data_3DUU # _model_server_result.job_id zGVU2p6tAr0rIJRPrHCHLw _model_server_result.datetime_utc '2024-11-22 23:06:08' _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 3duu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":114}' # _entry.id 3DUU # _exptl.entry_id 3DUU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.192 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' _entity.pdbx_number_of_molecules 2 _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 3DUU _cell.length_a 71.6 _cell.length_b 71.76 _cell.length_c 86.21 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DUU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 C,D,H,I,J,K,N,O 1 1 A,B,E,F,G,L,M 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 ? 4 F N N ? 4 J N 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 disulf ? disulf1 A SG CYS 23 A CYS 23 1_555 A SG CYS 94 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 22 B CYS 22 1_555 B SG CYS 98 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 C SG CYS 23 C CYS 23 1_555 C SG CYS 94 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 D SG CYS 22 D CYS 22 1_555 D SG CYS 98 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 H MG MG . C MG 111 1_555 N O HOH . C HOH 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? # _chem_comp.formula 'C8 H14 O8' _chem_comp.formula_weight 238.192 _chem_comp.id KDO _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '3-deoxy-d-manno-oct-2-ulopyranosonic acid;2-keto-3-deoxy-D-mannooctanoic acid;3-deoxy-alpha-D-manno-oct-2-ulosonic acid;3-deoxy-D-manno-oct-2-ulosonic acid;3-deoxy-manno-oct-2-ulosonic 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 C1 O1A KDO doub 152 n n C1 O1B KDO sing 153 n n C1 C2 KDO sing 154 n n O1B HO1B KDO sing 155 n n C2 O2 KDO sing 156 n n C2 C3 KDO sing 157 n n C2 O6 KDO sing 158 n n O2 HO2 KDO sing 159 n n C3 C4 KDO sing 160 n n C3 H31 KDO sing 161 n n C3 H32 KDO sing 162 n n C4 O4 KDO sing 163 n n C4 C5 KDO sing 164 n n C4 H4 KDO sing 165 n n O4 HO4 KDO sing 166 n n C5 O5 KDO sing 167 n n C5 C6 KDO sing 168 n n C5 H5 KDO sing 169 n n O5 HO5 KDO sing 170 n n C6 O6 KDO sing 171 n n C6 C7 KDO sing 172 n n C6 H6 KDO sing 173 n n C7 O7 KDO sing 174 n n C7 C8 KDO sing 175 n n C7 H7 KDO sing 176 n n O7 HO7 KDO sing 177 n n C8 O8 KDO sing 178 n n C8 H81 KDO sing 179 n n C8 H82 KDO sing 180 n n O8 HO8 KDO sing 181 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 KDO DKdopa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 KDO a-D-Kdop 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 KDO Kdo 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3DUU _atom_sites.fract_transf_matrix[1][1] 0.013966 _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] 0.013935 _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] 0.0116 _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 3 MG A 1 112 112 MG MG . F 4 KDO B 1 114 107 KDO KDO . G 5 PG4 B 1 115 109 PG4 PG4 . H 3 MG C 1 111 111 MG MG . I 3 MG C 1 113 113 MG MG . J 4 KDO D 1 114 108 KDO KDO . K 5 PG4 D 1 115 110 PG4 PG4 . L 6 HOH A 1 113 3 HOH HOH . L 6 HOH A 2 114 4 HOH HOH . L 6 HOH A 3 115 5 HOH HOH . L 6 HOH A 4 116 9 HOH HOH . L 6 HOH A 5 117 13 HOH HOH . L 6 HOH A 6 118 17 HOH HOH . L 6 HOH A 7 119 20 HOH HOH . L 6 HOH A 8 120 22 HOH HOH . L 6 HOH A 9 121 24 HOH HOH . L 6 HOH A 10 122 31 HOH HOH . L 6 HOH A 11 123 37 HOH HOH . L 6 HOH A 12 124 39 HOH HOH . L 6 HOH A 13 125 40 HOH HOH . L 6 HOH A 14 126 44 HOH HOH . L 6 HOH A 15 127 46 HOH HOH . L 6 HOH A 16 128 52 HOH HOH . L 6 HOH A 17 129 53 HOH HOH . L 6 HOH A 18 130 56 HOH HOH . L 6 HOH A 19 131 58 HOH HOH . L 6 HOH A 20 132 64 HOH HOH . L 6 HOH A 21 133 65 HOH HOH . L 6 HOH A 22 134 69 HOH HOH . L 6 HOH A 23 135 77 HOH HOH . L 6 HOH A 24 136 79 HOH HOH . L 6 HOH A 25 137 82 HOH HOH . L 6 HOH A 26 138 85 HOH HOH . L 6 HOH A 27 139 90 HOH HOH . L 6 HOH A 28 140 96 HOH HOH . L 6 HOH A 29 141 106 HOH HOH . L 6 HOH A 30 142 114 HOH HOH . L 6 HOH A 31 143 115 HOH HOH . L 6 HOH A 32 144 121 HOH HOH . L 6 HOH A 33 145 124 HOH HOH . L 6 HOH A 34 146 126 HOH HOH . L 6 HOH A 35 147 142 HOH HOH . L 6 HOH A 36 148 144 HOH HOH . L 6 HOH A 37 149 146 HOH HOH . L 6 HOH A 38 150 147 HOH HOH . L 6 HOH A 39 151 150 HOH HOH . L 6 HOH A 40 152 152 HOH HOH . L 6 HOH A 41 153 153 HOH HOH . L 6 HOH A 42 154 154 HOH HOH . L 6 HOH A 43 155 155 HOH HOH . L 6 HOH A 44 156 158 HOH HOH . L 6 HOH A 45 157 163 HOH HOH . L 6 HOH A 46 158 169 HOH HOH . L 6 HOH A 47 159 170 HOH HOH . L 6 HOH A 48 160 178 HOH HOH . L 6 HOH A 49 161 189 HOH HOH . L 6 HOH A 50 162 190 HOH HOH . L 6 HOH A 51 163 191 HOH HOH . M 6 HOH B 1 116 11 HOH HOH . M 6 HOH B 2 117 12 HOH HOH . M 6 HOH B 3 118 23 HOH HOH . M 6 HOH B 4 119 26 HOH HOH . M 6 HOH B 5 120 32 HOH HOH . M 6 HOH B 6 121 33 HOH HOH . M 6 HOH B 7 122 34 HOH HOH . M 6 HOH B 8 123 41 HOH HOH . M 6 HOH B 9 124 47 HOH HOH . M 6 HOH B 10 125 49 HOH HOH . M 6 HOH B 11 126 54 HOH HOH . M 6 HOH B 12 127 59 HOH HOH . M 6 HOH B 13 128 74 HOH HOH . M 6 HOH B 14 129 75 HOH HOH . M 6 HOH B 15 130 76 HOH HOH . M 6 HOH B 16 131 80 HOH HOH . M 6 HOH B 17 132 81 HOH HOH . M 6 HOH B 18 133 84 HOH HOH . M 6 HOH B 19 134 87 HOH HOH . M 6 HOH B 20 135 93 HOH HOH . M 6 HOH B 21 136 98 HOH HOH . M 6 HOH B 22 137 99 HOH HOH . M 6 HOH B 23 138 103 HOH HOH . M 6 HOH B 24 139 105 HOH HOH . M 6 HOH B 25 140 107 HOH HOH . M 6 HOH B 26 141 113 HOH HOH . M 6 HOH B 27 142 118 HOH HOH . M 6 HOH B 28 143 123 HOH HOH . M 6 HOH B 29 144 125 HOH HOH . M 6 HOH B 30 145 127 HOH HOH . M 6 HOH B 31 146 130 HOH HOH . M 6 HOH B 32 147 134 HOH HOH . M 6 HOH B 33 148 136 HOH HOH . M 6 HOH B 34 149 138 HOH HOH . M 6 HOH B 35 150 139 HOH HOH . M 6 HOH B 36 151 140 HOH HOH . M 6 HOH B 37 152 141 HOH HOH . M 6 HOH B 38 153 149 HOH HOH . M 6 HOH B 39 154 151 HOH HOH . M 6 HOH B 40 155 156 HOH HOH . M 6 HOH B 41 156 159 HOH HOH . M 6 HOH B 42 157 160 HOH HOH . M 6 HOH B 43 158 166 HOH HOH . M 6 HOH B 44 159 168 HOH HOH . M 6 HOH B 45 160 172 HOH HOH . M 6 HOH B 46 161 174 HOH HOH . M 6 HOH B 47 162 175 HOH HOH . M 6 HOH B 48 163 177 HOH HOH . M 6 HOH B 49 164 180 HOH HOH . M 6 HOH B 50 165 181 HOH HOH . M 6 HOH B 51 166 186 HOH HOH . M 6 HOH B 52 167 188 HOH HOH . N 6 HOH C 1 114 1 HOH HOH . N 6 HOH C 2 115 2 HOH HOH . N 6 HOH C 3 116 7 HOH HOH . N 6 HOH C 4 117 10 HOH HOH . N 6 HOH C 5 118 16 HOH HOH . N 6 HOH C 6 119 21 HOH HOH . N 6 HOH C 7 120 36 HOH HOH . N 6 HOH C 8 121 45 HOH HOH . N 6 HOH C 9 122 48 HOH HOH . N 6 HOH C 10 123 50 HOH HOH . N 6 HOH C 11 124 51 HOH HOH . N 6 HOH C 12 125 55 HOH HOH . N 6 HOH C 13 126 57 HOH HOH . N 6 HOH C 14 127 60 HOH HOH . N 6 HOH C 15 128 62 HOH HOH . N 6 HOH C 16 129 67 HOH HOH . N 6 HOH C 17 130 68 HOH HOH . N 6 HOH C 18 131 72 HOH HOH . N 6 HOH C 19 132 73 HOH HOH . N 6 HOH C 20 133 88 HOH HOH . N 6 HOH C 21 134 89 HOH HOH . N 6 HOH C 22 135 95 HOH HOH . N 6 HOH C 23 136 100 HOH HOH . N 6 HOH C 24 137 102 HOH HOH . N 6 HOH C 25 138 104 HOH HOH . N 6 HOH C 26 139 108 HOH HOH . N 6 HOH C 27 140 111 HOH HOH . N 6 HOH C 28 141 112 HOH HOH . N 6 HOH C 29 142 116 HOH HOH . N 6 HOH C 30 143 119 HOH HOH . N 6 HOH C 31 144 128 HOH HOH . N 6 HOH C 32 145 131 HOH HOH . N 6 HOH C 33 146 135 HOH HOH . N 6 HOH C 34 147 137 HOH HOH . N 6 HOH C 35 148 143 HOH HOH . N 6 HOH C 36 149 145 HOH HOH . N 6 HOH C 37 150 157 HOH HOH . N 6 HOH C 38 151 162 HOH HOH . N 6 HOH C 39 152 164 HOH HOH . N 6 HOH C 40 153 165 HOH HOH . N 6 HOH C 41 154 167 HOH HOH . N 6 HOH C 42 155 171 HOH HOH . N 6 HOH C 43 156 183 HOH HOH . N 6 HOH C 44 157 185 HOH HOH . N 6 HOH C 45 158 187 HOH HOH . O 6 HOH D 1 116 6 HOH HOH . O 6 HOH D 2 117 8 HOH HOH . O 6 HOH D 3 118 14 HOH HOH . O 6 HOH D 4 119 15 HOH HOH . O 6 HOH D 5 120 18 HOH HOH . O 6 HOH D 6 121 19 HOH HOH . O 6 HOH D 7 122 25 HOH HOH . O 6 HOH D 8 123 27 HOH HOH . O 6 HOH D 9 124 28 HOH HOH . O 6 HOH D 10 125 29 HOH HOH . O 6 HOH D 11 126 30 HOH HOH . O 6 HOH D 12 127 35 HOH HOH . O 6 HOH D 13 128 38 HOH HOH . O 6 HOH D 14 129 42 HOH HOH . O 6 HOH D 15 130 43 HOH HOH . O 6 HOH D 16 131 61 HOH HOH . O 6 HOH D 17 132 63 HOH HOH . O 6 HOH D 18 133 66 HOH HOH . O 6 HOH D 19 134 70 HOH HOH . O 6 HOH D 20 135 71 HOH HOH . O 6 HOH D 21 136 78 HOH HOH . O 6 HOH D 22 137 83 HOH HOH . O 6 HOH D 23 138 86 HOH HOH . O 6 HOH D 24 139 91 HOH HOH . O 6 HOH D 25 140 92 HOH HOH . O 6 HOH D 26 141 94 HOH HOH . O 6 HOH D 27 142 97 HOH HOH . O 6 HOH D 28 143 101 HOH HOH . O 6 HOH D 29 144 109 HOH HOH . O 6 HOH D 30 145 110 HOH HOH . O 6 HOH D 31 146 117 HOH HOH . O 6 HOH D 32 147 120 HOH HOH . O 6 HOH D 33 148 122 HOH HOH . O 6 HOH D 34 149 129 HOH HOH . O 6 HOH D 35 150 132 HOH HOH . O 6 HOH D 36 151 133 HOH HOH . O 6 HOH D 37 152 148 HOH HOH . O 6 HOH D 38 153 161 HOH HOH . O 6 HOH D 39 154 173 HOH HOH . O 6 HOH D 40 155 176 HOH HOH . O 6 HOH D 41 156 179 HOH HOH . O 6 HOH D 42 157 182 HOH HOH . O 6 HOH D 43 158 184 HOH HOH . O 6 HOH D 44 159 192 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 KDO . . . J 4 38.619 -23.407 42.96 1 30.64 ? C1 KDO 114 D 1 HETATM 2 O O1A KDO . . . J 4 39.021 -22.219 43.027 1 33.93 ? O1A KDO 114 D 1 HETATM 3 O O1B KDO . . . J 4 38.305 -24.065 43.977 1 28.77 ? O1B KDO 114 D 1 HETATM 4 C C2 KDO . . . J 4 38.969 -24.161 41.702 1 29.4 ? C2 KDO 114 D 1 HETATM 5 O O2 KDO . . . J 4 39.094 -25.56 41.987 1 29.65 ? O2 KDO 114 D 1 HETATM 6 C C3 KDO . . . J 4 37.872 -23.985 40.669 1 29.12 ? C3 KDO 114 D 1 HETATM 7 C C4 KDO . . . J 4 38.293 -24.79 39.455 1 28.25 ? C4 KDO 114 D 1 HETATM 8 O O4 KDO . . . J 4 37.287 -24.72 38.451 1 27.59 ? O4 KDO 114 D 1 HETATM 9 C C5 KDO . . . J 4 39.602 -24.216 38.939 1 28.92 ? C5 KDO 114 D 1 HETATM 10 O O5 KDO . . . J 4 39.43 -22.818 38.703 1 29.19 ? O5 KDO 114 D 1 HETATM 11 C C6 KDO . . . J 4 40.666 -24.361 40.01 1 30.45 ? C6 KDO 114 D 1 HETATM 12 O O6 KDO . . . J 4 40.197 -23.657 41.16 1 33.65 ? O6 KDO 114 D 1 HETATM 13 C C7 KDO . . . J 4 41.99 -23.751 39.552 1 29.61 ? C7 KDO 114 D 1 HETATM 14 O O7 KDO . . . J 4 42.422 -24.349 38.316 1 26.96 ? O7 KDO 114 D 1 HETATM 15 C C8 KDO . . . J 4 43.064 -23.992 40.597 1 27 ? C8 KDO 114 D 1 HETATM 16 O O8 KDO . . . J 4 43.485 -25.349 40.449 1 26.55 ? O8 KDO 114 D 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #