data_7UPG
#
_model_server_result.job_id            OcSVRIpFtbUVxyUKA641bg 
_model_server_result.datetime_utc      '2025-03-05 02:43:07' 
_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          7upg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
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_entry.id    7UPG 
#
_exptl.entry_id    7UPG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    10 
_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            7UPG 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7UPG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T 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 171 n n 
O1 HO1 KDH sing 172 n n 
C3 C6 KDH doub 173 n y 
C3 C4 KDH sing 174 n y 
C6 O7 KDH sing 175 n n 
C6 C9 KDH sing 176 n y 
O7 HO7 KDH sing 177 n n 
C9 O10 KDH sing 178 n n 
C9 C12 KDH doub 179 n y 
O10 HO10 KDH sing 180 n n 
C12 C14 KDH sing 181 n y 
C12 H12 KDH sing 182 n n 
C14 C15 KDH sing 183 n n 
C14 C4 KDH doub 184 n y 
C15 C33 KDH sing 185 n n 
C15 O01 KDH sing 186 n n 
C15 H15 KDH sing 187 n n 
C20 C21 KDH doub 188 n y 
C20 C31 KDH sing 189 n y 
C20 O01 KDH sing 190 n n 
C21 C24 KDH sing 191 n y 
C21 H21 KDH sing 192 n n 
C24 C26 KDH doub 193 n y 
C24 O02 KDH sing 194 n n 
C26 C29 KDH sing 195 n y 
C26 H26 KDH sing 196 n n 
C29 C31 KDH doub 197 n y 
C29 O03 KDH sing 198 n n 
C31 C01 KDH sing 199 n n 
C33 C01 KDH sing 200 n n 
C33 O35 KDH sing 201 n n 
C33 H33 KDH sing 202 n n 
C36 C38 KDH sing 203 n n 
C36 O35 KDH sing 204 n n 
C36 O37 KDH doub 205 n n 
C38 C39 KDH doub 206 n y 
C38 C41 KDH sing 207 n y 
C39 C49 KDH sing 208 n y 
C39 H39 KDH sing 209 n n 
C41 C43 KDH doub 210 n y 
C41 H41 KDH sing 211 n n 
C01 H01 KDH sing 212 n n 
C01 H01A KDH sing 213 n n 
O02 HO02 KDH sing 214 n n 
O03 HO03 KDH sing 215 n n 
C4 H4 KDH sing 216 n n 
C43 O44 KDH sing 217 n n 
C43 C46 KDH sing 218 n y 
O44 HO44 KDH sing 219 n n 
C46 O47 KDH sing 220 n n 
C46 C49 KDH doub 221 n y 
O47 HO47 KDH sing 222 n n 
C49 O50 KDH sing 223 n n 
O50 HO50 KDH sing 224 n n 
#
_atom_sites.entry_id                     7UPG 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
K 2 KDH A 1 501 401 KDH KDH . 
L 2 KDH A 1 502 401 KDH KDH . 
M 2 KDH B 1 501 401 KDH KDH . 
N 2 KDH C 1 501 401 KDH KDH . 
O 2 KDH D 1 501 401 KDH KDH . 
P 2 KDH E 1 501 401 KDH KDH . 
Q 2 KDH E 1 502 401 KDH KDH . 
R 2 KDH G 1 501 401 KDH KDH . 
S 2 KDH H 1 501 401 KDH KDH . 
T 2 KDH I 1 501 401 KDH KDH . 
#
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 . . . M 2 -14.122 -21.08 5.687 1 118.04 ? O1 KDH 501 B 1 
HETATM 2 C C3 KDH . . . M 2 -13.547 -22.156 5.063 1 118.04 ? C3 KDH 501 B 1 
HETATM 3 C C6 KDH . . . M 2 -14.344 -23.044 4.353 1 118.04 ? C6 KDH 501 B 1 
HETATM 4 O O7 KDH . . . M 2 -15.691 -22.844 4.274 1 118.04 ? O7 KDH 501 B 1 
HETATM 5 C C9 KDH . . . M 2 -13.753 -24.134 3.726 1 118.04 ? C9 KDH 501 B 1 
HETATM 6 O O10 KDH . . . M 2 -14.544 -25.005 3.021 1 118.04 ? O10 KDH 501 B 1 
HETATM 7 C C12 KDH . . . M 2 -12.388 -24.335 3.807 1 118.04 ? C12 KDH 501 B 1 
HETATM 8 C C14 KDH . . . M 2 -11.589 -23.443 4.518 1 118.04 ? C14 KDH 501 B 1 
HETATM 9 C C15 KDH . . . M 2 -10.103 -23.647 4.616 1 118.04 ? C15 KDH 501 B 1 
HETATM 10 C C20 KDH . . . M 2 -8.312 -24.746 3.539 1 118.04 ? C20 KDH 501 B 1 
HETATM 11 C C21 KDH . . . M 2 -7.894 -25.889 2.869 1 118.04 ? C21 KDH 501 B 1 
HETATM 12 C C24 KDH . . . M 2 -6.544 -26.187 2.831 1 118.04 ? C24 KDH 501 B 1 
HETATM 13 C C26 KDH . . . M 2 -5.619 -25.364 3.451 1 118.04 ? C26 KDH 501 B 1 
HETATM 14 C C29 KDH . . . M 2 -6.046 -24.23 4.114 1 118.04 ? C29 KDH 501 B 1 
HETATM 15 C C31 KDH . . . M 2 -7.405 -23.902 4.171 1 118.04 ? C31 KDH 501 B 1 
HETATM 16 C C33 KDH . . . M 2 -9.315 -22.348 4.564 1 118.04 ? C33 KDH 501 B 1 
HETATM 17 C C36 KDH . . . M 2 -9.985 -20.69 2.946 1 118.04 ? C36 KDH 501 B 1 
HETATM 18 C C38 KDH . . . M 2 -9.104 -19.523 3.193 1 118.04 ? C38 KDH 501 B 1 
HETATM 19 C C39 KDH . . . M 2 -7.895 -19.412 2.512 1 118.04 ? C39 KDH 501 B 1 
HETATM 20 C C41 KDH . . . M 2 -9.502 -18.543 4.099 1 118.04 ? C41 KDH 501 B 1 
HETATM 21 C C01 KDH . . . M 2 -7.867 -22.658 4.886 1 118.04 ? C01 KDH 501 B 1 
HETATM 22 O O01 KDH . . . M 2 -9.669 -24.499 3.547 1 118.04 ? O01 KDH 501 B 1 
HETATM 23 O O02 KDH . . . M 2 -6.118 -27.305 2.179 1 118.04 ? O02 KDH 501 B 1 
HETATM 24 O O03 KDH . . . M 2 -5.144 -23.413 4.73 1 118.04 ? O03 KDH 501 B 1 
HETATM 25 C C4 KDH . . . M 2 -12.185 -22.357 5.151 1 118.04 ? C4 KDH 501 B 1 
HETATM 26 O O35 KDH . . . M 2 -9.359 -21.855 3.189 1 118.04 ? O35 KDH 501 B 1 
HETATM 27 O O37 KDH . . . M 2 -11.121 -20.607 2.558 1 118.04 ? O37 KDH 501 B 1 
HETATM 28 C C43 KDH . . . M 2 -8.684 -17.457 4.323 1 118.04 ? C43 KDH 501 B 1 
HETATM 29 O O44 KDH . . . M 2 -9.017 -16.465 5.201 1 118.04 ? O44 KDH 501 B 1 
HETATM 30 C C46 KDH . . . M 2 -7.472 -17.337 3.649 1 118.04 ? C46 KDH 501 B 1 
HETATM 31 O O47 KDH . . . M 2 -6.676 -16.253 3.885 1 118.04 ? O47 KDH 501 B 1 
HETATM 32 C C49 KDH . . . M 2 -7.083 -18.321 2.743 1 118.04 ? C49 KDH 501 B 1 
HETATM 33 O O50 KDH . . . M 2 -5.885 -18.167 2.1 1 118.04 ? O50 KDH 501 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#