data_1WLJ # _model_server_result.job_id AyrbnyrmTzqgx8yb679jKg _model_server_result.datetime_utc '2025-02-05 03:56:46' _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 1wlj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":300}' # _entry.id 1WLJ # _exptl.entry_id 1WLJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _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 120 _cell.entry_id 1WLJ _cell.length_a 63.42 _cell.length_b 63.42 _cell.length_c 97.91 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WLJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 4 _struct_asym.id F _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 11 A ASP 11 1_555 B MN MN . A MN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 A OD1 ASP 11 A ASP 11 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc3 A OE2 GLU 13 A GLU 13 1_555 B MN MN . A MN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 A OD2 ASP 90 A ASP 90 1_555 D MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc5 A NE2 HIS 93 A HIS 93 1_555 D MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc6 A OD2 ASP 154 A ASP 154 1_555 B MN MN . A MN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 B MN MN . A MN 200 1_555 F O2P U5P . A U5P 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc8 B MN MN . A MN 200 1_555 F O3P U5P . A U5P 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc9 C MN MN . A MN 201 1_555 F O3P U5P . A U5P 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc10 C MN MN . A MN 201 1_555 G O HOH . A HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc11 C MN MN . A MN 201 1_555 G O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc12 C MN MN . A MN 201 1_555 G O HOH . A HOH 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc13 C MN MN . A MN 201 1_555 G O HOH . A HOH 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? # _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 364 n n N1 C6 U5P sing 365 n n N1 C1' U5P sing 366 n n C2 N3 U5P sing 367 n n C2 O2 U5P doub 368 n n N3 C4 U5P sing 369 n n N3 HN3 U5P sing 370 n n C4 C5 U5P sing 371 n n C4 O4 U5P doub 372 n n C5 C6 U5P doub 373 n n C5 H5 U5P sing 374 n n C6 H6 U5P sing 375 n n C1' C2' U5P sing 376 n n C1' O4' U5P sing 377 n n C1' H1' U5P sing 378 n n C2' O2' U5P sing 379 n n C2' C3' U5P sing 380 n n C2' H2' U5P sing 381 n n O2' HO2' U5P sing 382 n n C3' C4' U5P sing 383 n n C3' O3' U5P sing 384 n n C3' H3' U5P sing 385 n n C4' O4' U5P sing 386 n n C4' C5' U5P sing 387 n n C4' H4' U5P sing 388 n n O3' HO3' U5P sing 389 n n C5' O5' U5P sing 390 n n C5' "H5'1" U5P sing 391 n n C5' "H5'2" U5P sing 392 n n O5' P U5P sing 393 n n P O1P U5P doub 394 n n P O2P U5P sing 395 n n P O3P U5P sing 396 n n O2P HOP2 U5P sing 397 n n O3P HOP3 U5P sing 398 n n # _atom_sites.entry_id 1WLJ _atom_sites.fract_transf_matrix[1][1] 0.015768 _atom_sites.fract_transf_matrix[1][2] 0.009104 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018207 _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] 0.010213 _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 MN A 1 200 200 MN MN . C 2 MN A 1 201 201 MN MN . D 2 MN A 1 202 202 MN MN . E 3 ACT A 1 203 80 ACT ACT . F 4 U5P A 1 300 300 U5P U5P . G 5 HOH A 1 301 1 HOH HOH . G 5 HOH A 2 302 2 HOH HOH . G 5 HOH A 3 303 3 HOH HOH . G 5 HOH A 4 304 4 HOH HOH . G 5 HOH A 5 305 5 HOH HOH . G 5 HOH A 6 306 6 HOH HOH . G 5 HOH A 7 307 7 HOH HOH . G 5 HOH A 8 308 8 HOH HOH . G 5 HOH A 9 309 9 HOH HOH . G 5 HOH A 10 310 10 HOH HOH . G 5 HOH A 11 311 11 HOH HOH . G 5 HOH A 12 312 12 HOH HOH . G 5 HOH A 13 313 13 HOH HOH . G 5 HOH A 14 314 14 HOH HOH . G 5 HOH A 15 315 15 HOH HOH . G 5 HOH A 16 316 16 HOH HOH . G 5 HOH A 17 317 17 HOH HOH . G 5 HOH A 18 318 18 HOH HOH . G 5 HOH A 19 319 19 HOH HOH . G 5 HOH A 20 320 20 HOH HOH . G 5 HOH A 21 321 21 HOH HOH . G 5 HOH A 22 322 22 HOH HOH . G 5 HOH A 23 323 23 HOH HOH . G 5 HOH A 24 324 24 HOH HOH . G 5 HOH A 25 325 25 HOH HOH . G 5 HOH A 26 326 26 HOH HOH . G 5 HOH A 27 327 27 HOH HOH . G 5 HOH A 28 328 28 HOH HOH . G 5 HOH A 29 329 29 HOH HOH . G 5 HOH A 30 330 30 HOH HOH . G 5 HOH A 31 331 31 HOH HOH . G 5 HOH A 32 332 32 HOH HOH . G 5 HOH A 33 333 33 HOH HOH . G 5 HOH A 34 334 34 HOH HOH . G 5 HOH A 35 335 35 HOH HOH . G 5 HOH A 36 336 36 HOH HOH . G 5 HOH A 37 337 37 HOH HOH . G 5 HOH A 38 338 38 HOH HOH . G 5 HOH A 39 339 39 HOH HOH . G 5 HOH A 40 340 40 HOH HOH . G 5 HOH A 41 341 41 HOH HOH . G 5 HOH A 42 342 42 HOH HOH . G 5 HOH A 43 343 43 HOH HOH . G 5 HOH A 44 344 44 HOH HOH . G 5 HOH A 45 345 45 HOH HOH . G 5 HOH A 46 346 46 HOH HOH . G 5 HOH A 47 347 47 HOH HOH . G 5 HOH A 48 348 48 HOH HOH . G 5 HOH A 49 349 49 HOH HOH . G 5 HOH A 50 350 50 HOH HOH . G 5 HOH A 51 351 51 HOH HOH . G 5 HOH A 52 352 52 HOH HOH . G 5 HOH A 53 353 53 HOH HOH . G 5 HOH A 54 354 54 HOH HOH . G 5 HOH A 55 355 55 HOH HOH . G 5 HOH A 56 356 56 HOH HOH . G 5 HOH A 57 357 57 HOH HOH . G 5 HOH A 58 358 58 HOH HOH . G 5 HOH A 59 359 59 HOH HOH . G 5 HOH A 60 360 60 HOH HOH . G 5 HOH A 61 361 61 HOH HOH . G 5 HOH A 62 362 62 HOH HOH . G 5 HOH A 63 363 63 HOH HOH . G 5 HOH A 64 364 64 HOH HOH . G 5 HOH A 65 365 65 HOH HOH . G 5 HOH A 66 366 66 HOH HOH . G 5 HOH A 67 367 67 HOH HOH . G 5 HOH A 68 368 68 HOH HOH . G 5 HOH A 69 369 69 HOH HOH . G 5 HOH A 70 370 70 HOH HOH . G 5 HOH A 71 371 71 HOH HOH . G 5 HOH A 72 372 72 HOH HOH . G 5 HOH A 73 373 73 HOH HOH . G 5 HOH A 74 374 74 HOH HOH . G 5 HOH A 75 375 75 HOH HOH . G 5 HOH A 76 376 76 HOH HOH . G 5 HOH A 77 377 77 HOH HOH . G 5 HOH A 78 378 78 HOH HOH . G 5 HOH A 79 379 79 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 . . . F 4 9.222 45.248 30.539 1 23.95 ? N1 U5P 300 A 1 HETATM 2 C C2 U5P . . . F 4 9.499 46.505 31.044 1 27.1 ? C2 U5P 300 A 1 HETATM 3 N N3 U5P . . . F 4 10.305 47.284 30.253 1 27.04 ? N3 U5P 300 A 1 HETATM 4 C C4 U5P . . . F 4 10.854 46.941 29.034 1 29.17 ? C4 U5P 300 A 1 HETATM 5 C C5 U5P . . . F 4 10.531 45.617 28.582 1 26.81 ? C5 U5P 300 A 1 HETATM 6 C C6 U5P . . . F 4 9.745 44.836 29.333 1 25.83 ? C6 U5P 300 A 1 HETATM 7 O O2 U5P . . . F 4 9.061 46.899 32.112 1 28.52 ? O2 U5P 300 A 1 HETATM 8 O O4 U5P . . . F 4 11.526 47.772 28.42 1 28.88 ? O4 U5P 300 A 1 HETATM 9 C C1' U5P . . . F 4 8.346 44.377 31.333 1 22.45 ? C1' U5P 300 A 1 HETATM 10 C C2' U5P . . . F 4 6.878 44.807 31.286 1 19.55 ? C2' U5P 300 A 1 HETATM 11 O O2' U5P . . . F 4 6.266 44.504 32.525 1 20.76 ? O2' U5P 300 A 1 HETATM 12 C C3' U5P . . . F 4 6.354 43.943 30.147 1 18.98 ? C3' U5P 300 A 1 HETATM 13 C C4' U5P . . . F 4 7.095 42.638 30.375 1 18.66 ? C4' U5P 300 A 1 HETATM 14 O O3' U5P . . . F 4 4.936 43.762 30.115 1 18.59 ? O3' U5P 300 A 1 HETATM 15 O O4' U5P . . . F 4 8.418 43.064 30.8 1 19.47 ? O4' U5P 300 A 1 HETATM 16 C C5' U5P . . . F 4 7.22 41.75 29.163 1 17.85 ? C5' U5P 300 A 1 HETATM 17 O O5' U5P . . . F 4 7.995 42.411 28.147 1 19.24 ? O5' U5P 300 A 1 HETATM 18 P P U5P . . . F 4 7.997 41.877 26.609 1 19.1 ? P U5P 300 A 1 HETATM 19 O O1P U5P . . . F 4 9.434 42.054 26.141 1 19.82 ? O1P U5P 300 A 1 HETATM 20 O O2P U5P . . . F 4 7.032 42.779 25.854 1 18.95 ? O2P U5P 300 A 1 HETATM 21 O O3P U5P . . . F 4 7.529 40.428 26.643 1 18.62 ? O3P U5P 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 21 #