data_5X5Q # _model_server_result.job_id WAjROMQ2TU-poFUGsdYMjg _model_server_result.datetime_utc '2025-07-28 00:37:15' _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 5x5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 5X5Q # _exptl.entry_id 5X5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 5X5Q _cell.length_a 107.835 _cell.length_b 107.835 _cell.length_c 314.951 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X5Q _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_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,D,G,H,M,N,S,V 1 1 B,E,I,J,O,P,T 2 1 C,F,K,L,Q,R,U,W 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 414 n n N1 C6 UMP sing 415 n n N1 C1' UMP sing 416 n n C2 N3 UMP sing 417 n n C2 O2 UMP doub 418 n n N3 C4 UMP sing 419 n n N3 HN3 UMP sing 420 n n C4 C5 UMP sing 421 n n C4 O4 UMP doub 422 n n C5 C6 UMP doub 423 n n C5 H5 UMP sing 424 n n C6 H6 UMP sing 425 n n C1' C2' UMP sing 426 n n C1' O4' UMP sing 427 n n C1' H1' UMP sing 428 n n C2' C3' UMP sing 429 n n C2' H2' UMP sing 430 n n C2' "H2''" UMP sing 431 n n C3' C4' UMP sing 432 n n C3' O3' UMP sing 433 n n C3' H3' UMP sing 434 n n C4' O4' UMP sing 435 n n C4' C5' UMP sing 436 n n C4' H4' UMP sing 437 n n O3' HO3' UMP sing 438 n n C5' O5' UMP sing 439 n n C5' H5' UMP sing 440 n n C5' "H5''" UMP sing 441 n n O5' P UMP sing 442 n n P OP1 UMP doub 443 n n P OP2 UMP sing 444 n n P OP3 UMP sing 445 n n OP2 HOP2 UMP sing 446 n n OP3 HOP3 UMP sing 447 n n # _atom_sites.entry_id 5X5Q _atom_sites.fract_transf_matrix[1][1] 0.009273 _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] 0.009273 _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] 0.003175 _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 G 2 UMP A 1 401 1 UMP UMP . H 3 D16 A 1 402 1 D16 RTX . I 2 UMP B 1 401 2 UMP UMP . J 3 D16 B 1 402 2 D16 RTX . K 2 UMP C 1 401 3 UMP UMP . L 3 D16 C 1 402 3 D16 RTX . M 2 UMP D 1 401 4 UMP UMP . N 3 D16 D 1 402 4 D16 RTX . O 2 UMP E 1 401 5 UMP UMP . P 3 D16 E 1 402 5 D16 RTX . Q 2 UMP F 1 401 6 UMP UMP . R 3 D16 F 1 402 6 D16 RTX . S 4 HOH A 1 501 1 HOH HOH . S 4 HOH A 2 502 9 HOH HOH . T 4 HOH B 1 501 5 HOH HOH . T 4 HOH B 2 502 8 HOH HOH . T 4 HOH B 3 503 2 HOH HOH . T 4 HOH B 4 504 4 HOH HOH . U 4 HOH C 1 501 3 HOH HOH . V 4 HOH D 1 501 7 HOH HOH . V 4 HOH D 2 502 10 HOH HOH . W 4 HOH F 1 501 6 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 UMP . . . O 2 92.475 16.813 -0.406 1 42.77 ? N1 UMP 401 E 1 HETATM 2 C C2 UMP . . . O 2 91.412 16.492 -1.366 1 42.07 ? C2 UMP 401 E 1 HETATM 3 N N3 UMP . . . O 2 90.267 15.783 -0.802 1 44.1 ? N3 UMP 401 E 1 HETATM 4 C C4 UMP . . . O 2 90.124 15.409 0.574 1 46.7 ? C4 UMP 401 E 1 HETATM 5 C C5 UMP . . . O 2 91.197 15.766 1.505 1 43.92 ? C5 UMP 401 E 1 HETATM 6 C C6 UMP . . . O 2 92.372 16.478 1.001 1 43.34 ? C6 UMP 401 E 1 HETATM 7 O O2 UMP . . . O 2 91.47 16.737 -2.563 1 37.51 ? O2 UMP 401 E 1 HETATM 8 O O4 UMP . . . O 2 89.129 14.829 0.981 1 53.05 ? O4 UMP 401 E 1 HETATM 9 C C1' UMP . . . O 2 93.655 17.515 -0.83 1 45.75 ? C1' UMP 401 E 1 HETATM 10 C C2' UMP . . . O 2 93.832 18.81 -1.542 1 46.7 ? C2' UMP 401 E 1 HETATM 11 C C3' UMP . . . O 2 95.17 19.255 -1.233 1 45.16 ? C3' UMP 401 E 1 HETATM 12 C C4' UMP . . . O 2 95.504 18.541 0.025 1 46.35 ? C4' UMP 401 E 1 HETATM 13 O O3' UMP . . . O 2 95.985 18.803 -2.269 1 43.58 ? O3' UMP 401 E 1 HETATM 14 O O4' UMP . . . O 2 94.769 17.302 0.009 1 46.58 ? O4' UMP 401 E 1 HETATM 15 C C5' UMP . . . O 2 95.155 19.367 1.216 1 45.54 ? C5' UMP 401 E 1 HETATM 16 O O5' UMP . . . O 2 96.021 20.386 1.508 1 43.19 ? O5' UMP 401 E 1 HETATM 17 P P UMP . . . O 2 95.503 21.681 2.196 1 41.95 ? P UMP 401 E 1 HETATM 18 O OP1 UMP . . . O 2 94.542 22.346 1.228 1 40.59 -1 OP1 UMP 401 E 1 HETATM 19 O OP2 UMP . . . O 2 96.592 22.697 2.463 1 39.82 ? OP2 UMP 401 E 1 HETATM 20 O OP3 UMP . . . O 2 94.866 21.258 3.491 1 38.63 -1 OP3 UMP 401 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 94 _model_server_stats.query_time_ms 482 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #