data_5XAI # _model_server_result.job_id rtWkEOx2D-SEto69hWHOYg _model_server_result.datetime_utc '2024-11-05 10:56:00' _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 5xai # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5XAI # _exptl.entry_id 5XAI _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 92.17 _cell.angle_beta 92.1 _cell.angle_gamma 111.14 _cell.entry_id 5XAI _cell.length_a 42.634 _cell.length_b 52.118 _cell.length_c 53.394 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XAI _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 276 n n P O2P TMP sing 277 n n P O3P TMP sing 278 n n P O5' TMP sing 279 n n O2P HOP2 TMP sing 280 n n O3P HOP3 TMP sing 281 n n O5' C5' TMP sing 282 n n C5' C4' TMP sing 283 n n C5' "H5'1" TMP sing 284 n n C5' "H5'2" TMP sing 285 n n C4' O4' TMP sing 286 n n C4' C3' TMP sing 287 n n C4' H4' TMP sing 288 n n O4' C1' TMP sing 289 n n C3' O3' TMP sing 290 n n C3' C2' TMP sing 291 n n C3' H3' TMP sing 292 n n O3' HO3' TMP sing 293 n n C2' C1' TMP sing 294 n n C2' "H2'1" TMP sing 295 n n C2' "H2'2" TMP sing 296 n n C1' N1 TMP sing 297 n n C1' H1' TMP sing 298 n n N1 C2 TMP sing 299 n n N1 C6 TMP sing 300 n n C2 O2 TMP doub 301 n n C2 N3 TMP sing 302 n n N3 C4 TMP sing 303 n n N3 HN3 TMP sing 304 n n C4 O4 TMP doub 305 n n C4 C5 TMP sing 306 n n C5 C5M TMP sing 307 n n C5 C6 TMP doub 308 n n C5M H51 TMP sing 309 n n C5M H52 TMP sing 310 n n C5M H53 TMP sing 311 n n C6 H6 TMP sing 312 n n # _atom_sites.entry_id 5XAI _atom_sites.fract_transf_matrix[1][1] 0.023455 _atom_sites.fract_transf_matrix[1][2] 0.00907 _atom_sites.fract_transf_matrix[1][3] 0.001358 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020572 _atom_sites.fract_transf_matrix[2][3] 0.001127 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018769 _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 PO4 B 1 201 1 PO4 PO4 . D 3 TMP B 1 202 2 TMP TMP . E 2 PO4 A 1 201 2 PO4 PO4 . F 3 TMP A 1 202 1 TMP TMP . G 4 HOH B 1 301 90 HOH HOH . G 4 HOH B 2 302 96 HOH HOH . G 4 HOH B 3 303 77 HOH HOH . G 4 HOH B 4 304 15 HOH HOH . G 4 HOH B 5 305 75 HOH HOH . G 4 HOH B 6 306 35 HOH HOH . G 4 HOH B 7 307 27 HOH HOH . G 4 HOH B 8 308 11 HOH HOH . G 4 HOH B 9 309 9 HOH HOH . G 4 HOH B 10 310 145 HOH HOH . G 4 HOH B 11 311 109 HOH HOH . G 4 HOH B 12 312 38 HOH HOH . G 4 HOH B 13 313 5 HOH HOH . G 4 HOH B 14 314 83 HOH HOH . G 4 HOH B 15 315 157 HOH HOH . G 4 HOH B 16 316 8 HOH HOH . G 4 HOH B 17 317 29 HOH HOH . G 4 HOH B 18 318 93 HOH HOH . G 4 HOH B 19 319 52 HOH HOH . G 4 HOH B 20 320 137 HOH HOH . G 4 HOH B 21 321 154 HOH HOH . G 4 HOH B 22 322 70 HOH HOH . G 4 HOH B 23 323 78 HOH HOH . G 4 HOH B 24 324 37 HOH HOH . G 4 HOH B 25 325 25 HOH HOH . G 4 HOH B 26 326 54 HOH HOH . G 4 HOH B 27 327 140 HOH HOH . G 4 HOH B 28 328 18 HOH HOH . G 4 HOH B 29 329 53 HOH HOH . G 4 HOH B 30 330 156 HOH HOH . G 4 HOH B 31 331 69 HOH HOH . G 4 HOH B 32 332 158 HOH HOH . G 4 HOH B 33 333 105 HOH HOH . G 4 HOH B 34 334 76 HOH HOH . G 4 HOH B 35 335 22 HOH HOH . G 4 HOH B 36 336 3 HOH HOH . G 4 HOH B 37 337 136 HOH HOH . G 4 HOH B 38 338 91 HOH HOH . G 4 HOH B 39 339 95 HOH HOH . G 4 HOH B 40 340 49 HOH HOH . G 4 HOH B 41 341 30 HOH HOH . G 4 HOH B 42 342 79 HOH HOH . G 4 HOH B 43 343 110 HOH HOH . G 4 HOH B 44 344 86 HOH HOH . G 4 HOH B 45 345 144 HOH HOH . G 4 HOH B 46 346 88 HOH HOH . G 4 HOH B 47 347 16 HOH HOH . G 4 HOH B 48 348 97 HOH HOH . G 4 HOH B 49 349 107 HOH HOH . G 4 HOH B 50 350 155 HOH HOH . G 4 HOH B 51 351 71 HOH HOH . G 4 HOH B 52 352 36 HOH HOH . G 4 HOH B 53 353 98 HOH HOH . G 4 HOH B 54 354 131 HOH HOH . G 4 HOH B 55 355 106 HOH HOH . G 4 HOH B 56 356 89 HOH HOH . G 4 HOH B 57 357 85 HOH HOH . G 4 HOH B 58 358 82 HOH HOH . G 4 HOH B 59 359 138 HOH HOH . G 4 HOH B 60 360 100 HOH HOH . H 4 HOH A 1 301 67 HOH HOH . H 4 HOH A 2 302 73 HOH HOH . H 4 HOH A 3 303 142 HOH HOH . H 4 HOH A 4 304 117 HOH HOH . H 4 HOH A 5 305 32 HOH HOH . H 4 HOH A 6 306 72 HOH HOH . H 4 HOH A 7 307 124 HOH HOH . H 4 HOH A 8 308 44 HOH HOH . H 4 HOH A 9 309 1 HOH HOH . H 4 HOH A 10 310 118 HOH HOH . H 4 HOH A 11 311 143 HOH HOH . H 4 HOH A 12 312 153 HOH HOH . H 4 HOH A 13 313 61 HOH HOH . H 4 HOH A 14 314 13 HOH HOH . H 4 HOH A 15 315 116 HOH HOH . H 4 HOH A 16 316 33 HOH HOH . H 4 HOH A 17 317 10 HOH HOH . H 4 HOH A 18 318 39 HOH HOH . H 4 HOH A 19 319 121 HOH HOH . H 4 HOH A 20 320 7 HOH HOH . H 4 HOH A 21 321 115 HOH HOH . H 4 HOH A 22 322 102 HOH HOH . H 4 HOH A 23 323 108 HOH HOH . H 4 HOH A 24 324 6 HOH HOH . H 4 HOH A 25 325 51 HOH HOH . H 4 HOH A 26 326 151 HOH HOH . H 4 HOH A 27 327 99 HOH HOH . H 4 HOH A 28 328 103 HOH HOH . H 4 HOH A 29 329 147 HOH HOH . H 4 HOH A 30 330 41 HOH HOH . H 4 HOH A 31 331 20 HOH HOH . H 4 HOH A 32 332 133 HOH HOH . H 4 HOH A 33 333 120 HOH HOH . H 4 HOH A 34 334 152 HOH HOH . H 4 HOH A 35 335 104 HOH HOH . H 4 HOH A 36 336 2 HOH HOH . H 4 HOH A 37 337 148 HOH HOH . H 4 HOH A 38 338 23 HOH HOH . H 4 HOH A 39 339 132 HOH HOH . H 4 HOH A 40 340 48 HOH HOH . H 4 HOH A 41 341 68 HOH HOH . H 4 HOH A 42 342 26 HOH HOH . H 4 HOH A 43 343 4 HOH HOH . H 4 HOH A 44 344 64 HOH HOH . H 4 HOH A 45 345 24 HOH HOH . H 4 HOH A 46 346 128 HOH HOH . H 4 HOH A 47 347 12 HOH HOH . H 4 HOH A 48 348 34 HOH HOH . H 4 HOH A 49 349 101 HOH HOH . H 4 HOH A 50 350 94 HOH HOH . H 4 HOH A 51 351 28 HOH HOH . H 4 HOH A 52 352 150 HOH HOH . H 4 HOH A 53 353 81 HOH HOH . H 4 HOH A 54 354 80 HOH HOH . H 4 HOH A 55 355 56 HOH HOH . H 4 HOH A 56 356 31 HOH HOH . H 4 HOH A 57 357 129 HOH HOH . H 4 HOH A 58 358 113 HOH HOH . H 4 HOH A 59 359 114 HOH HOH . H 4 HOH A 60 360 92 HOH HOH . H 4 HOH A 61 361 43 HOH HOH . H 4 HOH A 62 362 134 HOH HOH . H 4 HOH A 63 363 135 HOH HOH . H 4 HOH A 64 364 126 HOH HOH . H 4 HOH A 65 365 65 HOH HOH . H 4 HOH A 66 366 87 HOH HOH . H 4 HOH A 67 367 63 HOH HOH . H 4 HOH A 68 368 119 HOH HOH . H 4 HOH A 69 369 58 HOH HOH . H 4 HOH A 70 370 122 HOH HOH . H 4 HOH A 71 371 74 HOH HOH . H 4 HOH A 72 372 123 HOH HOH . H 4 HOH A 73 373 66 HOH HOH . H 4 HOH A 74 374 125 HOH HOH . H 4 HOH A 75 375 149 HOH HOH . H 4 HOH A 76 376 84 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 -3.922 -6.818 -5.112 1 71.31 ? P TMP 202 B 1 HETATM 2 O O1P TMP . . . D 3 -2.989 -7.649 -5.934 1 60.83 ? O1P TMP 202 B 1 HETATM 3 O O2P TMP . . . D 3 -3.192 -5.591 -4.509 1 53.8 ? O2P TMP 202 B 1 HETATM 4 O O3P TMP . . . D 3 -5.229 -6.667 -5.869 1 71.16 ? O3P TMP 202 B 1 HETATM 5 O O5' TMP . . . D 3 -4.306 -7.832 -3.876 1 68.31 ? O5' TMP 202 B 1 HETATM 6 C C5' TMP . . . D 3 -4.422 -7.513 -2.484 1 50.68 ? C5' TMP 202 B 1 HETATM 7 C C4' TMP . . . D 3 -5.911 -7.441 -2.106 1 45.14 ? C4' TMP 202 B 1 HETATM 8 O O4' TMP . . . D 3 -6.055 -7.737 -0.695 1 39.23 ? O4' TMP 202 B 1 HETATM 9 C C3' TMP . . . D 3 -6.499 -6.053 -2.342 1 35.14 ? C3' TMP 202 B 1 HETATM 10 O O3' TMP . . . D 3 -7.896 -6.058 -2.458 1 37.7 ? O3' TMP 202 B 1 HETATM 11 C C2' TMP . . . D 3 -6.17 -5.417 -1.002 1 38.82 ? C2' TMP 202 B 1 HETATM 12 C C1' TMP . . . D 3 -6.342 -6.535 0.017 1 36.91 ? C1' TMP 202 B 1 HETATM 13 N N1 TMP . . . D 3 -5.441 -6.481 1.203 1 36.76 ? N1 TMP 202 B 1 HETATM 14 C C2 TMP . . . D 3 -6.045 -6.423 2.464 1 39.18 ? C2 TMP 202 B 1 HETATM 15 O O2 TMP . . . D 3 -7.309 -6.424 2.536 1 37.7 ? O2 TMP 202 B 1 HETATM 16 N N3 TMP . . . D 3 -5.311 -6.374 3.58 1 36.74 ? N3 TMP 202 B 1 HETATM 17 C C4 TMP . . . D 3 -3.986 -6.424 3.627 1 40.92 ? C4 TMP 202 B 1 HETATM 18 O O4 TMP . . . D 3 -3.357 -6.392 4.753 1 33.56 ? O4 TMP 202 B 1 HETATM 19 C C5 TMP . . . D 3 -3.319 -6.491 2.286 1 36.44 ? C5 TMP 202 B 1 HETATM 20 C C5M TMP . . . D 3 -1.82 -6.527 2.228 1 39.09 ? C5M TMP 202 B 1 HETATM 21 C C6 TMP . . . D 3 -4.1 -6.532 1.134 1 37.65 ? C6 TMP 202 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 21 #