data_3TP5 # _model_server_result.job_id XfE2cKnuUYzvDRS4gre7Iw _model_server_result.datetime_utc '2024-10-20 00:53:57' _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 3tp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3TP5 # _exptl.entry_id 3TP5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 3TP5 _cell.length_a 30.941 _cell.length_b 60.666 _cell.length_c 78.979 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TP5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna linking' _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 P2 O4P THP doub 298 n n P2 O5P THP sing 299 n n P2 O6P THP sing 300 n n P2 O5' THP sing 301 n n O5P HOP5 THP sing 302 n n O6P HOP6 THP sing 303 n n P1 O1P THP doub 304 n n P1 O2P THP sing 305 n n P1 O3P THP sing 306 n n P1 O3' THP sing 307 n n O2P HOP2 THP sing 308 n n O3P HOP3 THP sing 309 n n O5' C5' THP sing 310 n n C5' C4' THP sing 311 n n C5' "H5'1" THP sing 312 n n C5' "H5'2" THP sing 313 n n C4' O4' THP sing 314 n n C4' C3' THP sing 315 n n C4' H4' THP sing 316 n n O4' C1' THP sing 317 n n C3' O3' THP sing 318 n n C3' C2' THP sing 319 n n C3' H3' THP sing 320 n n C2' C1' THP sing 321 n n C2' "H2'1" THP sing 322 n n C2' "H2'2" THP sing 323 n n C1' N1 THP sing 324 n n C1' H1' THP sing 325 n n N1 C2 THP sing 326 n n N1 C6 THP sing 327 n n C2 O2 THP doub 328 n n C2 N3 THP sing 329 n n N3 C4 THP sing 330 n n N3 H3 THP sing 331 n n C4 O4 THP doub 332 n n C4 C5 THP sing 333 n n C5 C5M THP sing 334 n n C5 C6 THP doub 335 n n C5M H51 THP sing 336 n n C5M H52 THP sing 337 n n C5M H53 THP sing 338 n n C6 H6 THP sing 339 n n # _atom_sites.entry_id 3TP5 _atom_sites.fract_transf_matrix[1][1] 0.03232 _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] 0.016484 _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] 0.012662 _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 THP A 1 150 142 THP THP . C 3 MPD A 1 151 1 MPD MPD . D 4 HOH A 1 152 45 HOH HOH . D 4 HOH A 2 153 46 HOH HOH . D 4 HOH A 3 154 47 HOH HOH . D 4 HOH A 4 155 48 HOH HOH . D 4 HOH A 5 156 1 HOH HOH . D 4 HOH A 6 157 2 HOH HOH . D 4 HOH A 7 158 3 HOH HOH . D 4 HOH A 8 159 4 HOH HOH . D 4 HOH A 9 160 5 HOH HOH . D 4 HOH A 10 161 6 HOH HOH . D 4 HOH A 11 162 7 HOH HOH . D 4 HOH A 12 163 8 HOH HOH . D 4 HOH A 13 164 9 HOH HOH . D 4 HOH A 14 165 10 HOH HOH . D 4 HOH A 15 166 11 HOH HOH . D 4 HOH A 16 167 12 HOH HOH . D 4 HOH A 17 168 13 HOH HOH . D 4 HOH A 18 169 14 HOH HOH . D 4 HOH A 19 170 15 HOH HOH . D 4 HOH A 20 171 17 HOH HOH . D 4 HOH A 21 172 18 HOH HOH . D 4 HOH A 22 173 19 HOH HOH . D 4 HOH A 23 174 20 HOH HOH . D 4 HOH A 24 175 21 HOH HOH . D 4 HOH A 25 176 24 HOH HOH . D 4 HOH A 26 177 25 HOH HOH . D 4 HOH A 27 178 26 HOH HOH . D 4 HOH A 28 179 28 HOH HOH . D 4 HOH A 29 180 29 HOH HOH . D 4 HOH A 30 181 30 HOH HOH . D 4 HOH A 31 182 31 HOH HOH . D 4 HOH A 32 183 32 HOH HOH . D 4 HOH A 33 184 33 HOH HOH . D 4 HOH A 34 185 37 HOH HOH . D 4 HOH A 35 186 38 HOH HOH . D 4 HOH A 36 187 39 HOH HOH . D 4 HOH A 37 188 41 HOH HOH . D 4 HOH A 38 189 43 HOH HOH . D 4 HOH A 39 190 51 HOH HOH . D 4 HOH A 40 191 52 HOH HOH . D 4 HOH A 41 192 56 HOH HOH . D 4 HOH A 42 193 57 HOH HOH . D 4 HOH A 43 194 62 HOH HOH . D 4 HOH A 44 195 63 HOH HOH . D 4 HOH A 45 196 65 HOH HOH . D 4 HOH A 46 197 68 HOH HOH . D 4 HOH A 47 198 70 HOH HOH . D 4 HOH A 48 199 77 HOH HOH . D 4 HOH A 49 200 81 HOH HOH . D 4 HOH A 50 201 82 HOH HOH . D 4 HOH A 51 202 83 HOH HOH . D 4 HOH A 52 203 85 HOH HOH . D 4 HOH A 53 204 86 HOH HOH . D 4 HOH A 54 205 87 HOH HOH . D 4 HOH A 55 206 88 HOH HOH . D 4 HOH A 56 207 89 HOH HOH . D 4 HOH A 57 208 92 HOH HOH . D 4 HOH A 58 209 94 HOH HOH . D 4 HOH A 59 210 95 HOH HOH . D 4 HOH A 60 211 96 HOH HOH . D 4 HOH A 61 212 97 HOH HOH . D 4 HOH A 62 213 98 HOH HOH . D 4 HOH A 63 214 99 HOH HOH . D 4 HOH A 64 215 100 HOH HOH . D 4 HOH A 65 216 101 HOH HOH . D 4 HOH A 66 217 102 HOH HOH . D 4 HOH A 67 218 103 HOH HOH . D 4 HOH A 68 219 104 HOH HOH . D 4 HOH A 69 220 105 HOH HOH . D 4 HOH A 70 221 106 HOH HOH . D 4 HOH A 71 222 107 HOH HOH . D 4 HOH A 72 223 108 HOH HOH . D 4 HOH A 73 224 109 HOH HOH . D 4 HOH A 74 225 110 HOH HOH . D 4 HOH A 75 226 111 HOH HOH . D 4 HOH A 76 227 112 HOH HOH . D 4 HOH A 77 228 113 HOH HOH . D 4 HOH A 78 229 114 HOH HOH . D 4 HOH A 79 230 115 HOH HOH . D 4 HOH A 80 231 116 HOH HOH . D 4 HOH A 81 232 117 HOH HOH . D 4 HOH A 82 233 118 HOH HOH . D 4 HOH A 83 234 119 HOH HOH . D 4 HOH A 84 235 120 HOH HOH . D 4 HOH A 85 236 121 HOH HOH . D 4 HOH A 86 237 122 HOH HOH . D 4 HOH A 87 238 123 HOH HOH . D 4 HOH A 88 239 124 HOH HOH . D 4 HOH A 89 240 125 HOH HOH . D 4 HOH A 90 241 1 HOH HOH . D 4 HOH A 91 242 2 HOH HOH . D 4 HOH A 92 243 3 HOH HOH . D 4 HOH A 93 244 4 HOH HOH . D 4 HOH A 94 245 5 HOH HOH . D 4 HOH A 95 246 1 HOH HOH . D 4 HOH A 96 247 2 HOH HOH . D 4 HOH A 97 248 3 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 P2 THP . . . B 2 17.916 -3.705 -15.294 1 14.34 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 17.931 -5.185 -14.988 1 10.04 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 16.63 -2.887 -14.812 1 17.04 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 19.225 -2.956 -14.729 1 14.97 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 21.104 -0.223 -19.571 1 17.87 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 22.1 0.274 -20.546 1 18.8 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 21.74 -1.157 -18.471 1 25.75 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 20.489 0.887 -18.658 1 20.03 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 17.963 -3.732 -16.917 1 14.54 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 17.967 -2.474 -17.573 1 11.25 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 18.879 -2.62 -18.793 1 13.13 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.342 -3.743 -19.516 1 12.76 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.828 -1.371 -19.708 1 10.39 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 20.073 -1.148 -20.39 1 14.75 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 17.861 -1.933 -20.824 1 12.87 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 18.05 -3.451 -20.868 1 8.74 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 16.763 -4.056 -21.235 1 12.04 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.52 -4.282 -22.558 1 18.06 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.384 -4.05 -23.443 1 18.67 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.305 -4.802 -22.939 1 13.47 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.306 -4.977 -22.052 1 11.41 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.259 -5.409 -22.485 1 11.47 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.545 -4.748 -20.654 1 11.87 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.469 -4.976 -19.605 1 9.55 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 15.773 -4.241 -20.257 1 9.98 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #