data_3QW4 # _model_server_result.job_id 5OMn7aBv-bRlFx21bMf1ag _model_server_result.datetime_utc '2025-02-26 12:42:47' _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":"C","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 . . . C 2 24.947 -20.387 -32.321 1 57.73 ? N1 U5P 7485 B 1 HETATM 2 C C2 U5P . . . C 2 26.262 -19.865 -32.157 1 57.23 ? C2 U5P 7485 B 1 HETATM 3 N N3 U5P . . . C 2 27.231 -20.617 -31.51 1 56.99 ? N3 U5P 7485 B 1 HETATM 4 C C4 U5P . . . C 2 26.919 -21.884 -31.021 1 57.49 ? C4 U5P 7485 B 1 HETATM 5 C C5 U5P . . . C 2 25.634 -22.401 -31.174 1 57.91 ? C5 U5P 7485 B 1 HETATM 6 C C6 U5P . . . C 2 24.647 -21.662 -31.819 1 57.83 ? C6 U5P 7485 B 1 HETATM 7 O O2 U5P . . . C 2 26.591 -18.759 -32.568 1 57.47 ? O2 U5P 7485 B 1 HETATM 8 O O4 U5P . . . C 2 27.785 -22.547 -30.458 1 57.55 ? O4 U5P 7485 B 1 HETATM 9 C C1' U5P . . . C 2 23.846 -19.642 -33 1 57.34 ? C1' U5P 7485 B 1 HETATM 10 C C2' U5P . . . C 2 23.293 -18.565 -32.091 1 58.89 ? C2' U5P 7485 B 1 HETATM 11 O O2' U5P . . . C 2 22.425 -19.141 -31.113 1 60.13 ? O2' U5P 7485 B 1 HETATM 12 C C3' U5P . . . C 2 22.513 -17.737 -33.099 1 58.81 ? C3' U5P 7485 B 1 HETATM 13 C C4' U5P . . . C 2 23.2 -18.004 -34.435 1 56.43 ? C4' U5P 7485 B 1 HETATM 14 O O3' U5P . . . C 2 21.163 -18.189 -33.173 1 60.58 ? O3' U5P 7485 B 1 HETATM 15 O O4' U5P . . . C 2 24.256 -18.888 -34.152 1 55.99 ? O4' U5P 7485 B 1 HETATM 16 C C5' U5P . . . C 2 23.788 -16.644 -34.69 1 58.28 ? C5' U5P 7485 B 1 HETATM 17 O O5' U5P . . . C 2 24.664 -16.618 -35.804 1 58.29 ? O5' U5P 7485 B 1 HETATM 18 P P U5P . . . C 2 25.33 -15.211 -36.185 1 58.54 ? P U5P 7485 B 1 HETATM 19 O O1P U5P . . . C 2 24.54 -14.071 -35.668 1 59.33 ? O1P U5P 7485 B 1 HETATM 20 O O2P U5P . . . C 2 26.864 -15.23 -35.636 1 59.5 ? O2P U5P 7485 B 1 HETATM 21 O O3P U5P . . . C 2 25.452 -15.165 -37.799 1 58.17 ? O3P U5P 7485 B 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #