data_8YQ0 # _model_server_result.job_id tZC4HoINGTK6E2raEdLy5Q _model_server_result.datetime_utc '2025-07-19 05:49:57' _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 8yq0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":1001}' # _entry.id 8YQ0 # _exptl.entry_id 8YQ0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.11 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-O-phosphono-alpha-D-ribofuranose _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 8YQ0 _cell.length_a 108.083 _cell.length_b 108.083 _cell.length_c 659.674 _cell.Z_PDB 72 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YQ0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # 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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 PISA hexameric 6 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,B,C,D,E,F,S,T 1 1 G,H,I,J,K,L 2 1 M,N,O,P,Q,R,U 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 S N N ? 2 T N N ? 2 U N N # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id HSX _chem_comp.mon_nstd_flag n _chem_comp.name 5-O-phosphono-alpha-D-ribofuranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 5-O-phosphono-alpha-D-ribose;5-O-phosphono-D-ribose;5-O-phosphono-ribose # 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 O4 C1 HSX sing 150 n n C1 O1 HSX sing 151 n n C1 C2 HSX sing 152 n n C1 H1 HSX sing 153 n n O4 C4 HSX sing 154 n n C3 C2 HSX sing 155 n n C2 O2 HSX sing 156 n n C2 H2 HSX sing 157 n n O2 HO2 HSX sing 158 n n C4 C3 HSX sing 159 n n C3 O3 HSX sing 160 n n C3 H3 HSX sing 161 n n O3 HO3 HSX sing 162 n n C5 C4 HSX sing 163 n n C4 H4 HSX sing 164 n n O5 C5 HSX sing 165 n n C5 H51 HSX sing 166 n n C5 H52 HSX sing 167 n n P' O5 HSX sing 168 n n O1X P' HSX doub 169 n n O3X P' HSX sing 170 n n P' O2X HSX sing 171 n n O2X HO2X HSX sing 172 n n O3X HO3X HSX sing 173 n n O1 HO1 HSX sing 174 n n # _pdbx_chem_comp_identifier.comp_id HSX _pdbx_chem_comp_identifier.identifier a-D-Ribf5PO3 _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 8YQ0 _atom_sites.fract_transf_matrix[1][1] 0.009252 _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] 0.009252 _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] 0.001516 _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 S 2 HSX B 1 1001 1001 HSX HSX . T 2 HSX F 1 1001 1001 HSX HSX . U 2 HSX O 1 1001 1001 HSX HSX . # 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 C C1 HSX . . . S 2 28.855 146.323 89.451 1 118.2 ? C1 HSX 1001 B 1 HETATM 2 O O4 HSX . . . S 2 28.579 145.861 90.776 1 118.69 ? O4 HSX 1001 B 1 HETATM 3 C C2 HSX . . . S 2 27.673 145.869 88.594 1 108.49 ? C2 HSX 1001 B 1 HETATM 4 O O2 HSX . . . S 2 26.901 146.97 88.054 1 114.46 ? O2 HSX 1001 B 1 HETATM 5 C C3 HSX . . . S 2 26.825 145.025 89.532 1 96.17 ? C3 HSX 1001 B 1 HETATM 6 O O3 HSX . . . S 2 25.411 145.17 89.401 1 83.96 ? O3 HSX 1001 B 1 HETATM 7 C C4 HSX . . . S 2 27.191 145.558 90.882 1 100.12 ? C4 HSX 1001 B 1 HETATM 8 C C5 HSX . . . S 2 26.867 144.498 91.897 1 93.62 ? C5 HSX 1001 B 1 HETATM 9 O O5 HSX . . . S 2 26.462 145.124 93.071 1 97.75 ? O5 HSX 1001 B 1 HETATM 10 P P' HSX . . . S 2 27.599 145.138 94.122 1 136.17 ? P' HSX 1001 B 1 HETATM 11 O O1X HSX . . . S 2 28.489 146.062 93.38 1 119.64 ? O1X HSX 1001 B 1 HETATM 12 O O2X HSX . . . S 2 28.029 143.716 94.205 1 93.4 ? O2X HSX 1001 B 1 HETATM 13 O O3X HSX . . . S 2 27.005 145.668 95.382 1 105.77 ? O3X HSX 1001 B 1 HETATM 14 O O1 HSX . . . S 2 29.047 147.754 89.453 1 109.87 ? O1 HSX 1001 B 1 # _model_server_stats.io_time_ms 106 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #