data_1LCB # _model_server_result.job_id IiAZ2_kQvZi6u2FNGmATNg _model_server_result.datetime_utc '2024-10-10 13:25:44' _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 1lcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1LCB # _exptl.entry_id 1LCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 120 _cell.entry_id 1LCB _cell.length_a 78.6 _cell.length_b 78.6 _cell.length_c 229.4 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -114.7 # _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 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-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 P O1P TMP doub 361 n n P O2P TMP sing 362 n n P O3P TMP sing 363 n n P O5' TMP sing 364 n n O2P HOP2 TMP sing 365 n n O3P HOP3 TMP sing 366 n n O5' C5' TMP sing 367 n n C5' C4' TMP sing 368 n n C5' "H5'1" TMP sing 369 n n C5' "H5'2" TMP sing 370 n n C4' O4' TMP sing 371 n n C4' C3' TMP sing 372 n n C4' H4' TMP sing 373 n n O4' C1' TMP sing 374 n n C3' O3' TMP sing 375 n n C3' C2' TMP sing 376 n n C3' H3' TMP sing 377 n n O3' HO3' TMP sing 378 n n C2' C1' TMP sing 379 n n C2' "H2'1" TMP sing 380 n n C2' "H2'2" TMP sing 381 n n C1' N1 TMP sing 382 n n C1' H1' TMP sing 383 n n N1 C2 TMP sing 384 n n N1 C6 TMP sing 385 n n C2 O2 TMP doub 386 n n C2 N3 TMP sing 387 n n N3 C4 TMP sing 388 n n N3 HN3 TMP sing 389 n n C4 O4 TMP doub 390 n n C4 C5 TMP sing 391 n n C5 C5M TMP sing 392 n n C5 C6 TMP doub 393 n n C5M H51 TMP sing 394 n n C5M H52 TMP sing 395 n n C5M H53 TMP sing 396 n n C6 H6 TMP sing 397 n n # _atom_sites.entry_id 1LCB _atom_sites.fract_transf_matrix[1][1] 0.012723 _atom_sites.fract_transf_matrix[1][2] 0.007345 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014691 _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] 0.004359 _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 TMP A 1 317 317 TMP TMP . C 3 DHF A 1 318 318 DHF DHF . D 4 HOH A 1 319 319 HOH HOH . D 4 HOH A 2 320 320 HOH HOH . D 4 HOH A 3 321 321 HOH HOH . D 4 HOH A 4 322 322 HOH HOH . D 4 HOH A 5 323 323 HOH HOH . D 4 HOH A 6 324 324 HOH HOH . D 4 HOH A 7 325 325 HOH HOH . D 4 HOH A 8 326 326 HOH HOH . D 4 HOH A 9 328 328 HOH HOH . D 4 HOH A 10 329 329 HOH HOH . D 4 HOH A 11 330 330 HOH HOH . D 4 HOH A 12 331 331 HOH HOH . D 4 HOH A 13 332 332 HOH HOH . D 4 HOH A 14 333 333 HOH HOH . D 4 HOH A 15 334 334 HOH HOH . D 4 HOH A 16 335 335 HOH HOH . D 4 HOH A 17 336 336 HOH HOH . D 4 HOH A 18 337 337 HOH HOH . D 4 HOH A 19 338 338 HOH HOH . D 4 HOH A 20 339 339 HOH HOH . D 4 HOH A 21 340 340 HOH HOH . D 4 HOH A 22 341 341 HOH HOH . D 4 HOH A 23 342 342 HOH HOH . D 4 HOH A 24 343 343 HOH HOH . D 4 HOH A 25 344 344 HOH HOH . D 4 HOH A 26 345 345 HOH HOH . D 4 HOH A 27 346 346 HOH HOH . D 4 HOH A 28 347 347 HOH HOH . D 4 HOH A 29 348 348 HOH HOH . D 4 HOH A 30 349 349 HOH HOH . D 4 HOH A 31 351 351 HOH HOH . D 4 HOH A 32 352 352 HOH HOH . D 4 HOH A 33 353 353 HOH HOH . D 4 HOH A 34 355 355 HOH HOH . D 4 HOH A 35 356 356 HOH HOH . D 4 HOH A 36 357 357 HOH HOH . D 4 HOH A 37 358 358 HOH HOH . D 4 HOH A 38 359 359 HOH HOH . D 4 HOH A 39 360 360 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 P TMP . . . B 2 15.578 49.192 -57.614 1 12.83 ? P TMP 317 A 1 HETATM 2 O O1P TMP . . . B 2 14.439 48.358 -58.144 1 2 ? O1P TMP 317 A 1 HETATM 3 O O2P TMP . . . B 2 15.069 50.407 -56.912 1 2 ? O2P TMP 317 A 1 HETATM 4 O O3P TMP . . . B 2 16.666 49.414 -58.661 1 2 ? O3P TMP 317 A 1 HETATM 5 O O5' TMP . . . B 2 16.31 48.273 -56.49 1 2 ? O5' TMP 317 A 1 HETATM 6 C C5' TMP . . . B 2 17.536 48.535 -55.719 1 2 ? C5' TMP 317 A 1 HETATM 7 C C4' TMP . . . B 2 17.384 47.633 -54.577 1 2 ? C4' TMP 317 A 1 HETATM 8 O O4' TMP . . . B 2 16.248 48.169 -53.819 1 2 ? O4' TMP 317 A 1 HETATM 9 C C3' TMP . . . B 2 16.916 46.198 -54.944 1 2 ? C3' TMP 317 A 1 HETATM 10 O O3' TMP . . . B 2 17.971 45.305 -55.371 1 2 ? O3' TMP 317 A 1 HETATM 11 C C2' TMP . . . B 2 16.047 45.764 -53.754 1 2 ? C2' TMP 317 A 1 HETATM 12 C C1' TMP . . . B 2 15.641 47.071 -53.058 1 2 ? C1' TMP 317 A 1 HETATM 13 N N1 TMP . . . B 2 14.823 47.292 -51.795 1 2 ? N1 TMP 317 A 1 HETATM 14 C C2 TMP . . . B 2 14.21 46.22 -51.074 1 2 ? C2 TMP 317 A 1 HETATM 15 O O2 TMP . . . B 2 14.389 45.006 -51.282 1 2 ? O2 TMP 317 A 1 HETATM 16 N N3 TMP . . . B 2 13.406 46.625 -49.978 1 2 ? N3 TMP 317 A 1 HETATM 17 C C4 TMP . . . B 2 13.143 47.966 -49.565 1 2 ? C4 TMP 317 A 1 HETATM 18 O O4 TMP . . . B 2 12.289 48.245 -48.717 1 2 ? O4 TMP 317 A 1 HETATM 19 C C5 TMP . . . B 2 13.827 49.001 -50.34 1 2 ? C5 TMP 317 A 1 HETATM 20 C C5M TMP . . . B 2 13.846 50.348 -49.745 1 2 ? C5M TMP 317 A 1 HETATM 21 C C6 TMP . . . B 2 14.616 48.599 -51.448 1 2 ? C6 TMP 317 A 1 HETATM 22 H HO3' TMP . . . B 2 18.645 45.85 -55.8 1 15 ? HO3' TMP 317 A 1 HETATM 23 H HN3 TMP . . . B 2 13.096 45.883 -49.421 1 15 ? HN3 TMP 317 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #