data_3QW4 # _model_server_result.job_id OVEa7rgaq_4hsdDX7HspMA _model_server_result.datetime_utc '2025-02-27 02:24:53' _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 3qw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":7485}' # _entry.id 3QW4 # _exptl.entry_id 3QW4 _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 3 _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 3QW4 _cell.length_a 64.722 _cell.length_b 64.722 _cell.length_c 477.596 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QW4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1,2 A,B,C,D,E,F,G,H 2 1 B,D,E,F,H 3 1 A,C,G 3 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' 7_645 y+1,x-1,-z 0 1 0 1 0 0 0 0 -1 64.722 -64.722 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N ? 2 F N N # _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 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 3QW4 _atom_sites.fract_transf_matrix[1][1] 0.015451 _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] 0.015451 _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] 0.002094 _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 U5P B 1 7485 7485 U5P U5P . D 3 CL C 1 453 453 CL CL . E 2 U5P C 1 7485 7485 U5P U5P . F 2 U5P C 1 454 454 U5P U5P . G 4 HOH B 1 453 453 HOH HOH . G 4 HOH B 2 454 454 HOH HOH . G 4 HOH B 3 455 455 HOH HOH . G 4 HOH B 4 456 456 HOH HOH . G 4 HOH B 5 457 457 HOH HOH . G 4 HOH B 6 458 458 HOH HOH . G 4 HOH B 7 459 459 HOH HOH . G 4 HOH B 8 460 460 HOH HOH . G 4 HOH B 9 461 461 HOH HOH . G 4 HOH B 10 462 462 HOH HOH . G 4 HOH B 11 463 463 HOH HOH . G 4 HOH B 12 464 464 HOH HOH . G 4 HOH B 13 465 465 HOH HOH . G 4 HOH B 14 466 466 HOH HOH . G 4 HOH B 15 467 467 HOH HOH . G 4 HOH B 16 468 468 HOH HOH . G 4 HOH B 17 469 469 HOH HOH . G 4 HOH B 18 470 470 HOH HOH . G 4 HOH B 19 471 471 HOH HOH . G 4 HOH B 20 472 472 HOH HOH . G 4 HOH B 21 473 473 HOH HOH . G 4 HOH B 22 474 474 HOH HOH . H 4 HOH C 1 455 455 HOH HOH . H 4 HOH C 2 456 456 HOH HOH . H 4 HOH C 3 457 457 HOH HOH . H 4 HOH C 4 458 458 HOH HOH . H 4 HOH C 5 459 459 HOH HOH . H 4 HOH C 6 460 460 HOH HOH . H 4 HOH C 7 461 461 HOH HOH . H 4 HOH C 8 462 462 HOH HOH . H 4 HOH C 9 463 463 HOH HOH . H 4 HOH C 10 464 464 HOH HOH . H 4 HOH C 11 465 465 HOH HOH . H 4 HOH C 12 466 466 HOH HOH . H 4 HOH C 13 467 467 HOH HOH . H 4 HOH C 14 468 468 HOH HOH . H 4 HOH C 15 469 469 HOH HOH . H 4 HOH C 16 470 470 HOH HOH . H 4 HOH C 17 471 471 HOH HOH . H 4 HOH C 18 472 472 HOH HOH . H 4 HOH C 19 473 473 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 . . . E 2 0.175 -16.929 30.969 1 88.76 ? N1 U5P 7485 C 1 HETATM 2 C C2 U5P . . . E 2 0.599 -18.172 31.521 1 86.96 ? C2 U5P 7485 C 1 HETATM 3 N N3 U5P . . . E 2 -0.054 -19.352 31.16 1 86.98 ? N3 U5P 7485 C 1 HETATM 4 C C4 U5P . . . E 2 -1.118 -19.316 30.262 1 88.65 ? C4 U5P 7485 C 1 HETATM 5 C C5 U5P . . . E 2 -1.543 -18.114 29.718 1 90.72 ? C5 U5P 7485 C 1 HETATM 6 C C6 U5P . . . E 2 -0.903 -16.929 30.069 1 90.79 ? C6 U5P 7485 C 1 HETATM 7 O O2 U5P . . . E 2 1.532 -18.263 32.316 1 85.72 ? O2 U5P 7485 C 1 HETATM 8 O O4 U5P . . . E 2 -1.685 -20.355 29.953 1 89.25 ? O4 U5P 7485 C 1 HETATM 9 C C1' U5P . . . E 2 0.822 -15.614 31.278 1 88.55 ? C1' U5P 7485 C 1 HETATM 10 C C2' U5P . . . E 2 2.354 -15.741 31.12 1 86.78 ? C2' U5P 7485 C 1 HETATM 11 O O2' U5P . . . E 2 3.008 -15.529 32.379 1 86.24 ? O2' U5P 7485 C 1 HETATM 12 C C3' U5P . . . E 2 2.778 -14.679 30.107 1 87.17 ? C3' U5P 7485 C 1 HETATM 13 C C4' U5P . . . E 2 1.526 -13.846 29.901 1 89.3 ? C4' U5P 7485 C 1 HETATM 14 O O3' U5P . . . E 2 3.842 -13.867 30.631 1 86.16 ? O3' U5P 7485 C 1 HETATM 15 O O4' U5P . . . E 2 0.401 -14.7 30.239 1 90.08 ? O4' U5P 7485 C 1 HETATM 16 C C5' U5P . . . E 2 1.668 -13.649 28.413 1 89.33 ? C5' U5P 7485 C 1 HETATM 17 O O5' U5P . . . E 2 0.533 -13.034 27.831 1 90.74 ? O5' U5P 7485 C 1 HETATM 18 P P U5P . . . E 2 0.648 -12.554 26.307 1 91.17 ? P U5P 7485 C 1 HETATM 19 O O1P U5P . . . E 2 2.037 -12.417 25.808 1 89.98 ? O1P U5P 7485 C 1 HETATM 20 O O2P U5P . . . E 2 -0.157 -13.602 25.404 1 91.28 ? O2P U5P 7485 C 1 HETATM 21 O O3P U5P . . . E 2 -0.198 -11.199 26.232 1 94 ? O3P U5P 7485 C 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #