data_7EXU # _model_server_result.job_id leMEFfQsaLvd4cpwNjCkAw _model_server_result.datetime_utc '2025-02-25 20:15:56' _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 7exu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 7EXU # _exptl.entry_id 7EXU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 271.223 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol _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 120 _cell.entry_id 7EXU _cell.length_a 78.182 _cell.length_b 78.182 _cell.length_c 253.502 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EXU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 84.500667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OE2 GLU 338 A GLU 338 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 A SG CYS 340 A CYS 340 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc3 A SG CYS 417 A CYS 417 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 A SG CYS 418 A CYS 418 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _chem_comp.formula 'C11 H13 N O7' _chem_comp.formula_weight 271.223 _chem_comp.id 07Y _chem_comp.mon_nstd_flag . _chem_comp.name (2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol _chem_comp.type saccharide _chem_comp.pdbx_synonyms ? # 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 07Y sing 1 n n C5 C4 07Y sing 2 n n C5 O5 07Y sing 3 n n C4 C3 07Y sing 4 n n C4 O4 07Y sing 5 n n C3 C2 07Y sing 6 n n C2 O2 07Y sing 7 n n C2 C1 07Y sing 8 n n O4 C1 07Y sing 9 n n C1 O1 07Y sing 10 n n C18 C19 07Y doub 11 n y C18 C17 07Y sing 12 n y O1 C17 07Y sing 13 n n C19 C20 07Y sing 14 n y C17 C22 07Y doub 15 n y O18 N11 07Y sing 16 n n C20 N11 07Y sing 17 n n C20 C21 07Y doub 18 n y C22 C21 07Y sing 19 n y N11 O17 07Y doub 20 n n C1 H1 07Y sing 21 n n C2 H2 07Y sing 22 n n O2 H3 07Y sing 23 n n C3 H4 07Y sing 24 n n C4 H5 07Y sing 25 n n C5 H6 07Y sing 26 n n C5 H7 07Y sing 27 n n O5 H8 07Y sing 28 n n C18 H9 07Y sing 29 n n C19 H10 07Y sing 30 n n C21 H11 07Y sing 31 n n C22 H12 07Y sing 32 n n O3 H13 07Y sing 33 n n # _atom_sites.entry_id 7EXU _atom_sites.fract_transf_matrix[1][1] 0.012791 _atom_sites.fract_transf_matrix[1][2] 0.007385 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014769 _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] 0.003945 _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 ZN A 1 701 702 ZN ZN . C 3 07Y A 1 702 801 07Y PA3 . D 4 HOH A 1 801 10 HOH HOH . D 4 HOH A 2 802 16 HOH HOH . D 4 HOH A 3 803 13 HOH HOH . D 4 HOH A 4 804 25 HOH HOH . D 4 HOH A 5 805 22 HOH HOH . D 4 HOH A 6 806 12 HOH HOH . D 4 HOH A 7 807 20 HOH HOH . D 4 HOH A 8 808 15 HOH HOH . D 4 HOH A 9 809 9 HOH HOH . D 4 HOH A 10 810 8 HOH HOH . D 4 HOH A 11 811 17 HOH HOH . D 4 HOH A 12 812 1 HOH HOH . D 4 HOH A 13 813 14 HOH HOH . D 4 HOH A 14 814 2 HOH HOH . D 4 HOH A 15 815 4 HOH HOH . D 4 HOH A 16 816 24 HOH HOH . D 4 HOH A 17 817 18 HOH HOH . D 4 HOH A 18 818 7 HOH HOH . D 4 HOH A 19 819 21 HOH HOH . D 4 HOH A 20 820 3 HOH HOH . D 4 HOH A 21 821 11 HOH HOH . D 4 HOH A 22 822 19 HOH HOH . D 4 HOH A 23 823 23 HOH HOH . D 4 HOH A 24 824 6 HOH HOH . D 4 HOH A 25 825 5 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 07Y . . . C 3 21.16 -8.481 28.123 1 69.9 ? C1 07Y 702 A 1 HETATM 2 C C2 07Y . . . C 3 22.165 -7.938 27.146 1 69.33 ? C2 07Y 702 A 1 HETATM 3 O O2 07Y . . . C 3 23.148 -7.048 27.862 1 62.45 ? O2 07Y 702 A 1 HETATM 4 C C3 07Y . . . C 3 21.289 -7.195 26.16 1 67.21 ? C3 07Y 702 A 1 HETATM 5 C C4 07Y . . . C 3 20.07 -8.145 26.104 1 66.08 ? C4 07Y 702 A 1 HETATM 6 O O4 07Y . . . C 3 19.84 -8.444 27.506 1 74.11 ? O4 07Y 702 A 1 HETATM 7 C C5 07Y . . . C 3 18.795 -7.585 25.569 1 66.47 ? C5 07Y 702 A 1 HETATM 8 O O5 07Y . . . C 3 18.474 -6.429 26.329 1 63.73 ? O5 07Y 702 A 1 HETATM 9 C C18 07Y . . . C 3 19.754 -5.857 28.99 1 84.67 ? C18 07Y 702 A 1 HETATM 10 C C19 07Y . . . C 3 18.611 -5.226 29.44 1 93.08 ? C19 07Y 702 A 1 HETATM 11 C C20 07Y . . . C 3 17.949 -5.729 30.571 1 97.3 ? C20 07Y 702 A 1 HETATM 12 N N11 07Y . . . C 3 16.863 -5.114 31.005 1 101.09 ? N11 07Y 702 A 1 HETATM 13 O O18 07Y . . . C 3 16.473 -3.867 30.392 1 102.67 ? O18 07Y 702 A 1 HETATM 14 O O17 07Y . . . C 3 16.116 -5.695 32.067 1 108.58 ? O17 07Y 702 A 1 HETATM 15 C C21 07Y . . . C 3 18.413 -6.86 31.252 1 90.41 ? C21 07Y 702 A 1 HETATM 16 C C22 07Y . . . C 3 19.552 -7.491 30.788 1 91.9 ? C22 07Y 702 A 1 HETATM 17 C C17 07Y . . . C 3 20.199 -6.988 29.659 1 86.22 ? C17 07Y 702 A 1 HETATM 18 O O1 07Y . . . C 3 21.308 -7.619 29.246 1 84.9 ? O1 07Y 702 A 1 HETATM 19 O O3 07Y . . . C 3 22.02 -7.124 24.951 1 67.72 ? O3 07Y 702 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #