data_3TME # _model_server_result.job_id 00GkXNV2S2Z107_QwzuQHw _model_server_result.datetime_utc '2024-10-11 10:25:07' _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 3tme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3TME # _exptl.entry_id 3TME _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 3TME _cell.length_a 31.12 _cell.length_b 60.109 _cell.length_c 78.707 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TME _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 3TME _atom_sites.fract_transf_matrix[1][1] 0.032134 _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] 0.016636 _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] 0.012705 _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 MRD A 1 151 1 MRD MPD . D 4 HOH A 1 44 44 HOH HOH . D 4 HOH A 2 48 48 HOH HOH . D 4 HOH A 3 49 49 HOH HOH . D 4 HOH A 4 152 1 HOH HOH . D 4 HOH A 5 153 2 HOH HOH . D 4 HOH A 6 154 3 HOH HOH . D 4 HOH A 7 155 4 HOH HOH . D 4 HOH A 8 156 5 HOH HOH . D 4 HOH A 9 157 6 HOH HOH . D 4 HOH A 10 158 7 HOH HOH . D 4 HOH A 11 159 8 HOH HOH . D 4 HOH A 12 160 9 HOH HOH . D 4 HOH A 13 161 10 HOH HOH . D 4 HOH A 14 162 11 HOH HOH . D 4 HOH A 15 163 1 HOH HOH . D 4 HOH A 16 164 2 HOH HOH . D 4 HOH A 17 165 5 HOH HOH . D 4 HOH A 18 166 7 HOH HOH . D 4 HOH A 19 167 8 HOH HOH . D 4 HOH A 20 168 9 HOH HOH . D 4 HOH A 21 169 11 HOH HOH . D 4 HOH A 22 170 12 HOH HOH . D 4 HOH A 23 171 13 HOH HOH . D 4 HOH A 24 172 15 HOH HOH . D 4 HOH A 25 173 16 HOH HOH . D 4 HOH A 26 174 17 HOH HOH . D 4 HOH A 27 175 18 HOH HOH . D 4 HOH A 28 176 20 HOH HOH . D 4 HOH A 29 177 22 HOH HOH . D 4 HOH A 30 178 23 HOH HOH . D 4 HOH A 31 179 24 HOH HOH . D 4 HOH A 32 180 25 HOH HOH . D 4 HOH A 33 181 26 HOH HOH . D 4 HOH A 34 182 27 HOH HOH . D 4 HOH A 35 183 28 HOH HOH . D 4 HOH A 36 184 30 HOH HOH . D 4 HOH A 37 185 31 HOH HOH . D 4 HOH A 38 186 32 HOH HOH . D 4 HOH A 39 187 34 HOH HOH . D 4 HOH A 40 188 35 HOH HOH . D 4 HOH A 41 189 39 HOH HOH . D 4 HOH A 42 190 40 HOH HOH . D 4 HOH A 43 191 41 HOH HOH . D 4 HOH A 44 192 42 HOH HOH . D 4 HOH A 45 193 43 HOH HOH . D 4 HOH A 46 194 51 HOH HOH . D 4 HOH A 47 195 54 HOH HOH . D 4 HOH A 48 196 55 HOH HOH . D 4 HOH A 49 197 56 HOH HOH . D 4 HOH A 50 198 59 HOH HOH . D 4 HOH A 51 199 60 HOH HOH . D 4 HOH A 52 200 61 HOH HOH . D 4 HOH A 53 201 63 HOH HOH . D 4 HOH A 54 202 66 HOH HOH . D 4 HOH A 55 203 67 HOH HOH . D 4 HOH A 56 204 70 HOH HOH . D 4 HOH A 57 205 75 HOH HOH . D 4 HOH A 58 206 77 HOH HOH . D 4 HOH A 59 207 83 HOH HOH . D 4 HOH A 60 208 85 HOH HOH . D 4 HOH A 61 209 87 HOH HOH . D 4 HOH A 62 210 88 HOH HOH . D 4 HOH A 63 211 91 HOH HOH . D 4 HOH A 64 212 97 HOH HOH . D 4 HOH A 65 213 98 HOH HOH . D 4 HOH A 66 214 102 HOH HOH . D 4 HOH A 67 215 117 HOH HOH . D 4 HOH A 68 216 123 HOH HOH . D 4 HOH A 69 217 143 HOH HOH . D 4 HOH A 70 218 1 HOH HOH . D 4 HOH A 71 219 2 HOH HOH . D 4 HOH A 72 220 3 HOH HOH . D 4 HOH A 73 221 4 HOH HOH . D 4 HOH A 74 222 5 HOH HOH . D 4 HOH A 75 223 6 HOH HOH . D 4 HOH A 76 224 7 HOH HOH . D 4 HOH A 77 225 8 HOH HOH . D 4 HOH A 78 226 9 HOH HOH . D 4 HOH A 79 227 10 HOH HOH . D 4 HOH A 80 228 11 HOH HOH . D 4 HOH A 81 229 12 HOH HOH . D 4 HOH A 82 230 13 HOH HOH . D 4 HOH A 83 231 14 HOH HOH . D 4 HOH A 84 232 15 HOH HOH . D 4 HOH A 85 233 1 HOH HOH . D 4 HOH A 86 234 2 HOH HOH . D 4 HOH A 87 235 3 HOH HOH . D 4 HOH A 88 236 4 HOH HOH . D 4 HOH A 89 237 5 HOH HOH . D 4 HOH A 90 238 6 HOH HOH . D 4 HOH A 91 239 7 HOH HOH . D 4 HOH A 92 240 8 HOH HOH . D 4 HOH A 93 241 9 HOH HOH . D 4 HOH A 94 242 10 HOH HOH . D 4 HOH A 95 243 11 HOH HOH . D 4 HOH A 96 244 12 HOH HOH . D 4 HOH A 97 245 13 HOH HOH . D 4 HOH A 98 246 1 HOH HOH . D 4 HOH A 99 247 2 HOH HOH . D 4 HOH A 100 248 4 HOH HOH . D 4 HOH A 101 249 5 HOH HOH . D 4 HOH A 102 250 1 HOH HOH . D 4 HOH A 103 251 2 HOH HOH . D 4 HOH A 104 252 3 HOH HOH . D 4 HOH A 105 253 4 HOH HOH . D 4 HOH A 106 254 5 HOH HOH . D 4 HOH A 107 255 1 HOH HOH . D 4 HOH A 108 256 2 HOH HOH . D 4 HOH A 109 257 3 HOH HOH . D 4 HOH A 110 258 4 HOH HOH . D 4 HOH A 111 259 5 HOH HOH . D 4 HOH A 112 260 6 HOH HOH . D 4 HOH A 113 261 7 HOH HOH . D 4 HOH A 114 262 2 HOH HOH . D 4 HOH A 115 263 1 HOH HOH . D 4 HOH A 116 264 2 HOH HOH . D 4 HOH A 117 265 3 HOH HOH . D 4 HOH A 118 266 1 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 17.724 -6.285 -14.71 1 7.8 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 17.611 -7.743 -14.483 1 8.51 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 16.499 -5.469 -14.292 1 7.89 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 19.025 -5.685 -14.177 1 9.84 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 21.037 -2.854 -18.564 1 8.14 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 21.998 -2.256 -19.5 1 9.79 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 21.686 -4.031 -17.788 1 9.78 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 20.342 -1.947 -17.651 1 9.69 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 17.794 -6.257 -16.271 1 8.19 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 17.783 -4.98 -16.947 1 8.77 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 18.66 -5.067 -18.194 1 6.85 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.245 -6.161 -19.045 1 7.42 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.596 -3.789 -19.036 1 7.8 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 19.933 -3.516 -19.551 1 7.48 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 17.694 -4.287 -20.202 1 8.13 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 17.928 -5.76 -20.338 1 2.01 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 16.693 -6.405 -20.724 1 6.31 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.469 -6.643 -22.057 1 8.2 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.348 -6.338 -22.906 1 9.2 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.269 -7.173 -22.458 1 6.86 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.273 -7.453 -21.584 1 7.67 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.185 -7.838 -22.034 1 8.91 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.463 -7.201 -20.199 1 6.74 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.397 -7.537 -19.165 1 8.26 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 15.684 -6.719 -19.799 1 6.71 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #