data_7N67 # _model_server_result.job_id TobcGJvaFt2at3-5SoJZTg _model_server_result.datetime_utc '2024-10-11 07:17:43' _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 7n67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7N67 # _exptl.entry_id 7N67 _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-5'-DIPHOSPHATE" _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 90 _cell.angle_gamma 120 _cell.entry_id 7N67 _cell.length_a 92.944 _cell.length_b 92.944 _cell.length_c 85.55 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7N67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 28.516667 # 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 E N N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 TYD doub 350 n n PA O2A TYD sing 351 n n PA O3A TYD sing 352 n n PA O5' TYD sing 353 n n O2A HOA2 TYD sing 354 n n O3A PB TYD sing 355 n n PB O1B TYD doub 356 n n PB O2B TYD sing 357 n n PB O3B TYD sing 358 n n O2B HOB2 TYD sing 359 n n O3B HOB3 TYD sing 360 n n O5' C5' TYD sing 361 n n C5' C4' TYD sing 362 n n C5' "H5'1" TYD sing 363 n n C5' "H5'2" TYD sing 364 n n C4' O4' TYD sing 365 n n C4' C3' TYD sing 366 n n C4' H4' TYD sing 367 n n O4' C1' TYD sing 368 n n C3' O3' TYD sing 369 n n C3' C2' TYD sing 370 n n C3' H3' TYD sing 371 n n O3' HO3' TYD sing 372 n n C2' C1' TYD sing 373 n n C2' "H2'1" TYD sing 374 n n C2' "H2'2" TYD sing 375 n n C1' N1 TYD sing 376 n n C1' H1' TYD sing 377 n n N1 C2 TYD sing 378 n y N1 C6 TYD sing 379 n y C2 O2 TYD doub 380 n n C2 N3 TYD sing 381 n y N3 C4 TYD sing 382 n y N3 HN3 TYD sing 383 n n C4 O4 TYD doub 384 n n C4 C5 TYD sing 385 n y C5 C5M TYD sing 386 n n C5 C6 TYD doub 387 n y C5M H51 TYD sing 388 n n C5M H52 TYD sing 389 n n C5M H53 TYD sing 390 n n C6 H6 TYD sing 391 n n # _atom_sites.entry_id 7N67 _atom_sites.fract_transf_matrix[1][1] 0.010759 _atom_sites.fract_transf_matrix[1][2] 0.006212 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012424 _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] 0.011689 _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 TYD A 1 201 200 TYD TYD . D 3 TMA A 1 202 1 TMA TMA . E 2 TYD B 1 200 200 TYD TYD . F 4 HOH A 1 301 34 HOH HOH . F 4 HOH A 2 302 144 HOH HOH . F 4 HOH A 3 303 118 HOH HOH . F 4 HOH A 4 304 121 HOH HOH . F 4 HOH A 5 305 136 HOH HOH . F 4 HOH A 6 306 143 HOH HOH . F 4 HOH A 7 307 151 HOH HOH . F 4 HOH A 8 308 39 HOH HOH . F 4 HOH A 9 309 112 HOH HOH . F 4 HOH A 10 310 96 HOH HOH . F 4 HOH A 11 311 86 HOH HOH . F 4 HOH A 12 312 162 HOH HOH . F 4 HOH A 13 313 152 HOH HOH . F 4 HOH A 14 314 22 HOH HOH . F 4 HOH A 15 315 21 HOH HOH . F 4 HOH A 16 316 119 HOH HOH . F 4 HOH A 17 317 140 HOH HOH . F 4 HOH A 18 318 161 HOH HOH . F 4 HOH A 19 319 26 HOH HOH . F 4 HOH A 20 320 35 HOH HOH . F 4 HOH A 21 321 10 HOH HOH . F 4 HOH A 22 322 79 HOH HOH . F 4 HOH A 23 323 90 HOH HOH . F 4 HOH A 24 324 120 HOH HOH . F 4 HOH A 25 325 102 HOH HOH . F 4 HOH A 26 326 65 HOH HOH . F 4 HOH A 27 327 157 HOH HOH . F 4 HOH A 28 328 46 HOH HOH . F 4 HOH A 29 329 108 HOH HOH . F 4 HOH A 30 330 149 HOH HOH . F 4 HOH A 31 331 142 HOH HOH . F 4 HOH A 32 332 4 HOH HOH . F 4 HOH A 33 333 150 HOH HOH . F 4 HOH A 34 334 82 HOH HOH . F 4 HOH A 35 335 76 HOH HOH . F 4 HOH A 36 336 98 HOH HOH . F 4 HOH A 37 337 74 HOH HOH . F 4 HOH A 38 338 53 HOH HOH . F 4 HOH A 39 339 3 HOH HOH . F 4 HOH A 40 340 19 HOH HOH . F 4 HOH A 41 341 33 HOH HOH . F 4 HOH A 42 342 61 HOH HOH . F 4 HOH A 43 343 165 HOH HOH . F 4 HOH A 44 344 105 HOH HOH . F 4 HOH A 45 345 109 HOH HOH . F 4 HOH A 46 346 134 HOH HOH . F 4 HOH A 47 347 135 HOH HOH . F 4 HOH A 48 348 141 HOH HOH . F 4 HOH A 49 349 166 HOH HOH . F 4 HOH A 50 350 163 HOH HOH . F 4 HOH A 51 351 137 HOH HOH . F 4 HOH A 52 352 81 HOH HOH . G 4 HOH B 1 301 49 HOH HOH . G 4 HOH B 2 302 116 HOH HOH . G 4 HOH B 3 303 167 HOH HOH . G 4 HOH B 4 304 124 HOH HOH . G 4 HOH B 5 305 78 HOH HOH . G 4 HOH B 6 306 158 HOH HOH . G 4 HOH B 7 307 113 HOH HOH . G 4 HOH B 8 308 154 HOH HOH . G 4 HOH B 9 309 31 HOH HOH . G 4 HOH B 10 310 128 HOH HOH . G 4 HOH B 11 311 83 HOH HOH . G 4 HOH B 12 312 42 HOH HOH . G 4 HOH B 13 313 70 HOH HOH . G 4 HOH B 14 314 111 HOH HOH . G 4 HOH B 15 315 60 HOH HOH . G 4 HOH B 16 316 57 HOH HOH . G 4 HOH B 17 317 32 HOH HOH . G 4 HOH B 18 318 18 HOH HOH . G 4 HOH B 19 319 127 HOH HOH . G 4 HOH B 20 320 68 HOH HOH . G 4 HOH B 21 321 37 HOH HOH . G 4 HOH B 22 322 48 HOH HOH . G 4 HOH B 23 323 156 HOH HOH . G 4 HOH B 24 324 132 HOH HOH . G 4 HOH B 25 325 110 HOH HOH . G 4 HOH B 26 326 126 HOH HOH . G 4 HOH B 27 327 2 HOH HOH . G 4 HOH B 28 328 58 HOH HOH . G 4 HOH B 29 329 30 HOH HOH . G 4 HOH B 30 330 153 HOH HOH . G 4 HOH B 31 331 59 HOH HOH . G 4 HOH B 32 332 1 HOH HOH . G 4 HOH B 33 333 52 HOH HOH . G 4 HOH B 34 334 14 HOH HOH . G 4 HOH B 35 335 87 HOH HOH . G 4 HOH B 36 336 55 HOH HOH . G 4 HOH B 37 337 117 HOH HOH . G 4 HOH B 38 338 36 HOH HOH . G 4 HOH B 39 339 20 HOH HOH . G 4 HOH B 40 340 17 HOH HOH . G 4 HOH B 41 341 25 HOH HOH . G 4 HOH B 42 342 41 HOH HOH . G 4 HOH B 43 343 72 HOH HOH . G 4 HOH B 44 344 164 HOH HOH . G 4 HOH B 45 345 129 HOH HOH . G 4 HOH B 46 346 99 HOH HOH . G 4 HOH B 47 347 54 HOH HOH . G 4 HOH B 48 348 9 HOH HOH . G 4 HOH B 49 349 130 HOH HOH . G 4 HOH B 50 350 56 HOH HOH . G 4 HOH B 51 351 16 HOH HOH . G 4 HOH B 52 352 28 HOH HOH . G 4 HOH B 53 353 103 HOH HOH . G 4 HOH B 54 354 13 HOH HOH . G 4 HOH B 55 355 114 HOH HOH . G 4 HOH B 56 356 27 HOH HOH . G 4 HOH B 57 357 133 HOH HOH . G 4 HOH B 58 358 115 HOH HOH . G 4 HOH B 59 359 106 HOH HOH . G 4 HOH B 60 360 100 HOH HOH . G 4 HOH B 61 361 148 HOH HOH . G 4 HOH B 62 362 7 HOH HOH . G 4 HOH B 63 363 131 HOH HOH . G 4 HOH B 64 364 125 HOH HOH . G 4 HOH B 65 365 123 HOH HOH . G 4 HOH B 66 366 147 HOH HOH . G 4 HOH B 67 367 88 HOH HOH . G 4 HOH B 68 368 160 HOH HOH . G 4 HOH B 69 369 75 HOH HOH . G 4 HOH B 70 370 159 HOH HOH . G 4 HOH B 71 371 155 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 TYD . . . C 2 33.123 -34.138 1.516 1 42.98 ? PA TYD 201 A 1 HETATM 2 O O1A TYD . . . C 2 34.139 -34.519 0.493 1 44.82 ? O1A TYD 201 A 1 HETATM 3 O O2A TYD . . . C 2 33.088 -32.708 1.909 1 42.92 ? O2A TYD 201 A 1 HETATM 4 O O3A TYD . . . C 2 33.302 -35.049 2.837 1 44.16 ? O3A TYD 201 A 1 HETATM 5 P PB TYD . . . C 2 34.264 -35.052 4.166 1 46.14 ? PB TYD 201 A 1 HETATM 6 O O1B TYD . . . C 2 35.683 -34.879 3.639 1 46.83 ? O1B TYD 201 A 1 HETATM 7 O O2B TYD . . . C 2 34.066 -36.408 4.811 1 46.5 ? O2B TYD 201 A 1 HETATM 8 O O3B TYD . . . C 2 33.871 -33.915 5.103 1 42.19 ? O3B TYD 201 A 1 HETATM 9 O O5' TYD . . . C 2 31.67 -34.565 1.02 1 38.67 ? O5' TYD 201 A 1 HETATM 10 C C5' TYD . . . C 2 31.556 -35.687 0.123 1 38.1 ? C5' TYD 201 A 1 HETATM 11 C C4' TYD . . . C 2 30.471 -35.371 -0.873 1 38.5 ? C4' TYD 201 A 1 HETATM 12 O O4' TYD . . . C 2 29.195 -35.274 -0.197 1 36.82 ? O4' TYD 201 A 1 HETATM 13 C C3' TYD . . . C 2 30.681 -34.047 -1.6 1 39.17 ? C3' TYD 201 A 1 HETATM 14 O O3' TYD . . . C 2 30.305 -34.179 -2.964 1 38.55 ? O3' TYD 201 A 1 HETATM 15 C C2' TYD . . . C 2 29.736 -33.103 -0.88 1 39.28 ? C2' TYD 201 A 1 HETATM 16 C C1' TYD . . . C 2 28.585 -34.03 -0.51 1 39.41 ? C1' TYD 201 A 1 HETATM 17 N N1 TYD . . . C 2 27.784 -33.566 0.658 1 38.78 ? N1 TYD 201 A 1 HETATM 18 C C2 TYD . . . C 2 26.44 -33.306 0.479 1 36.91 ? C2 TYD 201 A 1 HETATM 19 O O2 TYD . . . C 2 25.854 -33.491 -0.579 1 40 ? O2 TYD 201 A 1 HETATM 20 N N3 TYD . . . C 2 25.791 -32.848 1.593 1 37.67 ? N3 TYD 201 A 1 HETATM 21 C C4 TYD . . . C 2 26.331 -32.641 2.845 1 38.78 ? C4 TYD 201 A 1 HETATM 22 O O4 TYD . . . C 2 25.606 -32.233 3.76 1 39.52 ? O4 TYD 201 A 1 HETATM 23 C C5 TYD . . . C 2 27.745 -32.926 2.958 1 36.48 ? C5 TYD 201 A 1 HETATM 24 C C5M TYD . . . C 2 28.428 -32.716 4.275 1 37.6 ? C5M TYD 201 A 1 HETATM 25 C C6 TYD . . . C 2 28.394 -33.359 1.875 1 35.69 ? C6 TYD 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #