data_7AGK # _model_server_result.job_id 19BeHGrYCxxxnGivQMOEug _model_server_result.datetime_utc '2024-12-04 06:18:34' _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 7agk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 7AGK # _exptl.entry_id 7AGK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.2 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid' _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 7AGK _cell.length_a 47.548 _cell.length_b 91.856 _cell.length_c 312.142 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,C,E,F 2 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 E N N ? 2 F N N ? 2 G N N # _chem_comp.formula 'C6 H13 O11 P S' _chem_comp.formula_weight 324.2 _chem_comp.id RAH _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '6-deoxy-6-sulfo-D-fructose 1-phosphate' # 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 P1 RAH doub 275 n n O6 P1 RAH sing 276 n n P1 O3 RAH sing 277 n n P1 O5 RAH sing 278 n n O3 C5 RAH sing 279 n n O2 C4 RAH sing 280 n n C5 C4 RAH sing 281 n n C4 O1 RAH sing 282 n n C4 C3 RAH sing 283 n n O1 C1 RAH sing 284 n n O7 C3 RAH sing 285 n n O11 S1 RAH doub 286 n n C3 C2 RAH sing 287 n n C1 C2 RAH sing 288 n n C1 C6 RAH sing 289 n n C2 O8 RAH sing 290 n n S1 C6 RAH sing 291 n n S1 O9 RAH doub 292 n n S1 O10 RAH sing 293 n n C1 H1 RAH sing 294 n n C2 H2 RAH sing 295 n n C3 H3 RAH sing 296 n n C5 H4 RAH sing 297 n n C5 H5 RAH sing 298 n n C6 H6 RAH sing 299 n n C6 H7 RAH sing 300 n n O2 H8 RAH sing 301 n n O5 H9 RAH sing 302 n n O6 H10 RAH sing 303 n n O7 H11 RAH sing 304 n n O8 H12 RAH sing 305 n n O10 H13 RAH sing 306 n n # _atom_sites.entry_id 7AGK _atom_sites.fract_transf_matrix[1][1] 0.021031 _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] 0.010887 _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] 0.003204 _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 E 2 RAH A 1 401 301 RAH SFP . F 2 RAH B 1 401 301 RAH SFP . G 2 RAH C 1 401 301 RAH SFP . # 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 RAH . . . F 2 14.585 4.113 100.281 0.7 36.86 ? C1 RAH 401 B 1 HETATM 2 C C2 RAH . . . F 2 15.55 5.229 100.634 0.7 40.38 ? C2 RAH 401 B 1 HETATM 3 C C3 RAH . . . F 2 14.768 6.041 101.654 0.7 44.97 ? C3 RAH 401 B 1 HETATM 4 C C4 RAH . . . F 2 13.791 5.013 102.283 0.7 50.08 ? C4 RAH 401 B 1 HETATM 5 C C5 RAH . . . F 2 12.366 5.503 102.169 0.7 59.26 ? C5 RAH 401 B 1 HETATM 6 C C6 RAH . . . F 2 15.267 2.898 99.789 0.7 34.57 ? C6 RAH 401 B 1 HETATM 7 S S1 RAH . . . F 2 14.235 1.505 99.503 0.7 32.39 ? S1 RAH 401 B 1 HETATM 8 O O2 RAH . . . F 2 14.045 4.788 103.635 0.7 48.97 ? O2 RAH 401 B 1 HETATM 9 O O3 RAH . . . F 2 11.457 4.995 103.175 0.7 74.76 ? O3 RAH 401 B 1 HETATM 10 O O4 RAH . . . F 2 9.917 6.873 102.291 0.7 95.72 -1 O4 RAH 401 B 1 HETATM 11 O O5 RAH . . . F 2 10.058 6.34 104.755 0.7 111.8 ? O5 RAH 401 B 1 HETATM 12 O O6 RAH . . . F 2 8.891 4.68 103.156 0.7 94.58 -1 O6 RAH 401 B 1 HETATM 13 O O7 RAH . . . F 2 15.578 6.717 102.591 0.7 46.24 ? O7 RAH 401 B 1 HETATM 14 O O8 RAH . . . F 2 15.882 5.938 99.455 0.7 38.83 ? O8 RAH 401 B 1 HETATM 15 O O9 RAH . . . F 2 13.138 1.852 98.708 0.7 33.23 ? O9 RAH 401 B 1 HETATM 16 O O10 RAH . . . F 2 15.036 0.542 98.836 0.7 32.44 ? O10 RAH 401 B 1 HETATM 17 O O11 RAH . . . F 2 13.908 1.162 100.951 0.7 25.6 ? O11 RAH 401 B 1 HETATM 18 O O1 RAH . . . F 2 13.942 3.819 101.532 0.7 43.36 ? O1 RAH 401 B 1 HETATM 19 P P1 RAH . . . F 2 10.003 5.753 103.34 0.7 123.1 ? P1 RAH 401 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 56 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 825 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #