data_8YQ0
#
_model_server_result.job_id            qzODY6s-BrBK_ftqPmEsCA 
_model_server_result.datetime_utc      '2025-07-17 06:55:16' 
_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":"U","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 . . . U 2 110.048 190.578 102.649 1 97.72 ? C1 HSX 1001 O 1 
HETATM 2 O O4 HSX . . . U 2 109.924 189.555 101.673 1 100.27 ? O4 HSX 1001 O 1 
HETATM 3 C C2 HSX . . . U 2 108.773 191.391 102.543 1 85.86 ? C2 HSX 1001 O 1 
HETATM 4 O O2 HSX . . . U 2 107.711 190.838 103.312 1 78.91 ? O2 HSX 1001 O 1 
HETATM 5 C C3 HSX . . . U 2 108.444 191.242 101.083 1 96.54 ? C3 HSX 1001 O 1 
HETATM 6 O O3 HSX . . . U 2 107.072 191.478 100.774 1 106.27 ? O3 HSX 1001 O 1 
HETATM 7 C C4 HSX . . . U 2 108.833 189.813 100.809 1 95.85 ? C4 HSX 1001 O 1 
HETATM 8 C C5 HSX . . . U 2 109.235 189.711 99.361 1 95.8 ? C5 HSX 1001 O 1 
HETATM 9 O O5 HSX . . . U 2 109.054 188.397 98.85 1 104.09 ? O5 HSX 1001 O 1 
HETATM 10 P P' HSX . . . U 2 110.313 187.446 98.685 1 144.38 ? P' HSX 1001 O 1 
HETATM 11 O O1X HSX . . . U 2 110.778 187.672 97.289 1 106.98 ? O1X HSX 1001 O 1 
HETATM 12 O O2X HSX . . . U 2 111.22 187.955 99.761 1 98.88 ? O2X HSX 1001 O 1 
HETATM 13 O O3X HSX . . . U 2 109.859 186.033 98.872 1 121.5 ? O3X HSX 1001 O 1 
HETATM 14 O O1 HSX . . . U 2 110.19 190.001 103.932 1 89.02 ? O1 HSX 1001 O 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           35 
_model_server_stats.create_model_time_ms    442 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#