data_4RDT # _model_server_result.job_id UI0M7LpnrcPi3MfH6d25Rg _model_server_result.datetime_utc '2024-11-21 14:34:25' _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 4rdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":804}' # _entry.id 4RDT # _exptl.entry_id 4RDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 4RDT _cell.length_a 101.34 _cell.length_b 156.227 _cell.length_c 158.075 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,L 1 1 B,J,K,M 2 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 ? 3 D N N ? 3 E N N ? 3 F 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 disulf ? disulf1 A SG CYS 262 A CYS 249 1_555 A SG CYS 299 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 262 B CYS 249 1_555 B SG CYS 299 B CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A OD1 ASP 113 A ASP 99 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 A OD2 ASP 113 A ASP 99 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A NE2 HIS 114 A HIS 100 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 A OE2 GLU 354 A GLU 340 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc5 A NE2 HIS 513 A HIS 499 1_555 C ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc6 B OD1 ASP 113 B ASP 99 1_555 J ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc7 B NE2 HIS 114 B HIS 100 1_555 J ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 B OE2 GLU 354 B GLU 340 1_555 J ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc9 B NE2 HIS 513 B HIS 499 1_555 J ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 183 n n C1 C2 GOL sing 184 n n C1 H11 GOL sing 185 n n C1 H12 GOL sing 186 n n O1 HO1 GOL sing 187 n n C2 O2 GOL sing 188 n n C2 C3 GOL sing 189 n n C2 H2 GOL sing 190 n n O2 HO2 GOL sing 191 n n C3 O3 GOL sing 192 n n C3 H31 GOL sing 193 n n C3 H32 GOL sing 194 n n O3 HO3 GOL sing 195 n n # _atom_sites.entry_id 4RDT _atom_sites.fract_transf_matrix[1][1] 0.009868 _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] 0.006401 _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] 0.006326 _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 ZN A 1 801 735 ZN ZN . D 3 GOL A 1 802 736 GOL GOL . E 3 GOL A 1 803 737 GOL GOL . F 3 GOL A 1 804 738 GOL GOL . G 4 C8E A 1 805 739 C8E C8E . H 4 C8E A 1 806 740 C8E C8E . I 5 SO4 A 1 807 741 SO4 SO4 . J 2 ZN B 1 801 735 ZN ZN . K 5 SO4 B 1 802 736 SO4 SO4 . L 6 HOH A 1 901 742 HOH HOH . L 6 HOH A 2 902 743 HOH HOH . L 6 HOH A 3 903 744 HOH HOH . L 6 HOH A 4 904 745 HOH HOH . L 6 HOH A 5 905 746 HOH HOH . L 6 HOH A 6 906 747 HOH HOH . L 6 HOH A 7 907 748 HOH HOH . L 6 HOH A 8 908 749 HOH HOH . L 6 HOH A 9 909 751 HOH HOH . M 6 HOH B 1 901 737 HOH HOH . M 6 HOH B 2 902 738 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 GOL . . . F 3 2.682 61.133 71.481 1 99.83 ? C1 GOL 804 A 1 HETATM 2 O O1 GOL . . . F 3 2.738 62.341 70.749 1 97.73 ? O1 GOL 804 A 1 HETATM 3 C C2 GOL . . . F 3 4.014 60.81 72.167 1 105 ? C2 GOL 804 A 1 HETATM 4 O O2 GOL . . . F 3 4.389 59.478 71.894 1 113.59 ? O2 GOL 804 A 1 HETATM 5 C C3 GOL . . . F 3 5.132 61.756 71.743 1 104.91 ? C3 GOL 804 A 1 HETATM 6 O O3 GOL . . . F 3 5.149 62.887 72.584 1 112.3 ? O3 GOL 804 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #