data_1U1B # _model_server_result.job_id nzH5rU75ZoHArcydIf0K-g _model_server_result.datetime_utc '2025-02-05 11:53:25' _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 1u1b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":902}' # _entry.id 1U1B # _exptl.entry_id 1U1B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 809.358 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-PHOSPHOTHYMIDINE (3'-5')-PYROPHOSPHATE ADENOSINE 3'-PHOSPHATE" _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 106.31 _cell.angle_gamma 90 _cell.entry_id 1U1B _cell.length_a 31.086 _cell.length_b 75.861 _cell.length_c 51.821 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U1B _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 ? 2 C N N ? 2 D 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C20 H27 N7 O20 P4 -2' _chem_comp.formula_weight 809.358 _chem_comp.id PAX _chem_comp.mon_nstd_flag . _chem_comp.name "5'-PHOSPHOTHYMIDINE (3'-5')-PYROPHOSPHATE ADENOSINE 3'-PHOSPHATE" _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 PA O1A PAX sing 237 n n PA O2A PAX doub 238 n n PA O5' PAX sing 239 n n PA O3A PAX sing 240 n n O5' C5' PAX sing 241 n n PB O1B PAX sing 242 n n PB O2B PAX doub 243 n n PB O3A PAX sing 244 n n PB O3 PAX sing 245 n n PG O1G PAX sing 246 n n PG O2G PAX sing 247 n n PG O3G PAX doub 248 n n PG O3' PAX sing 249 n n O1G H1G PAX sing 250 n n N9A C4A PAX sing 251 n y N9A C8A PAX sing 252 n y N9A C1' PAX sing 253 n n C4A N3A PAX doub 254 n y C4A C5A PAX sing 255 n y N3A C2A PAX sing 256 n y C2A N1A PAX doub 257 n y C2A H2A PAX sing 258 n n N1A C6A PAX sing 259 n y C6A N6A PAX sing 260 n n C6A C5A PAX doub 261 n y N6A H6A1 PAX sing 262 n n N6A H6A2 PAX sing 263 n n C5A N7A PAX sing 264 n y N7A C8A PAX doub 265 n y C8A H8A PAX sing 266 n n C5' C4' PAX sing 267 n n C5' "H5'1" PAX sing 268 n n C5' "H5'2" PAX sing 269 n n C4' O4' PAX sing 270 n n C4' C3' PAX sing 271 n n C4' H4' PAX sing 272 n n O4' C1' PAX sing 273 n n C1' C2' PAX sing 274 n n C1' H1' PAX sing 275 n n C2' O2' PAX sing 276 n n C2' C3' PAX sing 277 n n C2' H2' PAX sing 278 n n O2' H2 PAX sing 279 n n C3' O3' PAX sing 280 n n C3' H3' PAX sing 281 n n O5 C5 PAX sing 282 n n O5 PD PAX sing 283 n n C5 C4 PAX sing 284 n n C5 H51 PAX sing 285 n n C5 H52 PAX sing 286 n n C4 O4 PAX sing 287 n n C4 C3 PAX sing 288 n n C4 H4 PAX sing 289 n n O4 C1 PAX sing 290 n n C1 C2 PAX sing 291 n n C1 N1T PAX sing 292 n n C1 H1 PAX sing 293 n n C2 C3 PAX sing 294 n n C2 H21 PAX sing 295 n n C2 H22 PAX sing 296 n n C3 O3 PAX sing 297 n n C3 H3 PAX sing 298 n n PD O1D PAX sing 299 n n PD O2D PAX sing 300 n n PD O3D PAX doub 301 n n O2D H2D PAX sing 302 n n N1T C6T PAX sing 303 n y N1T C2T PAX sing 304 n y C6T C5T PAX doub 305 n y C6T H6T PAX sing 306 n n C2T O2T PAX doub 307 n n C2T N3T PAX sing 308 n y N3T C4T PAX sing 309 n y N3T H3T PAX sing 310 n n C4T O4T PAX doub 311 n n C4T C5T PAX sing 312 n y C5T CM5 PAX sing 313 n n CM5 HM51 PAX sing 314 n n CM5 HM52 PAX sing 315 n n CM5 HM53 PAX sing 316 n n HO1 O2G PAX sing 317 n n HO2 O1D PAX sing 318 n n # _atom_sites.entry_id 1U1B _atom_sites.fract_transf_matrix[1][1] 0.032169 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.009413 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013182 _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] 0.020106 _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 PAX A 1 901 901 PAX PTA . D 2 PAX B 1 902 902 PAX PTA . E 3 HOH A 1 902 2 HOH HOH . E 3 HOH A 2 903 4 HOH HOH . E 3 HOH A 3 904 5 HOH HOH . E 3 HOH A 4 905 9 HOH HOH . E 3 HOH A 5 906 10 HOH HOH . E 3 HOH A 6 907 12 HOH HOH . E 3 HOH A 7 908 13 HOH HOH . E 3 HOH A 8 909 14 HOH HOH . E 3 HOH A 9 910 18 HOH HOH . E 3 HOH A 10 911 19 HOH HOH . E 3 HOH A 11 912 20 HOH HOH . E 3 HOH A 12 913 21 HOH HOH . E 3 HOH A 13 914 23 HOH HOH . E 3 HOH A 14 915 24 HOH HOH . E 3 HOH A 15 916 25 HOH HOH . E 3 HOH A 16 917 28 HOH HOH . E 3 HOH A 17 918 29 HOH HOH . E 3 HOH A 18 919 33 HOH HOH . E 3 HOH A 19 920 35 HOH HOH . E 3 HOH A 20 921 37 HOH HOH . E 3 HOH A 21 922 38 HOH HOH . E 3 HOH A 22 923 39 HOH HOH . E 3 HOH A 23 924 40 HOH HOH . E 3 HOH A 24 925 41 HOH HOH . E 3 HOH A 25 926 42 HOH HOH . E 3 HOH A 26 927 43 HOH HOH . E 3 HOH A 27 928 44 HOH HOH . E 3 HOH A 28 929 45 HOH HOH . E 3 HOH A 29 930 46 HOH HOH . E 3 HOH A 30 931 47 HOH HOH . E 3 HOH A 31 932 48 HOH HOH . E 3 HOH A 32 933 49 HOH HOH . E 3 HOH A 33 934 50 HOH HOH . E 3 HOH A 34 935 53 HOH HOH . E 3 HOH A 35 936 55 HOH HOH . E 3 HOH A 36 937 56 HOH HOH . E 3 HOH A 37 938 58 HOH HOH . E 3 HOH A 38 939 61 HOH HOH . E 3 HOH A 39 940 63 HOH HOH . E 3 HOH A 40 941 64 HOH HOH . E 3 HOH A 41 942 65 HOH HOH . E 3 HOH A 42 943 66 HOH HOH . E 3 HOH A 43 944 72 HOH HOH . E 3 HOH A 44 945 74 HOH HOH . F 3 HOH B 1 903 1 HOH HOH . F 3 HOH B 2 904 3 HOH HOH . F 3 HOH B 3 905 6 HOH HOH . F 3 HOH B 4 906 7 HOH HOH . F 3 HOH B 5 907 11 HOH HOH . F 3 HOH B 6 908 17 HOH HOH . F 3 HOH B 7 909 22 HOH HOH . F 3 HOH B 8 910 26 HOH HOH . F 3 HOH B 9 911 27 HOH HOH . F 3 HOH B 10 912 30 HOH HOH . F 3 HOH B 11 913 31 HOH HOH . F 3 HOH B 12 914 51 HOH HOH . F 3 HOH B 13 915 52 HOH HOH . F 3 HOH B 14 916 54 HOH HOH . F 3 HOH B 15 917 57 HOH HOH . F 3 HOH B 16 918 59 HOH HOH . F 3 HOH B 17 919 60 HOH HOH . F 3 HOH B 18 920 68 HOH HOH . F 3 HOH B 19 921 69 HOH HOH . F 3 HOH B 20 922 70 HOH HOH . F 3 HOH B 21 923 71 HOH HOH . F 3 HOH B 22 924 73 HOH HOH . F 3 HOH B 23 925 75 HOH HOH . F 3 HOH B 24 926 76 HOH HOH . F 3 HOH B 25 927 77 HOH HOH . F 3 HOH B 26 928 79 HOH HOH . F 3 HOH B 27 929 80 HOH HOH . F 3 HOH B 28 930 81 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 PA PAX . . . D 2 -24.136 -18.73 -9.572 1 55.71 ? PA PAX 902 B 1 HETATM 2 O O1A PAX . . . D 2 -25.55 -19.31 -9.536 1 57.45 ? O1A PAX 902 B 1 HETATM 3 O O2A PAX . . . D 2 -23.71 -18.04 -10.873 1 55.62 ? O2A PAX 902 B 1 HETATM 4 O O5' PAX . . . D 2 -23.925 -17.704 -8.369 1 55.28 ? O5' PAX 902 B 1 HETATM 5 P PB PAX . . . D 2 -22.779 -20.736 -7.959 1 55.42 ? PB PAX 902 B 1 HETATM 6 O O1B PAX . . . D 2 -22.023 -19.881 -7.013 1 55.13 ? O1B PAX 902 B 1 HETATM 7 O O2B PAX . . . D 2 -24.034 -21.383 -7.523 1 54.77 ? O2B PAX 902 B 1 HETATM 8 O O3A PAX . . . D 2 -23.096 -19.879 -9.247 1 56.07 ? O3A PAX 902 B 1 HETATM 9 P PG PAX . . . D 2 -29.23 -15.857 -8.064 1 57.14 ? PG PAX 902 B 1 HETATM 10 O O1G PAX . . . D 2 -29.417 -15.806 -6.548 1 57.11 ? O1G PAX 902 B 1 HETATM 11 O O2G PAX . . . D 2 -30.184 -14.949 -8.831 1 56.94 ? O2G PAX 902 B 1 HETATM 12 O O3G PAX . . . D 2 -29.297 -17.307 -8.575 1 56.57 ? O3G PAX 902 B 1 HETATM 13 N N9A PAX . . . D 2 -24.014 -13.43 -9.846 1 40.17 ? N9A PAX 902 B 1 HETATM 14 C C4A PAX . . . D 2 -23.062 -13.762 -10.795 1 36.93 ? C4A PAX 902 B 1 HETATM 15 N N3A PAX . . . D 2 -22.842 -14.983 -11.376 1 35.83 ? N3A PAX 902 B 1 HETATM 16 C C2A PAX . . . D 2 -21.813 -14.942 -12.276 1 37.36 ? C2A PAX 902 B 1 HETATM 17 N N1A PAX . . . D 2 -21.038 -13.862 -12.619 1 38.97 ? N1A PAX 902 B 1 HETATM 18 C C6A PAX . . . D 2 -21.291 -12.649 -12.01 1 38.16 ? C6A PAX 902 B 1 HETATM 19 N N6A PAX . . . D 2 -20.536 -11.606 -12.348 1 36.9 ? N6A PAX 902 B 1 HETATM 20 C C5A PAX . . . D 2 -22.353 -12.571 -11.047 1 37.24 ? C5A PAX 902 B 1 HETATM 21 N N7A PAX . . . D 2 -22.848 -11.533 -10.284 1 36.62 ? N7A PAX 902 B 1 HETATM 22 C C8A PAX . . . D 2 -23.821 -12.086 -9.596 1 39.45 ? C8A PAX 902 B 1 HETATM 23 C C5' PAX . . . D 2 -24.982 -17.399 -7.471 1 52.2 ? C5' PAX 902 B 1 HETATM 24 C C4' PAX . . . D 2 -25.551 -16.033 -7.756 1 50.83 ? C4' PAX 902 B 1 HETATM 25 O O4' PAX . . . D 2 -24.5 -15.104 -8.197 1 48.07 ? O4' PAX 902 B 1 HETATM 26 C C1' PAX . . . D 2 -25.062 -14.247 -9.173 1 45.86 ? C1' PAX 902 B 1 HETATM 27 C C2' PAX . . . D 2 -25.924 -15.23 -9.986 1 49.11 ? C2' PAX 902 B 1 HETATM 28 O O2' PAX . . . D 2 -26.795 -14.589 -10.916 1 48.95 ? O2' PAX 902 B 1 HETATM 29 C C3' PAX . . . D 2 -26.63 -16.001 -8.863 1 51.53 ? C3' PAX 902 B 1 HETATM 30 O O3' PAX . . . D 2 -27.738 -15.238 -8.359 1 54.74 ? O3' PAX 902 B 1 HETATM 31 O O5 PAX . . . D 2 -19.696 -22.514 -12.32 1 57.16 ? O5 PAX 902 B 1 HETATM 32 C C5 PAX . . . D 2 -20.977 -23.003 -11.865 1 52.56 ? C5 PAX 902 B 1 HETATM 33 C C4 PAX . . . D 2 -20.989 -23.121 -10.352 1 47.45 ? C4 PAX 902 B 1 HETATM 34 O O4 PAX . . . D 2 -19.786 -23.773 -9.903 1 44.51 ? O4 PAX 902 B 1 HETATM 35 C C1 PAX . . . D 2 -19.121 -22.977 -8.945 1 39.51 ? C1 PAX 902 B 1 HETATM 36 C C2 PAX . . . D 2 -19.608 -21.559 -9.155 1 43.27 ? C2 PAX 902 B 1 HETATM 37 C C3 PAX . . . D 2 -21.04 -21.791 -9.614 1 47.16 ? C3 PAX 902 B 1 HETATM 38 O O3 PAX . . . D 2 -21.885 -21.95 -8.497 1 49.58 ? O3 PAX 902 B 1 HETATM 39 P PD PAX . . . D 2 -19.538 -21.643 -13.7 1 61.12 ? PD PAX 902 B 1 HETATM 40 O O1D PAX . . . D 2 -19.675 -22.675 -14.832 1 59.52 ? O1D PAX 902 B 1 HETATM 41 O O2D PAX . . . D 2 -18.134 -20.992 -13.636 1 59.86 ? O2D PAX 902 B 1 HETATM 42 O O3D PAX . . . D 2 -20.68 -20.612 -13.688 1 58.22 ? O3D PAX 902 B 1 HETATM 43 N N1T PAX . . . D 2 -17.662 -23.15 -9.151 1 34.84 ? N1T PAX 902 B 1 HETATM 44 C C6T PAX . . . D 2 -17.075 -23.076 -10.441 1 32.13 ? C6T PAX 902 B 1 HETATM 45 C C2T PAX . . . D 2 -16.875 -23.396 -8.006 1 31.49 ? C2T PAX 902 B 1 HETATM 46 O O2T PAX . . . D 2 -17.326 -23.463 -6.881 1 28.11 ? O2T PAX 902 B 1 HETATM 47 N N3T PAX . . . D 2 -15.522 -23.559 -8.269 1 29.48 ? N3T PAX 902 B 1 HETATM 48 C C4T PAX . . . D 2 -14.885 -23.499 -9.516 1 29.74 ? C4T PAX 902 B 1 HETATM 49 O O4T PAX . . . D 2 -13.671 -23.67 -9.558 1 29.62 ? O4T PAX 902 B 1 HETATM 50 C C5T PAX . . . D 2 -15.753 -23.233 -10.656 1 30.64 ? C5T PAX 902 B 1 HETATM 51 C CM5 PAX . . . D 2 -15.196 -23.139 -12.044 1 27.36 ? CM5 PAX 902 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 51 #