data_3NG5 # _model_server_result.job_id 7Tpj_rDjIFWXimUwBx6ZuQ _model_server_result.datetime_utc '2024-11-29 11:32:22' _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 3ng5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":129}' # _entry.id 3NG5 # _exptl.entry_id 3NG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.372 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate' _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 3NG5 _cell.length_a 86.074 _cell.length_b 44.189 _cell.length_c 65.141 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H _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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N N # _chem_comp.formula 'C22 H18 O11' _chem_comp.formula_weight 458.372 _chem_comp.id KDH _chem_comp.mon_nstd_flag . _chem_comp.name '(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (-)-Epigallocatechin-3-gallate;EGCG # 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 C3 KDH sing 167 n n O1 HO1 KDH sing 168 n n C3 C6 KDH doub 169 n y C3 C4 KDH sing 170 n y C6 O7 KDH sing 171 n n C6 C9 KDH sing 172 n y O7 HO7 KDH sing 173 n n C9 O10 KDH sing 174 n n C9 C12 KDH doub 175 n y O10 HO10 KDH sing 176 n n C12 C14 KDH sing 177 n y C12 H12 KDH sing 178 n n C14 C15 KDH sing 179 n n C14 C4 KDH doub 180 n y C15 C33 KDH sing 181 n n C15 O01 KDH sing 182 n n C15 H15 KDH sing 183 n n C20 C21 KDH doub 184 n y C20 C31 KDH sing 185 n y C20 O01 KDH sing 186 n n C21 C24 KDH sing 187 n y C21 H21 KDH sing 188 n n C24 C26 KDH doub 189 n y C24 O02 KDH sing 190 n n C26 C29 KDH sing 191 n y C26 H26 KDH sing 192 n n C29 C31 KDH doub 193 n y C29 O03 KDH sing 194 n n C31 C01 KDH sing 195 n n C33 C01 KDH sing 196 n n C33 O35 KDH sing 197 n n C33 H33 KDH sing 198 n n C36 C38 KDH sing 199 n n C36 O35 KDH sing 200 n n C36 O37 KDH doub 201 n n C38 C39 KDH doub 202 n y C38 C41 KDH sing 203 n y C39 C49 KDH sing 204 n y C39 H39 KDH sing 205 n n C41 C43 KDH doub 206 n y C41 H41 KDH sing 207 n n C01 H01 KDH sing 208 n n C01 H01A KDH sing 209 n n O02 HO02 KDH sing 210 n n O03 HO03 KDH sing 211 n n C4 H4 KDH sing 212 n n C43 O44 KDH sing 213 n n C43 C46 KDH sing 214 n y O44 HO44 KDH sing 215 n n C46 O47 KDH sing 216 n n C46 C49 KDH doub 217 n y O47 HO47 KDH sing 218 n n C49 O50 KDH sing 219 n n O50 HO50 KDH sing 220 n n # _atom_sites.entry_id 3NG5 _atom_sites.fract_transf_matrix[1][1] 0.011618 _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] 0.02263 _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] 0.015351 _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 C 2 KDH A 1 128 2 KDH EGT . D 2 KDH A 1 129 3 KDH EGT . E 3 GOL A 1 130 4 GOL GOL . F 2 KDH B 1 128 1 KDH EGT . G 4 HOH A 1 131 131 HOH HOH . G 4 HOH A 2 132 132 HOH HOH . G 4 HOH A 3 133 2 HOH HOH . G 4 HOH A 4 134 134 HOH HOH . G 4 HOH A 5 135 135 HOH HOH . G 4 HOH A 6 136 136 HOH HOH . G 4 HOH A 7 137 7 HOH HOH . G 4 HOH A 8 138 138 HOH HOH . G 4 HOH A 9 139 8 HOH HOH . G 4 HOH A 10 140 140 HOH HOH . G 4 HOH A 11 141 141 HOH HOH . G 4 HOH A 12 142 142 HOH HOH . G 4 HOH A 13 143 9 HOH HOH . G 4 HOH A 14 144 144 HOH HOH . G 4 HOH A 15 145 145 HOH HOH . G 4 HOH A 16 146 146 HOH HOH . G 4 HOH A 17 147 147 HOH HOH . G 4 HOH A 18 148 10 HOH HOH . G 4 HOH A 19 149 11 HOH HOH . G 4 HOH A 20 150 12 HOH HOH . G 4 HOH A 21 151 13 HOH HOH . G 4 HOH A 22 152 152 HOH HOH . G 4 HOH A 23 153 153 HOH HOH . G 4 HOH A 24 154 17 HOH HOH . G 4 HOH A 25 155 18 HOH HOH . G 4 HOH A 26 156 156 HOH HOH . G 4 HOH A 27 157 19 HOH HOH . G 4 HOH A 28 158 20 HOH HOH . G 4 HOH A 29 159 21 HOH HOH . G 4 HOH A 30 160 22 HOH HOH . G 4 HOH A 31 161 26 HOH HOH . G 4 HOH A 32 162 28 HOH HOH . G 4 HOH A 33 163 29 HOH HOH . G 4 HOH A 34 164 30 HOH HOH . G 4 HOH A 35 165 32 HOH HOH . G 4 HOH A 36 166 40 HOH HOH . G 4 HOH A 37 167 41 HOH HOH . G 4 HOH A 38 168 42 HOH HOH . G 4 HOH A 39 169 44 HOH HOH . G 4 HOH A 40 170 46 HOH HOH . G 4 HOH A 41 171 47 HOH HOH . G 4 HOH A 42 172 48 HOH HOH . G 4 HOH A 43 173 49 HOH HOH . G 4 HOH A 44 174 50 HOH HOH . G 4 HOH A 45 175 57 HOH HOH . G 4 HOH A 46 176 58 HOH HOH . G 4 HOH A 47 177 59 HOH HOH . G 4 HOH A 48 178 60 HOH HOH . G 4 HOH A 49 179 61 HOH HOH . G 4 HOH A 50 180 62 HOH HOH . G 4 HOH A 51 181 63 HOH HOH . G 4 HOH A 52 182 65 HOH HOH . G 4 HOH A 53 183 66 HOH HOH . G 4 HOH A 54 184 67 HOH HOH . G 4 HOH A 55 185 73 HOH HOH . G 4 HOH A 56 186 74 HOH HOH . G 4 HOH A 57 187 75 HOH HOH . G 4 HOH A 58 188 76 HOH HOH . G 4 HOH A 59 189 77 HOH HOH . G 4 HOH A 60 190 78 HOH HOH . G 4 HOH A 61 191 79 HOH HOH . G 4 HOH A 62 192 80 HOH HOH . G 4 HOH A 63 193 82 HOH HOH . G 4 HOH A 64 194 84 HOH HOH . G 4 HOH A 65 195 86 HOH HOH . G 4 HOH A 66 196 87 HOH HOH . G 4 HOH A 67 197 90 HOH HOH . G 4 HOH A 68 198 96 HOH HOH . G 4 HOH A 69 199 98 HOH HOH . G 4 HOH A 70 200 99 HOH HOH . G 4 HOH A 71 201 100 HOH HOH . G 4 HOH A 72 202 103 HOH HOH . G 4 HOH A 73 203 104 HOH HOH . G 4 HOH A 74 204 105 HOH HOH . G 4 HOH A 75 205 107 HOH HOH . G 4 HOH A 76 206 109 HOH HOH . G 4 HOH A 77 207 110 HOH HOH . G 4 HOH A 78 208 113 HOH HOH . G 4 HOH A 79 209 114 HOH HOH . G 4 HOH A 80 210 115 HOH HOH . G 4 HOH A 81 211 119 HOH HOH . G 4 HOH A 82 212 121 HOH HOH . G 4 HOH A 83 213 122 HOH HOH . G 4 HOH A 84 214 123 HOH HOH . G 4 HOH A 85 215 124 HOH HOH . G 4 HOH A 86 216 125 HOH HOH . G 4 HOH A 87 217 126 HOH HOH . G 4 HOH A 88 218 127 HOH HOH . H 4 HOH B 1 129 129 HOH HOH . H 4 HOH B 2 130 130 HOH HOH . H 4 HOH B 3 131 1 HOH HOH . H 4 HOH B 4 132 3 HOH HOH . H 4 HOH B 5 133 133 HOH HOH . H 4 HOH B 6 134 4 HOH HOH . H 4 HOH B 7 135 5 HOH HOH . H 4 HOH B 8 136 6 HOH HOH . H 4 HOH B 9 137 137 HOH HOH . H 4 HOH B 10 138 14 HOH HOH . H 4 HOH B 11 139 139 HOH HOH . H 4 HOH B 12 140 15 HOH HOH . H 4 HOH B 13 141 16 HOH HOH . H 4 HOH B 14 142 23 HOH HOH . H 4 HOH B 15 143 143 HOH HOH . H 4 HOH B 16 144 24 HOH HOH . H 4 HOH B 17 145 25 HOH HOH . H 4 HOH B 18 146 27 HOH HOH . H 4 HOH B 19 147 31 HOH HOH . H 4 HOH B 20 148 148 HOH HOH . H 4 HOH B 21 149 149 HOH HOH . H 4 HOH B 22 150 150 HOH HOH . H 4 HOH B 23 151 151 HOH HOH . H 4 HOH B 24 152 33 HOH HOH . H 4 HOH B 25 153 34 HOH HOH . H 4 HOH B 26 154 154 HOH HOH . H 4 HOH B 27 155 155 HOH HOH . H 4 HOH B 28 156 35 HOH HOH . H 4 HOH B 29 157 157 HOH HOH . H 4 HOH B 30 158 158 HOH HOH . H 4 HOH B 31 159 159 HOH HOH . H 4 HOH B 32 160 160 HOH HOH . H 4 HOH B 33 161 161 HOH HOH . H 4 HOH B 34 162 36 HOH HOH . H 4 HOH B 35 163 37 HOH HOH . H 4 HOH B 36 164 38 HOH HOH . H 4 HOH B 37 165 39 HOH HOH . H 4 HOH B 38 166 43 HOH HOH . H 4 HOH B 39 167 45 HOH HOH . H 4 HOH B 40 168 51 HOH HOH . H 4 HOH B 41 169 52 HOH HOH . H 4 HOH B 42 170 53 HOH HOH . H 4 HOH B 43 171 54 HOH HOH . H 4 HOH B 44 172 55 HOH HOH . H 4 HOH B 45 173 56 HOH HOH . H 4 HOH B 46 174 64 HOH HOH . H 4 HOH B 47 175 68 HOH HOH . H 4 HOH B 48 176 69 HOH HOH . H 4 HOH B 49 177 70 HOH HOH . H 4 HOH B 50 178 71 HOH HOH . H 4 HOH B 51 179 72 HOH HOH . H 4 HOH B 52 180 81 HOH HOH . H 4 HOH B 53 181 83 HOH HOH . H 4 HOH B 54 182 85 HOH HOH . H 4 HOH B 55 183 88 HOH HOH . H 4 HOH B 56 184 89 HOH HOH . H 4 HOH B 57 185 91 HOH HOH . H 4 HOH B 58 186 92 HOH HOH . H 4 HOH B 59 187 93 HOH HOH . H 4 HOH B 60 188 94 HOH HOH . H 4 HOH B 61 189 95 HOH HOH . H 4 HOH B 62 190 97 HOH HOH . H 4 HOH B 63 191 101 HOH HOH . H 4 HOH B 64 192 102 HOH HOH . H 4 HOH B 65 193 106 HOH HOH . H 4 HOH B 66 194 108 HOH HOH . H 4 HOH B 67 195 111 HOH HOH . H 4 HOH B 68 196 112 HOH HOH . H 4 HOH B 69 197 116 HOH HOH . H 4 HOH B 70 198 117 HOH HOH . H 4 HOH B 71 199 118 HOH HOH . H 4 HOH B 72 200 120 HOH HOH . H 4 HOH B 73 201 128 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 KDH . . . D 2 -24.982 5.578 -1.849 1 62.87 ? O1 KDH 129 A 1 HETATM 2 C C3 KDH . . . D 2 -24.861 5.013 -3.081 1 54.78 ? C3 KDH 129 A 1 HETATM 3 C C6 KDH . . . D 2 -24.607 3.65 -3.211 1 49.79 ? C6 KDH 129 A 1 HETATM 4 O O7 KDH . . . D 2 -24.478 2.839 -2.114 1 87.56 ? O7 KDH 129 A 1 HETATM 5 C C9 KDH . . . D 2 -24.482 3.095 -4.469 1 52.65 ? C9 KDH 129 A 1 HETATM 6 O O10 KDH . . . D 2 -24.232 1.759 -4.579 1 62.44 ? O10 KDH 129 A 1 HETATM 7 C C12 KDH . . . D 2 -24.616 3.891 -5.603 1 45.57 ? C12 KDH 129 A 1 HETATM 8 C C14 KDH . . . D 2 -24.869 5.25 -5.478 1 56.67 ? C14 KDH 129 A 1 HETATM 9 C C15 KDH . . . D 2 -24.992 6.121 -6.677 1 58.71 ? C15 KDH 129 A 1 HETATM 10 C C20 KDH . . . D 2 -24.382 6.144 -9.03 1 62.31 ? C20 KDH 129 A 1 HETATM 11 C C21 KDH . . . D 2 -23.408 5.842 -9.979 1 51.65 ? C21 KDH 129 A 1 HETATM 12 C C24 KDH . . . D 2 -23.43 6.475 -11.218 1 68.43 ? C24 KDH 129 A 1 HETATM 13 C C26 KDH . . . D 2 -24.424 7.406 -11.507 1 69.63 ? C26 KDH 129 A 1 HETATM 14 C C29 KDH . . . D 2 -25.395 7.702 -10.559 1 65.34 ? C29 KDH 129 A 1 HETATM 15 C C31 KDH . . . D 2 -25.374 7.074 -9.319 1 55.58 ? C31 KDH 129 A 1 HETATM 16 C C33 KDH . . . D 2 -26.422 6.593 -6.995 1 53.39 ? C33 KDH 129 A 1 HETATM 17 C C36 KDH . . . D 2 -27.461 4.624 -8.033 1 70.87 ? C36 KDH 129 A 1 HETATM 18 C C38 KDH . . . D 2 -28.433 3.491 -8.125 1 65.62 ? C38 KDH 129 A 1 HETATM 19 C C39 KDH . . . D 2 -28.099 2.482 -9.013 1 61.45 ? C39 KDH 129 A 1 HETATM 20 C C41 KDH . . . D 2 -29.631 3.44 -7.415 1 69.09 ? C41 KDH 129 A 1 HETATM 21 C C01 KDH . . . D 2 -26.453 7.404 -8.304 1 53 ? C01 KDH 129 A 1 HETATM 22 O O01 KDH . . . D 2 -24.357 5.517 -7.81 1 68.37 ? O01 KDH 129 A 1 HETATM 23 O O02 KDH . . . D 2 -22.48 6.183 -12.151 1 76.75 ? O02 KDH 129 A 1 HETATM 24 O O03 KDH . . . D 2 -26.36 8.617 -10.855 1 67.38 ? O03 KDH 129 A 1 HETATM 25 C C4 KDH . . . D 2 -24.989 5.81 -4.212 1 60.08 ? C4 KDH 129 A 1 HETATM 26 O O35 KDH . . . D 2 -27.435 5.564 -6.925 1 71.74 ? O35 KDH 129 A 1 HETATM 27 O O37 KDH . . . D 2 -26.693 4.764 -8.965 1 107.04 ? O37 KDH 129 A 1 HETATM 28 C C43 KDH . . . D 2 -30.476 2.337 -7.591 1 74.53 ? C43 KDH 129 A 1 HETATM 29 O O44 KDH . . . D 2 -31.651 2.237 -6.896 1 83.13 ? O44 KDH 129 A 1 HETATM 30 C C46 KDH . . . D 2 -30.125 1.324 -8.479 1 71.56 ? C46 KDH 129 A 1 HETATM 31 O O47 KDH . . . D 2 -30.95 0.25 -8.653 1 87.86 ? O47 KDH 129 A 1 HETATM 32 C C49 KDH . . . D 2 -28.934 1.395 -9.19 1 62.78 ? C49 KDH 129 A 1 HETATM 33 O O50 KDH . . . D 2 -28.571 0.414 -10.062 1 83.14 ? O50 KDH 129 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #