26 O O3B UPA . . . D 3 -11.455 14.216 -3.845 1 16.96 ? O3B UPA 125 A 1 HETATM 27 C C2B UPA . . . D 3 -13.314 15.469 -3.2 1 17.32 ? C2B UPA 125 A 1 HETATM 28 O O2B UPA . . . D 3 -12.752 16.066 -4.412 1 17.29 ? O2B UPA 125 A 1 HETATM 29 C C1B UPA . . . D 3 -14.524 14.648 -3.733 1 17.39 ? C1B UPA 125 A 1 HETATM 30 N N9A UPA . . . D 3 -15.77 15.43 -3.7 1 17.67 ? N9A UPA 125 A 1 HETATM 31 C C8A UPA . . . D 3 -16.089 16.573 -2.973 1 17.5 ? C8A UPA 125 A 1 HETATM 32 N N7A UPA . . . D 3 -17.262 17.043 -3.198 1 17.35 ? N7A UPA 125 A 1 HETATM 33 C C6A UPA . . . D 3 -19.059 16.042 -4.772 1 17.41 ? C6A UPA 125 A 1 HETATM 34 N N6A UPA . . . D 3 -20.028 16.927 -4.518 1 17.31 ? N6A UPA 125 A 1 HETATM 35 C C5A UPA . . . D 3 -17.791 16.129 -4.14 1 17.79 ? C5A UPA 125 A 1 HETATM 36 C C4A UPA . . . D 3 -16.88 15.132 -4.457 1 17.61 ? C4A UPA 125 A 1 HETATM 37 N N3A UPA . . . D 3 -17.05 14.087 -5.317 1 17.46 ? N3A UPA 125 A 1 HETATM 38 C C2A UPA . . . D 3 -18.234 14.135 -5.863 1 17.55 ? C2A UPA 125 A 1 HETATM 39 N N1A UPA . . . D 3 -19.205 15.042 -5.659 1 17.35 ? N1A UPA 125 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #