data_3BGX # _model_server_result.job_id FGnQ8KGpYDL2_veOpeBVLQ _model_server_result.datetime_utc '2024-11-23 19:59:55' _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 3bgx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":265}' # _entry.id 3BGX # _exptl.entry_id 3BGX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _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 3BGX _cell.length_a 72.03 _cell.length_b 72.03 _cell.length_c 115.46 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BGX _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 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,E,F _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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 76.973333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id CXM _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CXM _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id LYS _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LYS _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.324 _struct_conn.pdbx_value_order ? # _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 391 n n P O2P TMP sing 392 n n P O3P TMP sing 393 n n P O5' TMP sing 394 n n O2P HOP2 TMP sing 395 n n O3P HOP3 TMP sing 396 n n O5' C5' TMP sing 397 n n C5' C4' TMP sing 398 n n C5' "H5'1" TMP sing 399 n n C5' "H5'2" TMP sing 400 n n C4' O4' TMP sing 401 n n C4' C3' TMP sing 402 n n C4' H4' TMP sing 403 n n O4' C1' TMP sing 404 n n C3' O3' TMP sing 405 n n C3' C2' TMP sing 406 n n C3' H3' TMP sing 407 n n O3' HO3' TMP sing 408 n n C2' C1' TMP sing 409 n n C2' "H2'1" TMP sing 410 n n C2' "H2'2" TMP sing 411 n n C1' N1 TMP sing 412 n n C1' H1' TMP sing 413 n n N1 C2 TMP sing 414 n n N1 C6 TMP sing 415 n n C2 O2 TMP doub 416 n n C2 N3 TMP sing 417 n n N3 C4 TMP sing 418 n n N3 HN3 TMP sing 419 n n C4 O4 TMP doub 420 n n C4 C5 TMP sing 421 n n C5 C5M TMP sing 422 n n C5 C6 TMP doub 423 n n C5M H51 TMP sing 424 n n C5M H52 TMP sing 425 n n C5M H53 TMP sing 426 n n C6 H6 TMP sing 427 n n # _atom_sites.entry_id 3BGX _atom_sites.fract_transf_matrix[1][1] 0.013883 _atom_sites.fract_transf_matrix[1][2] 0.008015 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016031 _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] 0.008661 _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 SO4 A 1 267 267 SO4 SO4 . C 2 SO4 A 1 268 268 SO4 SO4 . D 3 TMP A 1 265 265 TMP TMP . E 4 MEF A 1 266 266 MEF MEF . F 5 HOH A 1 269 1 HOH HOH . F 5 HOH A 2 270 2 HOH HOH . F 5 HOH A 3 271 3 HOH HOH . F 5 HOH A 4 272 4 HOH HOH . F 5 HOH A 5 273 5 HOH HOH . F 5 HOH A 6 274 6 HOH HOH . F 5 HOH A 7 275 7 HOH HOH . F 5 HOH A 8 276 8 HOH HOH . F 5 HOH A 9 277 9 HOH HOH . F 5 HOH A 10 278 10 HOH HOH . F 5 HOH A 11 279 11 HOH HOH . F 5 HOH A 12 280 12 HOH HOH . F 5 HOH A 13 281 13 HOH HOH . F 5 HOH A 14 282 14 HOH HOH . F 5 HOH A 15 283 15 HOH HOH . F 5 HOH A 16 284 16 HOH HOH . F 5 HOH A 17 285 17 HOH HOH . F 5 HOH A 18 286 18 HOH HOH . F 5 HOH A 19 287 19 HOH HOH . F 5 HOH A 20 288 20 HOH HOH . F 5 HOH A 21 289 21 HOH HOH . F 5 HOH A 22 290 22 HOH HOH . F 5 HOH A 23 291 23 HOH HOH . F 5 HOH A 24 292 24 HOH HOH . F 5 HOH A 25 293 25 HOH HOH . F 5 HOH A 26 294 26 HOH HOH . F 5 HOH A 27 295 27 HOH HOH . F 5 HOH A 28 296 28 HOH HOH . F 5 HOH A 29 297 29 HOH HOH . F 5 HOH A 30 298 30 HOH HOH . F 5 HOH A 31 299 31 HOH HOH . F 5 HOH A 32 300 32 HOH HOH . F 5 HOH A 33 301 33 HOH HOH . F 5 HOH A 34 302 34 HOH HOH . F 5 HOH A 35 303 35 HOH HOH . F 5 HOH A 36 304 36 HOH HOH . F 5 HOH A 37 305 37 HOH HOH . F 5 HOH A 38 306 38 HOH HOH . F 5 HOH A 39 307 39 HOH HOH . F 5 HOH A 40 308 40 HOH HOH . F 5 HOH A 41 309 41 HOH HOH . F 5 HOH A 42 310 42 HOH HOH . F 5 HOH A 43 311 43 HOH HOH . F 5 HOH A 44 312 44 HOH HOH . F 5 HOH A 45 313 45 HOH HOH . F 5 HOH A 46 314 46 HOH HOH . F 5 HOH A 47 315 47 HOH HOH . F 5 HOH A 48 316 48 HOH HOH . F 5 HOH A 49 317 49 HOH HOH . F 5 HOH A 50 318 50 HOH HOH . F 5 HOH A 51 319 51 HOH HOH . F 5 HOH A 52 320 52 HOH HOH . F 5 HOH A 53 321 53 HOH HOH . F 5 HOH A 54 322 54 HOH HOH . F 5 HOH A 55 323 55 HOH HOH . F 5 HOH A 56 324 56 HOH HOH . F 5 HOH A 57 325 57 HOH HOH . F 5 HOH A 58 326 58 HOH HOH . F 5 HOH A 59 327 59 HOH HOH . F 5 HOH A 60 328 60 HOH HOH . F 5 HOH A 61 329 61 HOH HOH . F 5 HOH A 62 330 62 HOH HOH . F 5 HOH A 63 331 63 HOH HOH . F 5 HOH A 64 332 64 HOH HOH . F 5 HOH A 65 333 65 HOH HOH . F 5 HOH A 66 334 66 HOH HOH . F 5 HOH A 67 335 67 HOH HOH . F 5 HOH A 68 336 68 HOH HOH . F 5 HOH A 69 337 69 HOH HOH . F 5 HOH A 70 338 70 HOH HOH . F 5 HOH A 71 339 71 HOH HOH . F 5 HOH A 72 340 72 HOH HOH . F 5 HOH A 73 341 73 HOH HOH . F 5 HOH A 74 342 74 HOH HOH . F 5 HOH A 75 343 75 HOH HOH . F 5 HOH A 76 344 76 HOH HOH . F 5 HOH A 77 345 77 HOH HOH . F 5 HOH A 78 346 78 HOH HOH . F 5 HOH A 79 347 79 HOH HOH . F 5 HOH A 80 348 80 HOH HOH . F 5 HOH A 81 349 81 HOH HOH . F 5 HOH A 82 350 82 HOH HOH . F 5 HOH A 83 351 83 HOH HOH . F 5 HOH A 84 352 84 HOH HOH . F 5 HOH A 85 353 85 HOH HOH . F 5 HOH A 86 354 86 HOH HOH . F 5 HOH A 87 355 87 HOH HOH . F 5 HOH A 88 356 88 HOH HOH . F 5 HOH A 89 357 89 HOH HOH . F 5 HOH A 90 358 90 HOH HOH . F 5 HOH A 91 359 91 HOH HOH . F 5 HOH A 92 360 92 HOH HOH . F 5 HOH A 93 361 93 HOH HOH . F 5 HOH A 94 362 94 HOH HOH . F 5 HOH A 95 363 95 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 . . . D 3 40.695 13.879 31.278 1 16.31 ? P TMP 265 A 1 HETATM 2 O O1P TMP . . . D 3 41.841 12.973 31.571 1 15 ? O1P TMP 265 A 1 HETATM 3 O O2P TMP . . . D 3 40.613 14.271 29.795 1 18.34 ? O2P TMP 265 A 1 HETATM 4 O O3P TMP . . . D 3 39.399 13.483 31.929 1 17.88 ? O3P TMP 265 A 1 HETATM 5 O O5' TMP . . . D 3 41.149 15.271 31.839 1 20.07 ? O5' TMP 265 A 1 HETATM 6 C C5' TMP . . . D 3 41.118 15.642 33.233 1 18.97 ? C5' TMP 265 A 1 HETATM 7 C C4' TMP . . . D 3 42.431 15.523 33.964 1 19.49 ? C4' TMP 265 A 1 HETATM 8 O O4' TMP . . . D 3 42.616 16.432 35.04 1 18.64 ? O4' TMP 265 A 1 HETATM 9 C C3' TMP . . . D 3 43.863 15.295 33.421 1 16.06 ? C3' TMP 265 A 1 HETATM 10 O O3' TMP . . . D 3 44.831 16.289 33.13 1 15.13 ? O3' TMP 265 A 1 HETATM 11 C C2' TMP . . . D 3 44.325 14.806 34.807 1 16.49 ? C2' TMP 265 A 1 HETATM 12 C C1' TMP . . . D 3 43.544 15.692 35.732 1 17.74 ? C1' TMP 265 A 1 HETATM 13 N N1 TMP . . . D 3 43.308 15.424 37.107 1 16.89 ? N1 TMP 265 A 1 HETATM 14 C C2 TMP . . . D 3 44.286 15.017 37.985 1 17.61 ? C2 TMP 265 A 1 HETATM 15 O O2 TMP . . . D 3 45.475 14.857 37.624 1 17.4 ? O2 TMP 265 A 1 HETATM 16 N N3 TMP . . . D 3 43.952 14.816 39.28 1 17.19 ? N3 TMP 265 A 1 HETATM 17 C C4 TMP . . . D 3 42.722 14.974 39.752 1 18.04 ? C4 TMP 265 A 1 HETATM 18 O O4 TMP . . . D 3 42.429 14.803 40.981 1 17.6 ? O4 TMP 265 A 1 HETATM 19 C C5 TMP . . . D 3 41.661 15.359 38.823 1 17.54 ? C5 TMP 265 A 1 HETATM 20 C C5M TMP . . . D 3 40.274 15.538 39.356 1 17.42 ? C5M TMP 265 A 1 HETATM 21 C C6 TMP . . . D 3 42.019 15.567 37.512 1 18.56 ? C6 TMP 265 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #