data_5KRU # _model_server_result.job_id lZAi3zHelxD3UkFwA0FfYA _model_server_result.datetime_utc '2024-11-12 19:34:38' _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 5kru # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5KRU # _exptl.entry_id 5KRU _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 98.6 _cell.angle_gamma 90 _cell.entry_id 5KRU _cell.length_a 30.858 _cell.length_b 60.412 _cell.length_c 34.568 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KRU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,E _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc4 B O5P THP . A THP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc5 C CA CA . A CA 202 1_555 E O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc6 C CA CA . A CA 202 1_555 E O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc7 C CA CA . A CA 202 1_555 E O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? # _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 281 n n P2 O5P THP sing 282 n n P2 O6P THP sing 283 n n P2 O5' THP sing 284 n n O5P HOP5 THP sing 285 n n O6P HOP6 THP sing 286 n n P1 O1P THP doub 287 n n P1 O2P THP sing 288 n n P1 O3P THP sing 289 n n P1 O3' THP sing 290 n n O2P HOP2 THP sing 291 n n O3P HOP3 THP sing 292 n n O5' C5' THP sing 293 n n C5' C4' THP sing 294 n n C5' "H5'1" THP sing 295 n n C5' "H5'2" THP sing 296 n n C4' O4' THP sing 297 n n C4' C3' THP sing 298 n n C4' H4' THP sing 299 n n O4' C1' THP sing 300 n n C3' O3' THP sing 301 n n C3' C2' THP sing 302 n n C3' H3' THP sing 303 n n C2' C1' THP sing 304 n n C2' "H2'1" THP sing 305 n n C2' "H2'2" THP sing 306 n n C1' N1 THP sing 307 n n C1' H1' THP sing 308 n n N1 C2 THP sing 309 n n N1 C6 THP sing 310 n n C2 O2 THP doub 311 n n C2 N3 THP sing 312 n n N3 C4 THP sing 313 n n N3 H3 THP sing 314 n n C4 O4 THP doub 315 n n C4 C5 THP sing 316 n n C5 C5M THP sing 317 n n C5 C6 THP doub 318 n n C5M H51 THP sing 319 n n C5M H52 THP sing 320 n n C5M H53 THP sing 321 n n C6 H6 THP sing 322 n n # _atom_sites.entry_id 5KRU _atom_sites.fract_transf_matrix[1][1] 0.032407 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004903 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016553 _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] 0.029258 _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 1 201 142 THP THP . C 3 CA A 1 202 1 CA CA . D 4 PO4 A 1 203 1 PO4 PO4 . E 5 HOH A 1 301 128 HOH HOH . E 5 HOH A 2 302 58 HOH HOH . E 5 HOH A 3 303 98 HOH HOH . E 5 HOH A 4 304 2 HOH HOH . E 5 HOH A 5 305 131 HOH HOH . E 5 HOH A 6 306 132 HOH HOH . E 5 HOH A 7 307 14 HOH HOH . E 5 HOH A 8 308 130 HOH HOH . E 5 HOH A 9 309 62 HOH HOH . E 5 HOH A 10 310 105 HOH HOH . E 5 HOH A 11 311 72 HOH HOH . E 5 HOH A 12 312 87 HOH HOH . E 5 HOH A 13 313 67 HOH HOH . E 5 HOH A 14 314 76 HOH HOH . E 5 HOH A 15 315 90 HOH HOH . E 5 HOH A 16 316 115 HOH HOH . E 5 HOH A 17 317 83 HOH HOH . E 5 HOH A 18 318 93 HOH HOH . E 5 HOH A 19 319 53 HOH HOH . E 5 HOH A 20 320 113 HOH HOH . E 5 HOH A 21 321 17 HOH HOH . E 5 HOH A 22 322 12 HOH HOH . E 5 HOH A 23 323 107 HOH HOH . E 5 HOH A 24 324 64 HOH HOH . E 5 HOH A 25 325 74 HOH HOH . E 5 HOH A 26 326 15 HOH HOH . E 5 HOH A 27 327 69 HOH HOH . E 5 HOH A 28 328 18 HOH HOH . E 5 HOH A 29 329 84 HOH HOH . E 5 HOH A 30 330 54 HOH HOH . E 5 HOH A 31 331 125 HOH HOH . E 5 HOH A 32 332 77 HOH HOH . E 5 HOH A 33 333 101 HOH HOH . E 5 HOH A 34 334 104 HOH HOH . E 5 HOH A 35 335 61 HOH HOH . E 5 HOH A 36 336 50 HOH HOH . E 5 HOH A 37 337 5 HOH HOH . E 5 HOH A 38 338 133 HOH HOH . E 5 HOH A 39 339 88 HOH HOH . E 5 HOH A 40 340 11 HOH HOH . E 5 HOH A 41 341 6 HOH HOH . E 5 HOH A 42 342 79 HOH HOH . E 5 HOH A 43 343 70 HOH HOH . E 5 HOH A 44 344 95 HOH HOH . E 5 HOH A 45 345 60 HOH HOH . E 5 HOH A 46 346 123 HOH HOH . E 5 HOH A 47 347 63 HOH HOH . E 5 HOH A 48 348 122 HOH HOH . E 5 HOH A 49 349 65 HOH HOH . E 5 HOH A 50 350 10 HOH HOH . E 5 HOH A 51 351 92 HOH HOH . E 5 HOH A 52 352 119 HOH HOH . E 5 HOH A 53 353 102 HOH HOH . E 5 HOH A 54 354 134 HOH HOH . E 5 HOH A 55 355 80 HOH HOH . E 5 HOH A 56 356 97 HOH HOH . E 5 HOH A 57 357 85 HOH HOH . E 5 HOH A 58 358 78 HOH HOH . E 5 HOH A 59 359 20 HOH HOH . E 5 HOH A 60 360 82 HOH HOH . E 5 HOH A 61 361 66 HOH HOH . E 5 HOH A 62 362 100 HOH HOH . E 5 HOH A 63 363 118 HOH HOH . E 5 HOH A 64 364 109 HOH HOH . E 5 HOH A 65 365 121 HOH HOH . E 5 HOH A 66 366 81 HOH HOH . E 5 HOH A 67 367 75 HOH HOH . E 5 HOH A 68 368 55 HOH HOH . E 5 HOH A 69 369 106 HOH HOH . E 5 HOH A 70 370 3 HOH HOH . E 5 HOH A 71 371 59 HOH HOH . E 5 HOH A 72 372 52 HOH HOH . E 5 HOH A 73 373 71 HOH HOH . E 5 HOH A 74 374 8 HOH HOH . E 5 HOH A 75 375 126 HOH HOH . E 5 HOH A 76 376 110 HOH HOH . E 5 HOH A 77 377 49 HOH HOH . E 5 HOH A 78 378 57 HOH HOH . E 5 HOH A 79 379 116 HOH HOH . E 5 HOH A 80 380 4 HOH HOH . E 5 HOH A 81 381 19 HOH HOH . E 5 HOH A 82 382 96 HOH HOH . E 5 HOH A 83 383 117 HOH HOH . E 5 HOH A 84 384 103 HOH HOH . E 5 HOH A 85 385 129 HOH HOH . E 5 HOH A 86 386 99 HOH HOH . E 5 HOH A 87 387 91 HOH HOH . E 5 HOH A 88 388 124 HOH HOH . E 5 HOH A 89 389 127 HOH HOH . E 5 HOH A 90 390 108 HOH HOH . E 5 HOH A 91 391 94 HOH HOH . E 5 HOH A 92 392 111 HOH HOH . E 5 HOH A 93 393 112 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 43.569 9.391 39.981 1 13 ? P2 THP 201 A 1 HETATM 2 O O4P THP . . . B 2 43.466 7.972 39.961 1 11.34 ? O4P THP 201 A 1 HETATM 3 O O5P THP . . . B 2 42.309 10.077 40.422 1 12.7 ? O5P THP 201 A 1 HETATM 4 O O6P THP . . . B 2 44.88 9.911 40.711 1 15.73 ? O6P THP 201 A 1 HETATM 5 P P1 THP . . . B 2 46.405 13.933 35.878 1 22.7 ? P1 THP 201 A 1 HETATM 6 O O1P THP . . . B 2 45.752 15.136 35.179 1 30.82 ? O1P THP 201 A 1 HETATM 7 O O2P THP . . . B 2 46.314 14.004 37.268 1 17.21 ? O2P THP 201 A 1 HETATM 8 O O3P THP . . . B 2 47.77 13.756 35.213 1 27.76 ? O3P THP 201 A 1 HETATM 9 O O5' THP . . . B 2 43.727 9.795 38.46 1 12.17 ? O5' THP 201 A 1 HETATM 10 C C5' THP . . . B 2 43.582 11.148 37.953 1 15.26 ? C5' THP 201 A 1 HETATM 11 C C4' THP . . . B 2 44.287 11.301 36.629 1 14.66 ? C4' THP 201 A 1 HETATM 12 O O4' THP . . . B 2 43.661 10.391 35.71 1 17.24 ? O4' THP 201 A 1 HETATM 13 C C3' THP . . . B 2 44.27 12.664 35.971 1 18.22 ? C3' THP 201 A 1 HETATM 14 O O3' THP . . . B 2 45.539 12.774 35.353 1 24.82 ? O3' THP 201 A 1 HETATM 15 C C2' THP . . . B 2 43.351 12.478 34.775 1 15.05 ? C2' THP 201 A 1 HETATM 16 C C1' THP . . . B 2 43.408 10.996 34.49 1 14.39 ? C1' THP 201 A 1 HETATM 17 N N1 THP . . . B 2 42.096 10.485 34.015 1 12.46 ? N1 THP 201 A 1 HETATM 18 C C2 THP . . . B 2 41.872 10.521 32.629 1 11.55 ? C2 THP 201 A 1 HETATM 19 O O2 THP . . . B 2 42.794 10.936 31.849 1 13.45 ? O2 THP 201 A 1 HETATM 20 N N3 THP . . . B 2 40.684 10.173 32.115 1 12.09 ? N3 THP 201 A 1 HETATM 21 C C4 THP . . . B 2 39.683 9.792 32.926 1 9.42 ? C4 THP 201 A 1 HETATM 22 O O4 THP . . . B 2 38.594 9.48 32.375 1 9.9 ? O4 THP 201 A 1 HETATM 23 C C5 THP . . . B 2 39.902 9.644 34.348 1 10.49 ? C5 THP 201 A 1 HETATM 24 C C5M THP . . . B 2 38.79 9.168 35.245 1 9.76 ? C5M THP 201 A 1 HETATM 25 C C6 THP . . . B 2 41.122 10.089 34.881 1 10.64 ? C6 THP 201 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #