data_5VT4 # _model_server_result.job_id WIyH1xNTA18BJsZz2bwqgw _model_server_result.datetime_utc '2025-09-03 22:09:34' _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 5vt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 5VT4 # _exptl.entry_id 5VT4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 419.319 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid' _entity.pdbx_number_of_molecules 4 _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 5VT4 _cell.length_a 113.851 _cell.length_b 113.851 _cell.length_c 312.49 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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,B,E,F,I,J 1 1 C,D,G,H,K,L 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 ? 2 H N N # _chem_comp.formula 'C13 H26 N O12 P' _chem_comp.formula_weight 419.319 _chem_comp.id 9KJ _chem_comp.mon_nstd_flag n _chem_comp.name '{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '{[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid;{[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid;{[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid' # 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 O3 C3 9KJ sing 1 n n O4 C4 9KJ sing 2 n n O6 C6 9KJ sing 3 n n C4 C3 9KJ sing 4 n n C4 C5 9KJ sing 5 n n C6 C5 9KJ sing 6 n n C3 C2 9KJ sing 7 n n C2 C1 9KJ sing 8 n n C2 O2 9KJ sing 9 n n C5 O5 9KJ sing 10 n n O5 C1 9KJ sing 11 n n C1 O1 9KJ sing 12 n n O1 C07 9KJ sing 13 n n C07 C08 9KJ sing 14 n n C07 C19 9KJ sing 15 n n O09 C08 9KJ sing 16 n n C20 C19 9KJ sing 17 n n C20 O21 9KJ sing 18 n n C08 C10 9KJ sing 19 n n C19 N13 9KJ sing 20 n n C10 N13 9KJ sing 21 n n C10 C11 9KJ sing 22 n n N13 C14 9KJ sing 23 n n C14 P15 9KJ sing 24 n n C11 O12 9KJ sing 25 n n P15 O18 9KJ doub 26 n n P15 O16 9KJ sing 27 n n P15 O17 9KJ sing 28 n n C20 H1A 9KJ sing 29 n n C20 H2A 9KJ sing 30 n n C2 H2 9KJ sing 31 n n C3 H3 9KJ sing 32 n n C4 H4 9KJ sing 33 n n O4 HO4 9KJ sing 34 n n O6 HO6 9KJ sing 35 n n C6 H61 9KJ sing 36 n n C6 H62 9KJ sing 37 n n C5 H5 9KJ sing 38 n n C1 H1 9KJ sing 39 n n C07 H12 9KJ sing 40 n n C08 H13 9KJ sing 41 n n O09 H14 9KJ sing 42 n n C10 H15 9KJ sing 43 n n C11 H16 9KJ sing 44 n n C11 H17 9KJ sing 45 n n O12 H18 9KJ sing 46 n n C14 H20 9KJ sing 47 n n C14 H21 9KJ sing 48 n n O16 H22 9KJ sing 49 n n O17 H23 9KJ sing 50 n n C19 H24 9KJ sing 51 n n O21 H25 9KJ sing 52 n n O2 HO2 9KJ sing 53 n n O3 HO3 9KJ sing 54 n n # _atom_sites.entry_id 5VT4 _atom_sites.fract_transf_matrix[1][1] 0.008783 _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] 0.008783 _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] 0.0032 _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 9KJ A 1 701 703 9KJ DMP . F 2 9KJ B 1 701 703 9KJ DMP . G 2 9KJ C 1 701 703 9KJ DMP . H 2 9KJ D 1 701 703 9KJ DMP . I 3 HOH A 1 801 56 HOH HOH . I 3 HOH A 2 802 20 HOH HOH . I 3 HOH A 3 803 55 HOH HOH . I 3 HOH A 4 804 73 HOH HOH . I 3 HOH A 5 805 87 HOH HOH . I 3 HOH A 6 806 74 HOH HOH . I 3 HOH A 7 807 25 HOH HOH . I 3 HOH A 8 808 24 HOH HOH . I 3 HOH A 9 809 77 HOH HOH . I 3 HOH A 10 810 57 HOH HOH . I 3 HOH A 11 811 88 HOH HOH . I 3 HOH A 12 812 89 HOH HOH . I 3 HOH A 13 813 26 HOH HOH . I 3 HOH A 14 814 29 HOH HOH . I 3 HOH A 15 815 91 HOH HOH . I 3 HOH A 16 816 59 HOH HOH . I 3 HOH A 17 817 90 HOH HOH . I 3 HOH A 18 818 31 HOH HOH . J 3 HOH B 1 801 71 HOH HOH . J 3 HOH B 2 802 86 HOH HOH . J 3 HOH B 3 803 75 HOH HOH . J 3 HOH B 4 804 18 HOH HOH . J 3 HOH B 5 805 5 HOH HOH . J 3 HOH B 6 806 9 HOH HOH . J 3 HOH B 7 807 1 HOH HOH . J 3 HOH B 8 808 70 HOH HOH . J 3 HOH B 9 809 78 HOH HOH . J 3 HOH B 10 810 33 HOH HOH . J 3 HOH B 11 811 61 HOH HOH . J 3 HOH B 12 812 60 HOH HOH . J 3 HOH B 13 813 69 HOH HOH . J 3 HOH B 14 814 36 HOH HOH . J 3 HOH B 15 815 62 HOH HOH . J 3 HOH B 16 816 35 HOH HOH . J 3 HOH B 17 817 37 HOH HOH . J 3 HOH B 18 818 67 HOH HOH . J 3 HOH B 19 819 63 HOH HOH . J 3 HOH B 20 820 64 HOH HOH . K 3 HOH C 1 801 85 HOH HOH . K 3 HOH C 2 802 41 HOH HOH . K 3 HOH C 3 803 76 HOH HOH . K 3 HOH C 4 804 44 HOH HOH . K 3 HOH C 5 805 45 HOH HOH . K 3 HOH C 6 806 38 HOH HOH . K 3 HOH C 7 807 92 HOH HOH . L 3 HOH D 1 801 80 HOH HOH . L 3 HOH D 2 802 72 HOH HOH . L 3 HOH D 3 803 49 HOH HOH . L 3 HOH D 4 804 54 HOH HOH . L 3 HOH D 5 805 81 HOH HOH . L 3 HOH D 6 806 48 HOH HOH . L 3 HOH D 7 807 79 HOH HOH . L 3 HOH D 8 808 50 HOH HOH . L 3 HOH D 9 809 51 HOH HOH . L 3 HOH D 10 810 83 HOH HOH . L 3 HOH D 11 811 82 HOH HOH . L 3 HOH D 12 812 84 HOH HOH . L 3 HOH D 13 813 53 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 C20 9KJ . . . E 2 140.158 145.642 -342.805 1 59.94 ? C20 9KJ 701 A 1 HETATM 2 C C2 9KJ . . . E 2 136.887 148.539 -346.317 1 62.09 ? C2 9KJ 701 A 1 HETATM 3 C C3 9KJ . . . E 2 135.876 147.41 -346.589 1 63.14 ? C3 9KJ 701 A 1 HETATM 4 C C4 9KJ . . . E 2 136.579 146.156 -347.133 1 62.16 ? C4 9KJ 701 A 1 HETATM 5 O O4 9KJ . . . E 2 135.65 145.051 -347.198 1 68.96 ? O4 9KJ 701 A 1 HETATM 6 O O6 9KJ . . . E 2 139.797 145.016 -347.184 1 59.82 ? O6 9KJ 701 A 1 HETATM 7 C C6 9KJ . . . E 2 138.492 144.56 -346.838 1 59.29 ? C6 9KJ 701 A 1 HETATM 8 C C5 9KJ . . . E 2 137.78 145.783 -346.246 1 62.71 ? C5 9KJ 701 A 1 HETATM 9 O O5 9KJ . . . E 2 138.727 146.854 -346.098 1 60.55 ? O5 9KJ 701 A 1 HETATM 10 C C1 9KJ . . . E 2 138.164 148.076 -345.608 1 56.58 ? C1 9KJ 701 A 1 HETATM 11 O O1 9KJ . . . E 2 137.858 147.931 -344.225 1 66.65 ? O1 9KJ 701 A 1 HETATM 12 C C07 9KJ . . . E 2 139.095 147.805 -343.525 1 66.78 ? C07 9KJ 701 A 1 HETATM 13 C C08 9KJ . . . E 2 139.399 149.028 -342.627 1 64.7 ? C08 9KJ 701 A 1 HETATM 14 O O09 9KJ . . . E 2 140.244 149.972 -343.272 1 77.22 ? O09 9KJ 701 A 1 HETATM 15 C C10 9KJ . . . E 2 140.162 148.294 -341.528 1 64.55 ? C10 9KJ 701 A 1 HETATM 16 C C11 9KJ . . . E 2 140.514 149.238 -340.373 1 67.13 ? C11 9KJ 701 A 1 HETATM 17 O O12 9KJ . . . E 2 141.814 148.862 -339.915 1 73.07 ? O12 9KJ 701 A 1 HETATM 18 N N13 9KJ . . . E 2 139.189 147.25 -341.197 1 64.9 ? N13 9KJ 701 A 1 HETATM 19 C C14 9KJ . . . E 2 137.882 147.84 -340.855 1 75.12 ? C14 9KJ 701 A 1 HETATM 20 P P15 9KJ . . . E 2 137.67 147.996 -338.985 1 107.8 ? P15 9KJ 701 A 1 HETATM 21 O O16 9KJ . . . E 2 137.41 149.44 -338.561 1 61.07 ? O16 9KJ 701 A 1 HETATM 22 O O17 9KJ . . . E 2 138.928 147.506 -338.365 1 73.58 ? O17 9KJ 701 A 1 HETATM 23 O O18 9KJ . . . E 2 136.524 147.127 -338.567 1 72.56 ? O18 9KJ 701 A 1 HETATM 24 C C19 9KJ . . . E 2 139.024 146.634 -342.52 1 65.58 ? C19 9KJ 701 A 1 HETATM 25 O O21 9KJ . . . E 2 140.275 144.821 -341.656 1 60.49 ? O21 9KJ 701 A 1 HETATM 26 O O2 9KJ . . . E 2 136.272 149.484 -345.427 1 68.73 ? O2 9KJ 701 A 1 HETATM 27 O O3 9KJ . . . E 2 134.934 147.858 -347.568 1 65.62 ? O3 9KJ 701 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #