data_3NG5
#
_model_server_result.job_id            NPA23MX-XFE_PlySve7rIA 
_model_server_result.datetime_utc      '2024-10-31 15:27:13' 
_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":"C","auth_seq_id":128}' 
#
_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 . . . C 2 3.637 16.103 -11.047 1 28.64 ? O1 KDH 128 A 1 
HETATM 2 C C3 KDH . . . C 2 3.521 17.336 -11.586 1 27.18 ? C3 KDH 128 A 1 
HETATM 3 C C6 KDH . . . C 2 4.553 18.225 -11.394 1 39.8 ? C6 KDH 128 A 1 
HETATM 4 O O7 KDH . . . C 2 5.631 17.823 -10.661 1 32.17 ? O7 KDH 128 A 1 
HETATM 5 C C9 KDH . . . C 2 4.469 19.505 -11.921 1 25.36 ? C9 KDH 128 A 1 
HETATM 6 O O10 KDH . . . C 2 5.493 20.384 -11.737 1 31.96 ? O10 KDH 128 A 1 
HETATM 7 C C12 KDH . . . C 2 3.344 19.876 -12.654 1 45.43 ? C12 KDH 128 A 1 
HETATM 8 C C14 KDH . . . C 2 2.303 18.97 -12.859 1 32.31 ? C14 KDH 128 A 1 
HETATM 9 C C15 KDH . . . C 2 1.107 19.402 -13.625 1 41.16 ? C15 KDH 128 A 1 
HETATM 10 C C20 KDH . . . C 2 -0.762 18.664 -14.927 1 38.31 ? C20 KDH 128 A 1 
HETATM 11 C C21 KDH . . . C 2 -1.197 17.833 -15.95 1 29.95 ? C21 KDH 128 A 1 
HETATM 12 C C24 KDH . . . C 2 -2.353 18.17 -16.647 1 46.51 ? C24 KDH 128 A 1 
HETATM 13 C C26 KDH . . . C 2 -3.068 19.32 -16.337 1 34.81 ? C26 KDH 128 A 1 
HETATM 14 C C29 KDH . . . C 2 -2.627 20.153 -15.315 1 43.29 ? C29 KDH 128 A 1 
HETATM 15 C C31 KDH . . . C 2 -1.469 19.835 -14.627 1 35.19 ? C31 KDH 128 A 1 
HETATM 16 C C33 KDH . . . C 2 0.121 20.119 -12.709 1 44.07 ? C33 KDH 128 A 1 
HETATM 17 C C36 KDH . . . C 2 -1.21 19.698 -10.734 1 32.02 ? C36 KDH 128 A 1 
HETATM 18 C C38 KDH . . . C 2 -1.836 18.684 -9.851 1 25.4 ? C38 KDH 128 A 1 
HETATM 19 C C39 KDH . . . C 2 -2.114 17.477 -10.462 1 41.18 ? C39 KDH 128 A 1 
HETATM 20 C C41 KDH . . . C 2 -2.078 18.917 -8.5 1 48.94 ? C41 KDH 128 A 1 
HETATM 21 C C01 KDH . . . C 2 -1.018 20.748 -13.509 1 34.76 ? C01 KDH 128 A 1 
HETATM 22 O O01 KDH . . . C 2 0.384 18.339 -14.247 1 34.68 ? O01 KDH 128 A 1 
HETATM 23 O O02 KDH . . . C 2 -2.795 17.373 -17.648 1 40.39 ? O02 KDH 128 A 1 
HETATM 24 O O03 KDH . . . C 2 -3.323 21.296 -15.008 1 30.92 ? O03 KDH 128 A 1 
HETATM 25 C C4 KDH . . . C 2 2.389 17.697 -12.312 1 27.07 ? C4 KDH 128 A 1 
HETATM 26 O O35 KDH . . . C 2 -0.364 19.166 -11.766 1 27.09 ? O35 KDH 128 A 1 
HETATM 27 O O37 KDH . . . C 2 -1.377 20.894 -10.583 1 54.95 ? O37 KDH 128 A 1 
HETATM 28 C C43 KDH . . . C 2 -2.641 17.897 -7.76 1 39.45 ? C43 KDH 128 A 1 
HETATM 29 O O44 KDH . . . C 2 -2.918 18.077 -6.439 1 35.16 ? O44 KDH 128 A 1 
HETATM 30 C C46 KDH . . . C 2 -2.922 16.694 -8.379 1 23.97 ? C46 KDH 128 A 1 
HETATM 31 O O47 KDH . . . C 2 -3.478 15.698 -7.649 1 27.81 ? O47 KDH 128 A 1 
HETATM 32 C C49 KDH . . . C 2 -2.679 16.47 -9.721 1 29.21 ? C49 KDH 128 A 1 
HETATM 33 O O50 KDH . . . C 2 -2.96 15.261 -10.295 1 27.55 ? O50 KDH 128 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#