data_4GBY # _model_server_result.job_id ffITax4VruQnAkRGQfCaew _model_server_result.datetime_utc '2024-11-27 04:44:35' _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 4gby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4GBY # _exptl.entry_id 4GBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _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 4GBY _cell.length_a 95.29 _cell.length_b 95.29 _cell.length_c 168.181 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-xylopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-xylose;D-xylose;xylose # 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 O1 C1 XYP sing 427 n n O1 HO1 XYP sing 428 n n C1 C2 XYP sing 429 n n C1 O5 XYP sing 430 n n C1 H1 XYP sing 431 n n C2 C3 XYP sing 432 n n C2 O2 XYP sing 433 n n C2 H2 XYP sing 434 n n C3 C4 XYP sing 435 n n C3 O3 XYP sing 436 n n C3 H3 XYP sing 437 n n C4 C5 XYP sing 438 n n C4 O4 XYP sing 439 n n C4 H4 XYP sing 440 n n C5 O5 XYP sing 441 n n C5 H51 XYP sing 442 n n C5 H52 XYP sing 443 n n O2 HO2 XYP sing 444 n n O3 HO3 XYP sing 445 n n O4 HO4 XYP sing 446 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version XYP DXylpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYP b-D-xylopyranose 'COMMON NAME' GMML 1 XYP b-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYP Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4GBY _atom_sites.fract_transf_matrix[1][1] 0.010494 _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] 0.010494 _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] 0.005946 _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 XYP A 1 501 1 XYP DXY . C 3 BNG A 1 502 1 BNG BNG . D 3 BNG A 1 503 2 BNG BNG . E 3 BNG A 1 504 3 BNG BNG . F 3 BNG A 1 505 4 BNG BNG . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 2 HOH HOH . G 4 HOH A 3 603 3 HOH HOH . G 4 HOH A 4 604 4 HOH HOH . G 4 HOH A 5 605 5 HOH HOH . G 4 HOH A 6 606 6 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 XYP . . . B 2 16.4 -26.928 0.108 1 60.34 ? O1 XYP 501 A 1 HETATM 2 C C1 XYP . . . B 2 17.047 -25.823 -0.502 1 54.62 ? C1 XYP 501 A 1 HETATM 3 C C2 XYP . . . B 2 16.24 -25.551 -1.738 1 52.96 ? C2 XYP 501 A 1 HETATM 4 C C3 XYP . . . B 2 16.839 -24.358 -2.45 1 48.37 ? C3 XYP 501 A 1 HETATM 5 C C4 XYP . . . B 2 16.897 -23.152 -1.505 1 47.21 ? C4 XYP 501 A 1 HETATM 6 C C5 XYP . . . B 2 17.484 -23.503 -0.143 1 49.73 ? C5 XYP 501 A 1 HETATM 7 O O2 XYP . . . B 2 16.277 -26.739 -2.532 1 53.14 ? O2 XYP 501 A 1 HETATM 8 O O3 XYP . . . B 2 16.076 -24.14 -3.635 1 47.09 ? O3 XYP 501 A 1 HETATM 9 O O4 XYP . . . B 2 17.796 -22.179 -2.036 1 55.02 ? O4 XYP 501 A 1 HETATM 10 O O5 XYP . . . B 2 16.961 -24.715 0.386 1 56.75 ? O5 XYP 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #