data_8YQ0 # _model_server_result.job_id MzDTrtaOU5075OERzeisNw _model_server_result.datetime_utc '2025-07-16 14:26:56' _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":"T","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 . . . T 2 42.376 198.724 56.578 1 90.88 ? C1 HSX 1001 F 1 HETATM 2 O O4 HSX . . . T 2 42.79 199.542 57.737 1 95.36 ? O4 HSX 1001 F 1 HETATM 3 C C2 HSX . . . T 2 41.629 199.802 55.756 1 84.66 ? C2 HSX 1001 F 1 HETATM 4 O O2 HSX . . . T 2 41.519 199.453 54.345 1 80.07 ? O2 HSX 1001 F 1 HETATM 5 C C3 HSX . . . T 2 42.436 201.119 55.974 1 92.47 ? C3 HSX 1001 F 1 HETATM 6 O O3 HSX . . . T 2 42.919 201.755 54.675 1 76.39 ? O3 HSX 1001 F 1 HETATM 7 C C4 HSX . . . T 2 43.519 200.634 57.034 1 97.57 ? C4 HSX 1001 F 1 HETATM 8 C C5 HSX . . . T 2 44.116 201.767 57.932 1 90.71 ? C5 HSX 1001 F 1 HETATM 9 O O5 HSX . . . T 2 43.17 202.815 58.264 1 93.84 ? O5 HSX 1001 F 1 HETATM 10 P P' HSX . . . T 2 42.795 203.266 59.811 1 129.71 ? P' HSX 1001 F 1 HETATM 11 O O1X HSX . . . T 2 41.985 204.511 59.77 1 96.23 ? O1X HSX 1001 F 1 HETATM 12 O O2X HSX . . . T 2 41.824 202.076 60.285 1 108.36 ? O2X HSX 1001 F 1 HETATM 13 O O3X HSX . . . T 2 44.035 203.218 60.623 1 120.05 ? O3X HSX 1001 F 1 HETATM 14 O O1 HSX . . . T 2 43.48 198.132 55.802 1 96.77 ? O1 HSX 1001 F 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 492 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #