data_1RDY # _model_server_result.job_id FqvXRe7dMljrkNjlK5KEtw _model_server_result.datetime_utc '2024-11-24 00:57:30' _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 1rdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":338}' # _entry.id 1RDY # _exptl.entry_id 1RDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 260.136 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 6-O-phosphono-beta-D-fructofuranose _entity.pdbx_number_of_molecules 2 _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 1RDY _cell.length_a 61.2 _cell.length_b 166.75 _cell.length_c 79.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RDY _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,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 61.2 166.75 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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 112 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 112 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id F _struct_conn.ptnr2_label_atom_id O3P _struct_conn.ptnr2_label_comp_id AMP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id AMP _struct_conn.ptnr2_auth_seq_id 339 _struct_conn.ptnr2_symmetry 1_555 _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 1.864 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C6 H13 O9 P' _chem_comp.formula_weight 260.136 _chem_comp.id F6P _chem_comp.mon_nstd_flag n _chem_comp.name 6-O-phosphono-beta-D-fructofuranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms FRUCTOSE-6-PHOSPHATE;6-O-phosphono-beta-D-fructose;6-O-phosphono-D-fructose;6-O-phosphono-fructose # _pdbx_chem_comp_identifier.comp_id F6P _pdbx_chem_comp_identifier.identifier b-D-Fruf6PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1RDY _atom_sites.fract_transf_matrix[1][1] 0.01634 _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] 0.005997 _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] 0.012525 _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 F6P A 1 338 1 F6P F6P . D 3 AMP A 1 339 3 AMP AMP . E 2 F6P B 1 338 2 F6P F6P . F 3 AMP B 1 339 4 AMP AMP . G 4 HOH A 1 340 1 HOH HOH . G 4 HOH A 2 341 2 HOH HOH . G 4 HOH A 3 342 3 HOH HOH . G 4 HOH A 4 343 4 HOH HOH . G 4 HOH A 5 344 5 HOH HOH . G 4 HOH A 6 345 6 HOH HOH . G 4 HOH A 7 346 7 HOH HOH . G 4 HOH A 8 347 8 HOH HOH . G 4 HOH A 9 348 10 HOH HOH . G 4 HOH A 10 349 12 HOH HOH . G 4 HOH A 11 350 13 HOH HOH . G 4 HOH A 12 351 14 HOH HOH . G 4 HOH A 13 352 15 HOH HOH . G 4 HOH A 14 353 16 HOH HOH . G 4 HOH A 15 354 17 HOH HOH . G 4 HOH A 16 355 18 HOH HOH . G 4 HOH A 17 356 20 HOH HOH . G 4 HOH A 18 357 21 HOH HOH . G 4 HOH A 19 358 22 HOH HOH . G 4 HOH A 20 359 23 HOH HOH . G 4 HOH A 21 360 24 HOH HOH . G 4 HOH A 22 361 25 HOH HOH . G 4 HOH A 23 362 26 HOH HOH . G 4 HOH A 24 363 27 HOH HOH . G 4 HOH A 25 364 28 HOH HOH . G 4 HOH A 26 365 29 HOH HOH . G 4 HOH A 27 366 30 HOH HOH . G 4 HOH A 28 367 31 HOH HOH . G 4 HOH A 29 368 32 HOH HOH . G 4 HOH A 30 369 33 HOH HOH . G 4 HOH A 31 370 35 HOH HOH . G 4 HOH A 32 371 36 HOH HOH . G 4 HOH A 33 372 37 HOH HOH . G 4 HOH A 34 373 38 HOH HOH . G 4 HOH A 35 374 39 HOH HOH . G 4 HOH A 36 375 40 HOH HOH . G 4 HOH A 37 376 41 HOH HOH . G 4 HOH A 38 377 42 HOH HOH . G 4 HOH A 39 378 43 HOH HOH . G 4 HOH A 40 379 44 HOH HOH . G 4 HOH A 41 380 45 HOH HOH . G 4 HOH A 42 381 46 HOH HOH . G 4 HOH A 43 382 47 HOH HOH . G 4 HOH A 44 383 79 HOH HOH . G 4 HOH A 45 384 100 HOH HOH . G 4 HOH A 46 385 106 HOH HOH . G 4 HOH A 47 386 107 HOH HOH . G 4 HOH A 48 387 109 HOH HOH . G 4 HOH A 49 388 111 HOH HOH . H 4 HOH B 1 340 9 HOH HOH . H 4 HOH B 2 341 11 HOH HOH . H 4 HOH B 3 342 19 HOH HOH . H 4 HOH B 4 343 34 HOH HOH . H 4 HOH B 5 344 48 HOH HOH . H 4 HOH B 6 345 49 HOH HOH . H 4 HOH B 7 346 50 HOH HOH . H 4 HOH B 8 347 51 HOH HOH . H 4 HOH B 9 348 52 HOH HOH . H 4 HOH B 10 349 53 HOH HOH . H 4 HOH B 11 350 54 HOH HOH . H 4 HOH B 12 351 55 HOH HOH . H 4 HOH B 13 352 56 HOH HOH . H 4 HOH B 14 353 57 HOH HOH . H 4 HOH B 15 354 58 HOH HOH . H 4 HOH B 16 355 59 HOH HOH . H 4 HOH B 17 356 60 HOH HOH . H 4 HOH B 18 357 61 HOH HOH . H 4 HOH B 19 358 62 HOH HOH . H 4 HOH B 20 359 63 HOH HOH . H 4 HOH B 21 360 64 HOH HOH . H 4 HOH B 22 361 65 HOH HOH . H 4 HOH B 23 362 66 HOH HOH . H 4 HOH B 24 363 67 HOH HOH . H 4 HOH B 25 364 68 HOH HOH . H 4 HOH B 26 365 69 HOH HOH . H 4 HOH B 27 366 70 HOH HOH . H 4 HOH B 28 367 71 HOH HOH . H 4 HOH B 29 368 72 HOH HOH . H 4 HOH B 30 369 73 HOH HOH . H 4 HOH B 31 370 74 HOH HOH . H 4 HOH B 32 371 75 HOH HOH . H 4 HOH B 33 372 76 HOH HOH . H 4 HOH B 34 373 77 HOH HOH . H 4 HOH B 35 374 78 HOH HOH . H 4 HOH B 36 375 80 HOH HOH . H 4 HOH B 37 376 81 HOH HOH . H 4 HOH B 38 377 82 HOH HOH . H 4 HOH B 39 378 83 HOH HOH . H 4 HOH B 40 379 84 HOH HOH . H 4 HOH B 41 380 85 HOH HOH . H 4 HOH B 42 381 86 HOH HOH . H 4 HOH B 43 382 87 HOH HOH . H 4 HOH B 44 383 88 HOH HOH . H 4 HOH B 45 384 89 HOH HOH . H 4 HOH B 46 385 90 HOH HOH . H 4 HOH B 47 386 91 HOH HOH . H 4 HOH B 48 387 92 HOH HOH . H 4 HOH B 49 388 93 HOH HOH . H 4 HOH B 50 389 94 HOH HOH . H 4 HOH B 51 390 95 HOH HOH . H 4 HOH B 52 391 96 HOH HOH . H 4 HOH B 53 392 97 HOH HOH . H 4 HOH B 54 393 98 HOH HOH . H 4 HOH B 55 394 99 HOH HOH . H 4 HOH B 56 395 101 HOH HOH . H 4 HOH B 57 396 102 HOH HOH . H 4 HOH B 58 397 103 HOH HOH . H 4 HOH B 59 398 104 HOH HOH . H 4 HOH B 60 399 105 HOH HOH . H 4 HOH B 61 400 108 HOH HOH . H 4 HOH B 62 401 115 HOH HOH . H 4 HOH B 63 402 116 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 O O1 F6P . . . C 2 43.648 107.186 12.113 0.88 72.78 ? O1 F6P 338 A 1 HETATM 2 C C1 F6P . . . C 2 43.626 108.521 11.654 0.88 73.81 ? C1 F6P 338 A 1 HETATM 3 C C2 F6P . . . C 2 42.705 109.444 12.484 0.88 74.77 ? C2 F6P 338 A 1 HETATM 4 O O2 F6P . . . C 2 42.583 108.914 13.802 0.88 77.89 ? O2 F6P 338 A 1 HETATM 5 C C3 F6P . . . C 2 41.328 109.585 11.813 0.88 72.25 ? C3 F6P 338 A 1 HETATM 6 O O3 F6P . . . C 2 40.594 108.4 12.014 0.88 68.48 ? O3 F6P 338 A 1 HETATM 7 C C4 F6P . . . C 2 40.72 110.855 12.455 0.88 71.01 ? C4 F6P 338 A 1 HETATM 8 O O4 F6P . . . C 2 39.788 111.562 11.646 0.88 62.8 ? O4 F6P 338 A 1 HETATM 9 C C5 F6P . . . C 2 41.964 111.645 12.883 0.88 75.58 ? C5 F6P 338 A 1 HETATM 10 O O5 F6P . . . C 2 43.082 110.791 12.503 0.88 76.96 ? O5 F6P 338 A 1 HETATM 11 C C6 F6P . . . C 2 41.899 111.927 14.315 0.88 83.35 ? C6 F6P 338 A 1 HETATM 12 O O6 F6P . . . C 2 42.915 112.993 14.432 0.88 93.57 ? O6 F6P 338 A 1 HETATM 13 P P F6P . . . C 2 43.189 114.256 15.408 0.88 96.74 ? P F6P 338 A 1 HETATM 14 O O1P F6P . . . C 2 42.155 115.347 15.222 0.88 97.89 ? O1P F6P 338 A 1 HETATM 15 O O2P F6P . . . C 2 43.135 113.835 16.869 0.88 101.95 ? O2P F6P 338 A 1 HETATM 16 O O3P F6P . . . C 2 44.56 114.827 15.103 0.88 96.25 ? O3P F6P 338 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #