data_3WKU # _model_server_result.job_id 1V6ucnD4_c1droLHXQoRmg _model_server_result.datetime_utc '2024-10-13 11:18:39' _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 3wku # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 3WKU # _exptl.entry_id 3WKU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 170.12 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3,4,5-trihydroxybenzoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.58 _cell.angle_gamma 90 _cell.entry_id 3WKU _cell.length_a 57.435 _cell.length_b 60.765 _cell.length_c 117.986 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WKU _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A NE2 HIS 12 A HIS 12 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc2 A NE2 HIS 59 A HIS 59 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc3 A OE1 GLU 239 A GLU 239 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc4 A OE2 GLU 239 A GLU 239 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc5 D OAE GDE . A GDE 502 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.429 ? metalc ? metalc6 D OAD GDE . A GDE 502 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.793 ? metalc ? metalc7 B NE2 HIS 12 B HIS 12 1_555 E FE FE . B FE 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.188 ? metalc ? metalc8 B NE2 HIS 12 B HIS 12 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.558 ? metalc ? metalc9 B OD1 ASN 57 B ASN 57 1_555 E FE FE . B FE 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.854 ? metalc ? metalc10 B NE2 HIS 59 B HIS 59 1_555 E FE FE . B FE 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.206 ? metalc ? metalc11 B NE2 HIS 59 B HIS 59 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.413 ? metalc ? metalc12 B OE1 GLU 239 B GLU 239 1_555 E FE FE . B FE 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.79 ? metalc ? metalc13 B OE1 GLU 239 B GLU 239 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.647 ? metalc ? metalc14 B OE2 GLU 239 B GLU 239 1_555 E FE FE . B FE 501 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.664 ? metalc ? metalc15 E FE FE . B FE 501 1_555 F O HOH . B HOH 601 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc16 E FE FE . B FE 501 1_555 F O HOH . B HOH 602 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc17 E FE FE . B FE 501 1_555 F O HOH . B HOH 602 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.572 ? # _chem_comp.formula 'C7 H6 O5' _chem_comp.formula_weight 170.12 _chem_comp.id GDE _chem_comp.mon_nstd_flag . _chem_comp.name '3,4,5-trihydroxybenzoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Gallate # 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 OAA CAH GDE sing 83 n n OAB CAH GDE doub 84 n n OAC CAI GDE sing 85 n n OAD CAJ GDE sing 86 n n OAE CAL GDE sing 87 n n CAF CAI GDE doub 88 n y CAF CAK GDE sing 89 n y CAG CAJ GDE sing 90 n y CAG CAK GDE doub 91 n y CAH CAK GDE sing 92 n n CAI CAL GDE sing 93 n y CAJ CAL GDE doub 94 n y OAA HOAA GDE sing 95 n n OAC HOAC GDE sing 96 n n OAD HOAD GDE sing 97 n n OAE HOAE GDE sing 98 n n CAF HAF GDE sing 99 n n CAG HAG GDE sing 100 n n # _atom_sites.entry_id 3WKU _atom_sites.fract_transf_matrix[1][1] 0.017411 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002626 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016457 _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] 0.008571 _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 FE A 1 501 1 FE FE . D 3 GDE A 1 502 2 GDE GDE . E 2 FE B 1 501 2 FE FE . F 4 HOH B 1 601 2 HOH HOH . F 4 HOH B 2 602 3 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 OAA GDE . . . D 3 -2.621 3.403 7.627 1 27.36 ? OAA GDE 502 A 1 HETATM 2 O OAB GDE . . . D 3 -3.615 2.001 6.287 1 25.6 ? OAB GDE 502 A 1 HETATM 3 O OAC GDE . . . D 3 -6.214 4.03 11.156 1 30.87 ? OAC GDE 502 A 1 HETATM 4 O OAD GDE . . . D 3 -6.68 -0.428 9.665 1 31.74 ? OAD GDE 502 A 1 HETATM 5 O OAE GDE . . . D 3 -7.377 1.468 11.347 1 30.42 ? OAE GDE 502 A 1 HETATM 6 C CAF GDE . . . D 3 -4.934 3.278 9.317 1 27.44 ? CAF GDE 502 A 1 HETATM 7 C CAG GDE . . . D 3 -5.139 1.028 8.532 1 29.59 ? CAG GDE 502 A 1 HETATM 8 C CAH GDE . . . D 3 -3.54 2.575 7.388 1 26.19 ? CAH GDE 502 A 1 HETATM 9 C CAI GDE . . . D 3 -5.869 3.025 10.304 1 28.37 ? CAI GDE 502 A 1 HETATM 10 C CAJ GDE . . . D 3 -6.091 0.784 9.526 1 29.83 ? CAJ GDE 502 A 1 HETATM 11 C CAK GDE . . . D 3 -4.565 2.284 8.428 1 26.18 ? CAK GDE 502 A 1 HETATM 12 C CAL GDE . . . D 3 -6.451 1.774 10.397 1 28.81 ? CAL GDE 502 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #