data_1KSV # _model_server_result.job_id h3xRPeiRYOhRLksdBQmrRg _model_server_result.datetime_utc '2024-12-21 12:21:24' _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 1ksv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":232}' # _entry.id 1KSV # _exptl.entry_id 1KSV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 90 _cell.entry_id 1KSV _cell.length_a 48.061 _cell.length_b 147.58 _cell.length_c 34.879 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KSV _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 covale ? covale1 A C HIS 3 A HIS 1 1_555 A N MSE 4 A MSE 1 1_555 C ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C MSE 4 A MSE 1 1_555 A N ARG 5 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C PHE 66 A PHE 63 1_555 A N MSE 67 A MSE 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 A C MSE 67 A MSE 64 1_555 A N LEU 68 A LEU 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C LEU 113 A LEU 110 1_555 A N MSE 114 A MSE 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C MSE 114 A MSE 111 1_555 A N THR 115 A THR 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 A C ARG 191 A ARG 188 1_555 A N MSE 192 A MSE 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C MSE 192 A MSE 189 1_555 A N PHE 193 A PHE 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 377 n n N1 C6 U5P sing 378 n n N1 C1' U5P sing 379 n n C2 N3 U5P sing 380 n n C2 O2 U5P doub 381 n n N3 C4 U5P sing 382 n n N3 HN3 U5P sing 383 n n C4 C5 U5P sing 384 n n C4 O4 U5P doub 385 n n C5 C6 U5P doub 386 n n C5 H5 U5P sing 387 n n C6 H6 U5P sing 388 n n C1' C2' U5P sing 389 n n C1' O4' U5P sing 390 n n C1' H1' U5P sing 391 n n C2' O2' U5P sing 392 n n C2' C3' U5P sing 393 n n C2' H2' U5P sing 394 n n O2' HO2' U5P sing 395 n n C3' C4' U5P sing 396 n n C3' O3' U5P sing 397 n n C3' H3' U5P sing 398 n n C4' O4' U5P sing 399 n n C4' C5' U5P sing 400 n n C4' H4' U5P sing 401 n n O3' HO3' U5P sing 402 n n C5' O5' U5P sing 403 n n C5' "H5'1" U5P sing 404 n n C5' "H5'2" U5P sing 405 n n O5' P U5P sing 406 n n P O1P U5P doub 407 n n P O2P U5P sing 408 n n P O3P U5P sing 409 n n O2P HOP2 U5P sing 410 n n O3P HOP3 U5P sing 411 n n # _atom_sites.entry_id 1KSV _atom_sites.fract_transf_matrix[1][1] 0.020807 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006776 _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] 0.028671 _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 U5P A 1 232 232 U5P U . C 3 HOH A 1 301 301 HOH HOH . C 3 HOH A 2 302 302 HOH HOH . C 3 HOH A 3 303 303 HOH HOH . C 3 HOH A 4 304 304 HOH HOH . C 3 HOH A 5 305 305 HOH HOH . C 3 HOH A 6 306 306 HOH HOH . C 3 HOH A 7 307 307 HOH HOH . C 3 HOH A 8 308 308 HOH HOH . C 3 HOH A 9 309 309 HOH HOH . C 3 HOH A 10 310 310 HOH HOH . C 3 HOH A 11 311 311 HOH HOH . C 3 HOH A 12 312 312 HOH HOH . C 3 HOH A 13 315 315 HOH HOH . C 3 HOH A 14 316 316 HOH HOH . C 3 HOH A 15 317 317 HOH HOH . C 3 HOH A 16 318 318 HOH HOH . C 3 HOH A 17 319 319 HOH HOH . C 3 HOH A 18 320 320 HOH HOH . C 3 HOH A 19 321 321 HOH HOH . C 3 HOH A 20 322 322 HOH HOH . C 3 HOH A 21 323 323 HOH HOH . C 3 HOH A 22 324 324 HOH HOH . C 3 HOH A 23 325 325 HOH HOH . C 3 HOH A 24 326 326 HOH HOH . C 3 HOH A 25 327 327 HOH HOH . C 3 HOH A 26 328 328 HOH HOH . C 3 HOH A 27 329 329 HOH HOH . C 3 HOH A 28 330 330 HOH HOH . C 3 HOH A 29 331 331 HOH HOH . C 3 HOH A 30 332 332 HOH HOH . C 3 HOH A 31 333 333 HOH HOH . C 3 HOH A 32 334 334 HOH HOH . C 3 HOH A 33 335 335 HOH HOH . C 3 HOH A 34 336 336 HOH HOH . C 3 HOH A 35 337 337 HOH HOH . C 3 HOH A 36 338 338 HOH HOH . C 3 HOH A 37 339 339 HOH HOH . C 3 HOH A 38 340 340 HOH HOH . C 3 HOH A 39 341 341 HOH HOH . C 3 HOH A 40 342 342 HOH HOH . C 3 HOH A 41 343 343 HOH HOH . C 3 HOH A 42 344 344 HOH HOH . C 3 HOH A 43 345 345 HOH HOH . C 3 HOH A 44 346 346 HOH HOH . C 3 HOH A 45 347 347 HOH HOH . C 3 HOH A 46 348 348 HOH HOH . C 3 HOH A 47 349 349 HOH HOH . C 3 HOH A 48 350 350 HOH HOH . C 3 HOH A 49 351 351 HOH HOH . C 3 HOH A 50 352 352 HOH HOH . C 3 HOH A 51 353 353 HOH HOH . C 3 HOH A 52 354 354 HOH HOH . C 3 HOH A 53 355 355 HOH HOH . C 3 HOH A 54 356 356 HOH HOH . C 3 HOH A 55 357 357 HOH HOH . C 3 HOH A 56 358 358 HOH HOH . C 3 HOH A 57 359 359 HOH HOH . C 3 HOH A 58 360 360 HOH HOH . C 3 HOH A 59 361 361 HOH HOH . C 3 HOH A 60 362 362 HOH HOH . C 3 HOH A 61 363 363 HOH HOH . C 3 HOH A 62 364 364 HOH HOH . C 3 HOH A 63 365 365 HOH HOH . C 3 HOH A 64 366 366 HOH HOH . C 3 HOH A 65 367 367 HOH HOH . C 3 HOH A 66 368 368 HOH HOH . C 3 HOH A 67 369 369 HOH HOH . C 3 HOH A 68 370 370 HOH HOH . C 3 HOH A 69 371 371 HOH HOH . C 3 HOH A 70 372 372 HOH HOH . C 3 HOH A 71 373 373 HOH HOH . C 3 HOH A 72 374 374 HOH HOH . C 3 HOH A 73 375 375 HOH HOH . C 3 HOH A 74 376 376 HOH HOH . C 3 HOH A 75 377 377 HOH HOH . C 3 HOH A 76 378 378 HOH HOH . C 3 HOH A 77 379 379 HOH HOH . C 3 HOH A 78 380 380 HOH HOH . C 3 HOH A 79 381 381 HOH HOH . C 3 HOH A 80 382 382 HOH HOH . C 3 HOH A 81 383 383 HOH HOH . C 3 HOH A 82 384 384 HOH HOH . C 3 HOH A 83 385 385 HOH HOH . C 3 HOH A 84 386 386 HOH HOH . C 3 HOH A 85 387 387 HOH HOH . C 3 HOH A 86 388 388 HOH HOH . C 3 HOH A 87 389 389 HOH HOH . C 3 HOH A 88 390 390 HOH HOH . C 3 HOH A 89 391 391 HOH HOH . C 3 HOH A 90 392 392 HOH HOH . C 3 HOH A 91 393 393 HOH HOH . C 3 HOH A 92 394 394 HOH HOH . C 3 HOH A 93 395 395 HOH HOH . C 3 HOH A 94 396 396 HOH HOH . C 3 HOH A 95 397 397 HOH HOH . C 3 HOH A 96 398 398 HOH HOH . C 3 HOH A 97 399 399 HOH HOH . C 3 HOH A 98 400 400 HOH HOH . C 3 HOH A 99 401 401 HOH HOH . C 3 HOH A 100 402 402 HOH HOH . C 3 HOH A 101 403 403 HOH HOH . C 3 HOH A 102 404 404 HOH HOH . C 3 HOH A 103 405 405 HOH HOH . C 3 HOH A 104 406 406 HOH HOH . C 3 HOH A 105 407 407 HOH HOH . C 3 HOH A 106 408 408 HOH HOH . C 3 HOH A 107 409 409 HOH HOH . C 3 HOH A 108 410 410 HOH HOH . C 3 HOH A 109 411 411 HOH HOH . C 3 HOH A 110 412 412 HOH HOH . C 3 HOH A 111 413 413 HOH HOH . C 3 HOH A 112 414 414 HOH HOH . C 3 HOH A 113 415 415 HOH HOH . C 3 HOH A 114 416 416 HOH HOH . C 3 HOH A 115 417 417 HOH HOH . C 3 HOH A 116 418 418 HOH HOH . C 3 HOH A 117 419 419 HOH HOH . C 3 HOH A 118 420 420 HOH HOH . C 3 HOH A 119 421 421 HOH HOH . C 3 HOH A 120 422 422 HOH HOH . C 3 HOH A 121 423 423 HOH HOH . C 3 HOH A 122 424 424 HOH HOH . C 3 HOH A 123 425 425 HOH HOH . C 3 HOH A 124 426 426 HOH HOH . C 3 HOH A 125 427 427 HOH HOH . C 3 HOH A 126 428 428 HOH HOH . C 3 HOH A 127 429 429 HOH HOH . C 3 HOH A 128 430 430 HOH HOH . C 3 HOH A 129 431 431 HOH HOH . C 3 HOH A 130 432 432 HOH HOH . C 3 HOH A 131 433 433 HOH HOH . C 3 HOH A 132 434 434 HOH HOH . C 3 HOH A 133 435 435 HOH HOH . C 3 HOH A 134 436 436 HOH HOH . C 3 HOH A 135 437 437 HOH HOH . C 3 HOH A 136 438 438 HOH HOH . C 3 HOH A 137 439 439 HOH HOH . C 3 HOH A 138 440 440 HOH HOH . C 3 HOH A 139 441 441 HOH HOH . C 3 HOH A 140 442 442 HOH HOH . C 3 HOH A 141 443 443 HOH HOH . C 3 HOH A 142 444 444 HOH HOH . C 3 HOH A 143 445 445 HOH HOH . C 3 HOH A 144 446 446 HOH HOH . C 3 HOH A 145 447 447 HOH HOH . C 3 HOH A 146 448 448 HOH HOH . C 3 HOH A 147 449 449 HOH HOH . C 3 HOH A 148 450 450 HOH HOH . C 3 HOH A 149 451 451 HOH HOH . C 3 HOH A 150 452 452 HOH HOH . C 3 HOH A 151 453 453 HOH HOH . C 3 HOH A 152 454 454 HOH HOH . C 3 HOH A 153 455 455 HOH HOH . C 3 HOH A 154 456 456 HOH HOH . C 3 HOH A 155 457 457 HOH HOH . C 3 HOH A 156 458 458 HOH HOH . C 3 HOH A 157 459 459 HOH HOH . C 3 HOH A 158 460 460 HOH HOH . C 3 HOH A 159 461 461 HOH HOH . C 3 HOH A 160 462 462 HOH HOH . C 3 HOH A 161 463 463 HOH HOH . C 3 HOH A 162 464 464 HOH HOH . C 3 HOH A 163 465 465 HOH HOH . C 3 HOH A 164 466 466 HOH HOH . C 3 HOH A 165 467 467 HOH HOH . C 3 HOH A 166 468 468 HOH HOH . C 3 HOH A 167 469 469 HOH HOH . C 3 HOH A 168 470 470 HOH HOH . C 3 HOH A 169 471 471 HOH HOH . C 3 HOH A 170 472 472 HOH HOH . C 3 HOH A 171 473 473 HOH HOH . C 3 HOH A 172 474 474 HOH HOH . C 3 HOH A 173 475 475 HOH HOH . C 3 HOH A 174 476 476 HOH HOH . C 3 HOH A 175 477 477 HOH HOH . C 3 HOH A 176 478 478 HOH HOH . C 3 HOH A 177 479 479 HOH HOH . C 3 HOH A 178 480 480 HOH HOH . C 3 HOH A 179 481 481 HOH HOH . C 3 HOH A 180 482 482 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 N N1 U5P . . . B 2 50.742 8.281 -1.943 0.8 67.72 ? N1 U5P 232 A 1 HETATM 2 C C2 U5P . . . B 2 52.06 7.582 -1.961 0.8 67.44 ? C2 U5P 232 A 1 HETATM 3 N N3 U5P . . . B 2 52.822 7.942 -3.096 0.8 67.87 ? N3 U5P 232 A 1 HETATM 4 C C4 U5P . . . B 2 52.475 8.863 -4.18 0.8 68.67 ? C4 U5P 232 A 1 HETATM 5 C C5 U5P . . . B 2 51.195 9.512 -4.106 0.8 67.74 ? C5 U5P 232 A 1 HETATM 6 C C6 U5P . . . B 2 50.422 9.228 -3.07 0.8 67.07 ? C6 U5P 232 A 1 HETATM 7 O O2 U5P . . . B 2 52.505 6.731 -1.075 0.8 66.8 ? O2 U5P 232 A 1 HETATM 8 O O4 U5P . . . B 2 53.297 9.042 -5.107 0.8 70.21 ? O4 U5P 232 A 1 HETATM 9 C C1' U5P . . . B 2 49.942 7.971 -0.897 0.8 68.27 ? C1' U5P 232 A 1 HETATM 10 C C2' U5P . . . B 2 49.15 9.161 -0.283 0.8 68.16 ? C2' U5P 232 A 1 HETATM 11 O O2' U5P . . . B 2 49.087 8.967 1.092 0.8 67.49 ? O2' U5P 232 A 1 HETATM 12 C C3' U5P . . . B 2 47.816 9.128 -1.148 0.8 69.03 ? C3' U5P 232 A 1 HETATM 13 C C4' U5P . . . B 2 47.602 7.615 -1.435 0.8 69.55 ? C4' U5P 232 A 1 HETATM 14 O O3' U5P . . . B 2 46.852 9.223 -0.386 0.8 69.55 ? O3' U5P 232 A 1 HETATM 15 O O4' U5P . . . B 2 48.986 7.094 -1.563 0.8 68.93 ? O4' U5P 232 A 1 HETATM 16 C C5' U5P . . . B 2 46.369 7.186 -2.32 0.8 69.97 ? C5' U5P 232 A 1 HETATM 17 O O5' U5P . . . B 2 45.531 6.154 -1.966 0.8 71.19 ? O5' U5P 232 A 1 HETATM 18 P P U5P . . . B 2 44.105 6.385 -1.165 0.8 71.45 ? P U5P 232 A 1 HETATM 19 O O1P U5P . . . B 2 43.668 5.034 -0.356 0.8 71.37 ? O1P U5P 232 A 1 HETATM 20 O O2P U5P . . . B 2 42.945 6.616 -2.29 0.8 71.27 ? O2P U5P 232 A 1 HETATM 21 O O3P U5P . . . B 2 44.373 7.69 -0.167 0.8 71.07 ? O3P U5P 232 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #