data_5AJU # _model_server_result.job_id mJH6HU4SE9AVDddlS1ZcHw _model_server_result.datetime_utc '2025-05-17 12:37:57' _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 5aju # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1241}' # _entry.id 5AJU # _exptl.entry_id 5AJU _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-beta-D-ribofuranose _entity.pdbx_number_of_molecules 1 _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 5AJU _cell.length_a 78.97 _cell.length_b 78.97 _cell.length_c 144.64 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AJU _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H11 O8 P' _chem_comp.formula_weight 230.11 _chem_comp.id RP5 _chem_comp.mon_nstd_flag n _chem_comp.name 5-O-phosphono-beta-D-ribofuranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms '[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE;5-O-phosphono-beta-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 C1 O4 RP5 sing 277 n n C1 C2 RP5 sing 278 n n C1 O1 RP5 sing 279 n n C1 H1 RP5 sing 280 n n O4 C4 RP5 sing 281 n n C2 O2 RP5 sing 282 n n C2 C3 RP5 sing 283 n n C2 H2 RP5 sing 284 n n O2 HO2 RP5 sing 285 n n C3 O3 RP5 sing 286 n n C3 C4 RP5 sing 287 n n C3 H3 RP5 sing 288 n n O3 HO3 RP5 sing 289 n n C4 C5 RP5 sing 290 n n C4 H4 RP5 sing 291 n n C5 O5 RP5 sing 292 n n C5 H51 RP5 sing 293 n n C5 H52 RP5 sing 294 n n O5 P' RP5 sing 295 n n P' O1X RP5 doub 296 n n P' O2X RP5 sing 297 n n P' O3X RP5 sing 298 n n O2X HO' RP5 sing 299 n n O3X HOA RP5 sing 300 n n O1 HO1 RP5 sing 301 n n # _pdbx_chem_comp_identifier.comp_id RP5 _pdbx_chem_comp_identifier.identifier b-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 5AJU _atom_sites.fract_transf_matrix[1][1] 0.012663 _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] 0.012663 _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] 0.006914 _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 B 2 RP5 A 1 1241 1241 RP5 RP5 . C 3 SO4 A 1 1242 1242 SO4 SO4 . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 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 C C1 RP5 . . . B 2 -6.37 -9.184 -19.176 1 96.6 ? C1 RP5 1241 A 1 HETATM 2 O O4 RP5 . . . B 2 -6.729 -9.348 -20.624 1 102.5 ? O4 RP5 1241 A 1 HETATM 3 C C2 RP5 . . . B 2 -7.656 -8.438 -18.557 1 118.04 ? C2 RP5 1241 A 1 HETATM 4 O O2 RP5 . . . B 2 -7.454 -8.212 -17.09 1 118.48 ? O2 RP5 1241 A 1 HETATM 5 C C3 RP5 . . . B 2 -8.673 -9.081 -19.207 1 119.34 ? C3 RP5 1241 A 1 HETATM 6 O O3 RP5 . . . B 2 -9.047 -10.147 -18.242 1 116.21 ? O3 RP5 1241 A 1 HETATM 7 C C4 RP5 . . . B 2 -7.964 -9.741 -20.563 1 110.58 ? C4 RP5 1241 A 1 HETATM 8 C C5 RP5 . . . B 2 -8.689 -9.316 -21.792 1 113.82 ? C5 RP5 1241 A 1 HETATM 9 O O5 RP5 . . . B 2 -7.8 -8.62 -22.637 1 113.49 ? O5 RP5 1241 A 1 HETATM 10 P P' RP5 . . . B 2 -8.408 -7.768 -23.817 1 98.22 ? P' RP5 1241 A 1 HETATM 11 O O1X RP5 . . . B 2 -8.968 -8.681 -24.881 1 98.35 ? O1X RP5 1241 A 1 HETATM 12 O O2X RP5 . . . B 2 -9.517 -6.898 -23.282 1 102.46 ? O2X RP5 1241 A 1 HETATM 13 O O3X RP5 . . . B 2 -7.317 -6.893 -24.381 1 111.75 ? O3X RP5 1241 A 1 HETATM 14 O O1 RP5 . . . B 2 -5.32 -8.471 -19.042 1 92.46 ? O1 RP5 1241 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 1150 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #