data_3KGU
#
_model_server_result.job_id            Ps1ZhRXADKzFWjQyihBsRw 
_model_server_result.datetime_utc      '2024-10-12 01:27:16' 
_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          3kgu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":3071}' 
#
_entry.id    3KGU 
#
_exptl.entry_id    3KGU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              270.237 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GENISTEIN 
_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            3KGU 
_cell.length_a            43.53 
_cell.length_b            85.35 
_cell.length_c            64.97 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KGU 
_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 
_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 
#
_chem_comp.formula           'C15 H10 O5' 
_chem_comp.formula_weight    270.237 
_chem_comp.id                GEN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GENISTEIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE;4',5,7-TRIHYDROXYISOFLAVONE;PRUNETOL;GENISTEOL" 
#
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 C2 GEN doub 83 n y 
C1 C10 GEN sing 84 n y 
C1 H1 GEN sing 85 n n 
C2 O2 GEN sing 86 n n 
C2 C3 GEN sing 87 n y 
O2 H2 GEN sing 88 n n 
C3 C4 GEN doub 89 n y 
C3 H3 GEN sing 90 n n 
C4 O4 GEN sing 91 n n 
C4 C5 GEN sing 92 n y 
O4 H4 GEN sing 93 n n 
C5 C6 GEN sing 94 n y 
C5 C10 GEN doub 95 n y 
C6 O6 GEN doub 96 n n 
C6 C7 GEN sing 97 n y 
C7 C8 GEN doub 98 n y 
C7 C11 GEN sing 99 n y 
C8 O9 GEN sing 100 n y 
C8 H8 GEN sing 101 n n 
O9 C10 GEN sing 102 n y 
C11 C12 GEN doub 103 n y 
C11 C16 GEN sing 104 n y 
C12 C13 GEN sing 105 n y 
C12 H12 GEN sing 106 n n 
C13 C14 GEN doub 107 n y 
C13 H13 GEN sing 108 n n 
C14 O14 GEN sing 109 n n 
C14 C15 GEN sing 110 n y 
O14 H14 GEN sing 111 n n 
C15 C16 GEN doub 112 n y 
C15 H15 GEN sing 113 n n 
C16 H16 GEN sing 114 n n 
#
_atom_sites.entry_id                     3KGU 
_atom_sites.fract_transf_matrix[1][1]    0.022973 
_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]    0.011716 
_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]    0.015392 
_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 GEN A 1 3071 3071 GEN GEN . 
D 2 GEN B 1 3071 3071 GEN GEN . 
E 3 HOH A 1 128 2 HOH HOH . 
E 3 HOH A 2 129 3 HOH HOH . 
E 3 HOH A 3 130 4 HOH HOH . 
E 3 HOH A 4 131 131 HOH HOH . 
E 3 HOH A 5 132 132 HOH HOH . 
E 3 HOH A 6 133 133 HOH HOH . 
E 3 HOH A 7 134 6 HOH HOH . 
E 3 HOH A 8 135 10 HOH HOH . 
E 3 HOH A 9 136 11 HOH HOH . 
E 3 HOH A 10 137 13 HOH HOH . 
E 3 HOH A 11 138 15 HOH HOH . 
E 3 HOH A 12 139 16 HOH HOH . 
E 3 HOH A 13 140 17 HOH HOH . 
E 3 HOH A 14 141 19 HOH HOH . 
E 3 HOH A 15 142 142 HOH HOH . 
E 3 HOH A 16 143 21 HOH HOH . 
E 3 HOH A 17 144 22 HOH HOH . 
E 3 HOH A 18 145 145 HOH HOH . 
E 3 HOH A 19 146 24 HOH HOH . 
E 3 HOH A 20 147 25 HOH HOH . 
E 3 HOH A 21 148 28 HOH HOH . 
E 3 HOH A 22 149 29 HOH HOH . 
E 3 HOH A 23 150 30 HOH HOH . 
E 3 HOH A 24 151 33 HOH HOH . 
E 3 HOH A 25 152 36 HOH HOH . 
E 3 HOH A 26 153 38 HOH HOH . 
E 3 HOH A 27 154 40 HOH HOH . 
E 3 HOH A 28 155 41 HOH HOH . 
E 3 HOH A 29 156 45 HOH HOH . 
E 3 HOH A 30 157 157 HOH HOH . 
E 3 HOH A 31 158 46 HOH HOH . 
E 3 HOH A 32 159 47 HOH HOH . 
E 3 HOH A 33 160 49 HOH HOH . 
E 3 HOH A 34 161 50 HOH HOH . 
E 3 HOH A 35 162 52 HOH HOH . 
E 3 HOH A 36 163 53 HOH HOH . 
E 3 HOH A 37 164 54 HOH HOH . 
E 3 HOH A 38 165 55 HOH HOH . 
E 3 HOH A 39 166 57 HOH HOH . 
E 3 HOH A 40 167 59 HOH HOH . 
E 3 HOH A 41 168 60 HOH HOH . 
E 3 HOH A 42 169 169 HOH HOH . 
E 3 HOH A 43 170 61 HOH HOH . 
E 3 HOH A 44 171 171 HOH HOH . 
E 3 HOH A 45 172 63 HOH HOH . 
E 3 HOH A 46 173 65 HOH HOH . 
E 3 HOH A 47 174 174 HOH HOH . 
E 3 HOH A 48 175 68 HOH HOH . 
E 3 HOH A 49 176 70 HOH HOH . 
E 3 HOH A 50 177 71 HOH HOH . 
E 3 HOH A 51 178 73 HOH HOH . 
E 3 HOH A 52 179 74 HOH HOH . 
E 3 HOH A 53 180 75 HOH HOH . 
E 3 HOH A 54 181 76 HOH HOH . 
E 3 HOH A 55 182 77 HOH HOH . 
E 3 HOH A 56 183 78 HOH HOH . 
E 3 HOH A 57 184 79 HOH HOH . 
E 3 HOH A 58 185 83 HOH HOH . 
E 3 HOH A 59 186 85 HOH HOH . 
E 3 HOH A 60 187 86 HOH HOH . 
E 3 HOH A 61 188 87 HOH HOH . 
E 3 HOH A 62 189 89 HOH HOH . 
E 3 HOH A 63 190 91 HOH HOH . 
E 3 HOH A 64 191 93 HOH HOH . 
E 3 HOH A 65 192 95 HOH HOH . 
E 3 HOH A 66 193 97 HOH HOH . 
E 3 HOH A 67 194 99 HOH HOH . 
E 3 HOH A 68 195 101 HOH HOH . 
E 3 HOH A 69 196 103 HOH HOH . 
E 3 HOH A 70 197 106 HOH HOH . 
E 3 HOH A 71 198 108 HOH HOH . 
E 3 HOH A 72 199 111 HOH HOH . 
E 3 HOH A 73 200 112 HOH HOH . 
E 3 HOH A 74 201 114 HOH HOH . 
E 3 HOH A 75 202 115 HOH HOH . 
E 3 HOH A 76 203 116 HOH HOH . 
E 3 HOH A 77 204 118 HOH HOH . 
E 3 HOH A 78 205 119 HOH HOH . 
E 3 HOH A 79 206 120 HOH HOH . 
E 3 HOH A 80 207 122 HOH HOH . 
E 3 HOH A 81 208 123 HOH HOH . 
E 3 HOH A 82 209 124 HOH HOH . 
E 3 HOH A 83 210 126 HOH HOH . 
E 3 HOH A 84 211 127 HOH HOH . 
F 3 HOH B 1 128 128 HOH HOH . 
F 3 HOH B 2 129 1 HOH HOH . 
F 3 HOH B 3 130 130 HOH HOH . 
F 3 HOH B 4 131 5 HOH HOH . 
F 3 HOH B 5 132 7 HOH HOH . 
F 3 HOH B 6 133 8 HOH HOH . 
F 3 HOH B 7 134 134 HOH HOH . 
F 3 HOH B 8 135 135 HOH HOH . 
F 3 HOH B 9 136 136 HOH HOH . 
F 3 HOH B 10 137 9 HOH HOH . 
F 3 HOH B 11 138 138 HOH HOH . 
F 3 HOH B 12 139 139 HOH HOH . 
F 3 HOH B 13 140 14 HOH HOH . 
F 3 HOH B 14 141 18 HOH HOH . 
F 3 HOH B 15 142 20 HOH HOH . 
F 3 HOH B 16 143 23 HOH HOH . 
F 3 HOH B 17 144 26 HOH HOH . 
F 3 HOH B 18 145 27 HOH HOH . 
F 3 HOH B 19 146 31 HOH HOH . 
F 3 HOH B 20 147 147 HOH HOH . 
F 3 HOH B 21 148 32 HOH HOH . 
F 3 HOH B 22 149 34 HOH HOH . 
F 3 HOH B 23 150 35 HOH HOH . 
F 3 HOH B 24 151 37 HOH HOH . 
F 3 HOH B 25 152 39 HOH HOH . 
F 3 HOH B 26 153 42 HOH HOH . 
F 3 HOH B 27 154 43 HOH HOH . 
F 3 HOH B 28 155 48 HOH HOH . 
F 3 HOH B 29 156 51 HOH HOH . 
F 3 HOH B 30 157 56 HOH HOH . 
F 3 HOH B 31 158 158 HOH HOH . 
F 3 HOH B 32 159 58 HOH HOH . 
F 3 HOH B 33 160 62 HOH HOH . 
F 3 HOH B 34 161 64 HOH HOH . 
F 3 HOH B 35 162 66 HOH HOH . 
F 3 HOH B 36 163 67 HOH HOH . 
F 3 HOH B 37 164 72 HOH HOH . 
F 3 HOH B 38 165 80 HOH HOH . 
F 3 HOH B 39 166 166 HOH HOH . 
F 3 HOH B 40 167 81 HOH HOH . 
F 3 HOH B 41 168 168 HOH HOH . 
F 3 HOH B 42 169 82 HOH HOH . 
F 3 HOH B 43 170 170 HOH HOH . 
F 3 HOH B 44 171 84 HOH HOH . 
F 3 HOH B 45 172 88 HOH HOH . 
F 3 HOH B 46 173 173 HOH HOH . 
F 3 HOH B 47 174 90 HOH HOH . 
F 3 HOH B 48 175 92 HOH HOH . 
F 3 HOH B 49 176 176 HOH HOH . 
F 3 HOH B 50 177 177 HOH HOH . 
F 3 HOH B 51 178 94 HOH HOH . 
F 3 HOH B 52 179 96 HOH HOH . 
F 3 HOH B 53 180 100 HOH HOH . 
F 3 HOH B 54 181 102 HOH HOH . 
F 3 HOH B 55 182 104 HOH HOH . 
F 3 HOH B 56 183 105 HOH HOH . 
F 3 HOH B 57 184 109 HOH HOH . 
F 3 HOH B 58 185 110 HOH HOH . 
F 3 HOH B 59 186 113 HOH HOH . 
F 3 HOH B 60 187 117 HOH HOH . 
F 3 HOH B 61 188 121 HOH HOH . 
F 3 HOH B 62 189 125 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 GEN . . . D 2 0.588 0.548 -29.569 0.5 37.11 ? C1 GEN 3071 B 1 
HETATM 2 C C2 GEN . . . D 2 -0.242 -0.185 -30.411 0.5 37.33 ? C2 GEN 3071 B 1 
HETATM 3 O O2 GEN . . . D 2 -0.126 -0.061 -31.763 0.5 37.26 ? O2 GEN 3071 B 1 
HETATM 4 C C3 GEN . . . D 2 -1.19 -1.045 -29.871 0.5 36.98 ? C3 GEN 3071 B 1 
HETATM 5 C C4 GEN . . . D 2 -1.306 -1.17 -28.492 0.5 36.98 ? C4 GEN 3071 B 1 
HETATM 6 O O4 GEN . . . D 2 -2.244 -2.019 -27.988 0.5 36.67 ? O4 GEN 3071 B 1 
HETATM 7 C C5 GEN . . . D 2 -0.472 -0.434 -27.646 0.5 36.77 ? C5 GEN 3071 B 1 
HETATM 8 C C6 GEN . . . D 2 -0.577 -0.552 -26.264 0.5 36.56 ? C6 GEN 3071 B 1 
HETATM 9 O O6 GEN . . . D 2 -1.409 -1.306 -25.762 0.5 36.82 ? O6 GEN 3071 B 1 
HETATM 10 C C7 GEN . . . D 2 0.276 0.183 -25.452 0.5 36.1 ? C7 GEN 3071 B 1 
HETATM 11 C C8 GEN . . . D 2 1.206 1.028 -26.045 0.5 36.66 ? C8 GEN 3071 B 1 
HETATM 12 O O9 GEN . . . D 2 1.316 1.167 -27.4 0.5 37.31 ? O9 GEN 3071 B 1 
HETATM 13 C C10 GEN . . . D 2 0.477 0.428 -28.187 0.5 36.87 ? C10 GEN 3071 B 1 
HETATM 14 C C11 GEN . . . D 2 0.189 0.092 -24.061 0.5 35.52 ? C11 GEN 3071 B 1 
HETATM 15 C C12 GEN . . . D 2 0.141 1.25 -23.29 0.5 34.68 ? C12 GEN 3071 B 1 
HETATM 16 C C13 GEN . . . D 2 0.05 1.163 -21.904 0.5 34.54 ? C13 GEN 3071 B 1 
HETATM 17 C C14 GEN . . . D 2 0.003 -0.081 -21.283 0.5 34.21 ? C14 GEN 3071 B 1 
HETATM 18 O O14 GEN . . . D 2 -0.086 -0.162 -19.923 0.5 34.11 ? O14 GEN 3071 B 1 
HETATM 19 C C15 GEN . . . D 2 0.047 -1.238 -22.056 0.5 34.58 ? C15 GEN 3071 B 1 
HETATM 20 C C16 GEN . . . D 2 0.141 -1.154 -23.441 0.5 34.72 ? C16 GEN 3071 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#