data_3ZQ8 # _model_server_result.job_id 32q5-j18Dvqd8erNaoIdXg _model_server_result.datetime_utc '2025-03-24 02:21:54' _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 3zq8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1016}' # _entry.id 3ZQ8 # _exptl.entry_id 3ZQ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.54 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description MONOVACCENIN _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 107.25 _cell.angle_gamma 90 _cell.entry_id 3ZQ8 _cell.length_a 23.96 _cell.length_b 41.981 _cell.length_c 32.429 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZQ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 # _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 ? 2 E N N ? 2 F N N ? 2 G 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 covale ? covale1 A C FVA 1 A FVA 1 1_555 A N GLY 2 A GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C ALA 3 A ALA 3 1_555 A N DLE 4 A DLE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale3 A C DLE 4 A DLE 4 1_555 A N ALA 5 A ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C ALA 5 A ALA 5 1_555 A N DVA 6 A DVA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C DVA 6 A DVA 6 1_555 A N VAL 7 A VAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale6 A C VAL 7 A VAL 7 1_555 A N DVA 8 A DVA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 A C DVA 8 A DVA 8 1_555 A N TRP 9 A TRP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale8 A C TRP 9 A TRP 9 1_555 A N DLE 10 A DLE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C DLE 10 A DLE 10 1_555 A N TRP 11 A TRP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale10 A C TRP 11 A TRP 11 1_555 A N DLE 12 A DLE 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale11 A C DLE 12 A DLE 12 1_555 A N TRP 13 A TRP 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C TRP 13 A TRP 13 1_555 A N DLE 14 A DLE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C DLE 14 A DLE 14 1_555 A N TRP 15 A TRP 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale14 A C TRP 15 A TRP 15 1_555 A N ETA 16 A ETA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale15 B C FVA 1 B FVA 1 1_555 B N GLY 2 B GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 B C ALA 3 B ALA 3 1_555 B N DLE 4 B DLE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale17 B C DLE 4 B DLE 4 1_555 B N ALA 5 B ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale18 B C ALA 5 B ALA 5 1_555 B N DVA 6 B DVA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale19 B C DVA 6 B DVA 6 1_555 B N VAL 7 B VAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale20 B C VAL 7 B VAL 7 1_555 B N DVA 8 B DVA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale21 B C DVA 8 B DVA 8 1_555 B N TRP 9 B TRP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C TRP 9 B TRP 9 1_555 B N DLE 10 B DLE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale23 B C DLE 10 B DLE 10 1_555 B N TRP 11 B TRP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale24 B C TRP 11 B TRP 11 1_555 B N DLE 12 B DLE 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 B C DLE 12 B DLE 12 1_555 B N TRP 13 B TRP 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale26 B C TRP 13 B TRP 13 1_555 B N DLE 14 B DLE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale27 B C DLE 14 B DLE 14 1_555 B N TRP 15 B TRP 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale28 B C TRP 15 B TRP 15 1_555 B N ETA 16 B ETA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale29 C C FVA 1 C FVA 1 1_555 C N GLY 2 C GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale30 C C ALA 3 C ALA 3 1_555 C N DLE 4 C DLE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale31 C C DLE 4 C DLE 4 1_555 C N ALA 5 C ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale32 C C ALA 5 C ALA 5 1_555 C N DVA 6 C DVA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale33 C C DVA 6 C DVA 6 1_555 C N VAL 7 C VAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale34 C C VAL 7 C VAL 7 1_555 C N DVA 8 C DVA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale35 C C DVA 8 C DVA 8 1_555 C N TRP 9 C TRP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale36 C C TRP 9 C TRP 9 1_555 C N DLE 10 C DLE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale37 C C DLE 10 C DLE 10 1_555 C N TRP 11 C TRP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale38 C C TRP 11 C TRP 11 1_555 C N DLE 12 C DLE 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale39 C C DLE 12 C DLE 12 1_555 C N TRP 13 C TRP 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale40 C C TRP 13 C TRP 13 1_555 C N DLE 14 C DLE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale41 C C DLE 14 C DLE 14 1_555 C N TRP 15 C TRP 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale42 C C TRP 15 C TRP 15 1_555 C N ETA 16 C ETA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale43 D C FVA 1 D FVA 1 1_555 D N GLY 2 D GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale44 D C ALA 3 D ALA 3 1_555 D N DLE 4 D DLE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale45 D C DLE 4 D DLE 4 1_555 D N ALA 5 D ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale46 D C ALA 5 D ALA 5 1_555 D N DVA 6 D DVA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale47 D C DVA 6 D DVA 6 1_555 D N VAL 7 D VAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale48 D C VAL 7 D VAL 7 1_555 D N DVA 8 D DVA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale49 D C DVA 8 D DVA 8 1_555 D N TRP 9 D TRP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale50 D C TRP 9 D TRP 9 1_555 D N DLE 10 D DLE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale51 D C DLE 10 D DLE 10 1_555 D N TRP 11 D TRP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale52 D C TRP 11 D TRP 11 1_555 D N DLE 12 D DLE 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale53 D C DLE 12 D DLE 12 1_555 D N TRP 13 D TRP 13 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.333 ? covale ? covale54 D C DLE 12 D DLE 12 1_555 D N TRP 13 D TRP 13 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.33 ? covale ? covale55 D C TRP 13 D TRP 13 1_555 D N DLE 14 D DLE 14 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale56 D C TRP 13 D TRP 13 1_555 D N DLE 14 D DLE 14 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale57 D C DLE 14 D DLE 14 1_555 D N TRP 15 D TRP 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale58 D C TRP 15 D TRP 15 1_555 D N ETA 16 D ETA 16 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.322 ? covale ? covale59 D C TRP 15 D TRP 15 1_555 D N ETA 16 D ETA 16 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C21 H40 O4' _chem_comp.formula_weight 356.54 _chem_comp.id MVC _chem_comp.mon_nstd_flag . _chem_comp.name MONOVACCENIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '11.7 MAG' # 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 C10 C9 MVC sing 93 n n C10 C11 MVC sing 94 n n C9 C8 MVC sing 95 n n C17 C16 MVC sing 96 n n C11 C12 MVC sing 97 n n C8 C7 MVC sing 98 n n C24 C22 MVC sing 99 n n C24 O25 MVC sing 100 n n C16 C15 MVC sing 101 n n C12 C13 MVC doub 102 z n C7 C6 MVC sing 103 n n C15 C14 MVC sing 104 n n C13 C14 MVC sing 105 n n C6 C5 MVC sing 106 n n C5 C4 MVC sing 107 n n C4 C3 MVC sing 108 n n C3 C1 MVC sing 109 n n C21 C22 MVC sing 110 n n C21 O20 MVC sing 111 n n C22 O23 MVC sing 112 n n O19 C1 MVC doub 113 n n O25 C1 MVC sing 114 n n C17 C18 MVC sing 115 n n C18 C19 MVC sing 116 n n C10 H101 MVC sing 117 n n C10 H102 MVC sing 118 n n C9 H91C MVC sing 119 n n C9 H92C MVC sing 120 n n C11 H111 MVC sing 121 n n C11 H112 MVC sing 122 n n C8 H81C MVC sing 123 n n C8 H82C MVC sing 124 n n C17 H171 MVC sing 125 n n C17 H172 MVC sing 126 n n C16 H161 MVC sing 127 n n C16 H162 MVC sing 128 n n C12 H12 MVC sing 129 n n C7 H71C MVC sing 130 n n C7 H72C MVC sing 131 n n C24 H241 MVC sing 132 n n C24 H242 MVC sing 133 n n C22 H22 MVC sing 134 n n C15 H151 MVC sing 135 n n C15 H152 MVC sing 136 n n C13 H13 MVC sing 137 n n C6 H61C MVC sing 138 n n C6 H62C MVC sing 139 n n C14 H141 MVC sing 140 n n C14 H142 MVC sing 141 n n C5 H51C MVC sing 142 n n C5 H52C MVC sing 143 n n C4 H41C MVC sing 144 n n C4 H42C MVC sing 145 n n C3 H31C MVC sing 146 n n C3 H32C MVC sing 147 n n C21 H211 MVC sing 148 n n C21 H212 MVC sing 149 n n O20 H20 MVC sing 150 n n O23 H23 MVC sing 151 n n C18 H181 MVC sing 152 n n C18 H182 MVC sing 153 n n C19 H191 MVC sing 154 n n C19 H192 MVC sing 155 n n C19 H193 MVC sing 156 n n # _atom_sites.entry_id 3ZQ8 _atom_sites.fract_transf_matrix[1][1] 0.041736 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.012959 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02382 _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] 0.032289 _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 2 MVC C 1 1016 1016 MVC MVC . F 2 MVC C 1 1017 1017 MVC MVC . G 2 MVC C 1 1018 1018 MVC MVC . H 3 HOH C 1 2001 2001 HOH HOH . H 3 HOH C 2 2002 2002 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 C17 MVC . . . E 2 -12.418 -8.195 -15.264 1 53.73 ? C17 MVC 1016 C 1 HETATM 2 C C9 MVC . . . E 2 -13.709 -1.212 -16.219 1 38.65 ? C9 MVC 1016 C 1 HETATM 3 C C8 MVC . . . E 2 -14.676 -1.241 -15.03 1 29.3 ? C8 MVC 1016 C 1 HETATM 4 C C16 MVC . . . E 2 -12.044 -7.248 -16.401 1 52.75 ? C16 MVC 1016 C 1 HETATM 5 C C10 MVC . . . E 2 -14.312 -1.796 -17.496 1 41.87 ? C10 MVC 1016 C 1 HETATM 6 C C7 MVC . . . E 2 -13.966 -1.292 -13.688 1 33.22 ? C7 MVC 1016 C 1 HETATM 7 C C24 MVC . . . E 2 -16.391 0.728 -5.762 1 29.2 ? C24 MVC 1016 C 1 HETATM 8 C C15 MVC . . . E 2 -13.269 -6.517 -16.956 1 49.61 ? C15 MVC 1016 C 1 HETATM 9 C C11 MVC . . . E 2 -13.489 -2.991 -18.039 1 46.43 ? C11 MVC 1016 C 1 HETATM 10 C C6 MVC . . . E 2 -14.837 -0.808 -12.512 1 27.72 ? C6 MVC 1016 C 1 HETATM 11 C C14 MVC . . . E 2 -12.974 -5.991 -18.364 1 49.79 ? C14 MVC 1016 C 1 HETATM 12 C C12 MVC . . . E 2 -14.274 -3.899 -18.77 1 50.51 ? C12 MVC 1016 C 1 HETATM 13 C C5 MVC . . . E 2 -14.166 0.073 -11.435 1 28.94 ? C5 MVC 1016 C 1 HETATM 14 C C13 MVC . . . E 2 -14.053 -5.287 -18.902 1 50.42 ? C13 MVC 1016 C 1 HETATM 15 C C4 MVC . . . E 2 -15.041 0.045 -10.184 1 27.55 ? C4 MVC 1016 C 1 HETATM 16 C C3 MVC . . . E 2 -14.455 0.709 -8.896 1 29.19 ? C3 MVC 1016 C 1 HETATM 17 C C21 MVC . . . E 2 -15.9 2.741 -4.5 1 30.54 ? C21 MVC 1016 C 1 HETATM 18 C C22 MVC . . . E 2 -16.034 1.227 -4.366 1 31.77 ? C22 MVC 1016 C 1 HETATM 19 O O19 MVC . . . E 2 -16.626 0.321 -8.132 1 25.92 ? O19 MVC 1016 C 1 HETATM 20 C C1 MVC . . . E 2 -15.59 0.947 -7.912 1 28.52 ? C1 MVC 1016 C 1 HETATM 21 O O25 MVC . . . E 2 -15.246 0.849 -6.518 1 25.97 ? O25 MVC 1016 C 1 HETATM 22 O O23 MVC . . . E 2 -17.074 0.871 -3.447 1 36.43 ? O23 MVC 1016 C 1 HETATM 23 O O20 MVC . . . E 2 -15.458 3.275 -3.23 1 39.63 ? O20 MVC 1016 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #