data_6PD8 # _model_server_result.job_id Zk9cbZSLKUEh3IXDIdDzMA _model_server_result.datetime_utc '2024-11-26 05:37:58' _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 6pd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":804}' # _entry.id 6PD8 # _exptl.entry_id 6PD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 6PD8 _cell.length_a 46.067 _cell.length_b 56.656 _cell.length_c 123.041 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 4 D N N ? 4 E 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 HIS 97 A HIS 603 1_555 A N ALY 98 A ALY 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C ALY 98 A ALY 604 1_555 A N THR 99 A THR 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A SG CYS 34 A CYS 540 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc2 A SG CYS 37 A CYS 543 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 A NE2 HIS 50 A HIS 556 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc4 A SG CYS 54 A CYS 560 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? # _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 157 n n C1 C2 GOL sing 158 n n C1 H11 GOL sing 159 n n C1 H12 GOL sing 160 n n O1 HO1 GOL sing 161 n n C2 O2 GOL sing 162 n n C2 C3 GOL sing 163 n n C2 H2 GOL sing 164 n n O2 HO2 GOL sing 165 n n C3 O3 GOL sing 166 n n C3 H31 GOL sing 167 n n C3 H32 GOL sing 168 n n O3 HO3 GOL sing 169 n n # _atom_sites.entry_id 6PD8 _atom_sites.fract_transf_matrix[1][1] 0.021708 _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] 0.01765 _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] 0.008127 _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 B 2 ZN A 1 801 506 ZN ZN . C 3 NA A 1 802 507 NA NA . D 4 GOL A 1 803 510 GOL GOL . E 4 GOL A 1 804 511 GOL GOL . F 5 O9D A 1 805 506 O9D LIG . G 6 HOH A 1 901 39 HOH HOH . G 6 HOH A 2 902 1 HOH HOH . G 6 HOH A 3 903 14 HOH HOH . G 6 HOH A 4 904 32 HOH HOH . G 6 HOH A 5 905 7 HOH HOH . G 6 HOH A 6 906 41 HOH HOH . G 6 HOH A 7 907 18 HOH HOH . G 6 HOH A 8 908 42 HOH HOH . G 6 HOH A 9 909 8 HOH HOH . G 6 HOH A 10 910 12 HOH HOH . G 6 HOH A 11 911 15 HOH HOH . G 6 HOH A 12 912 29 HOH HOH . G 6 HOH A 13 913 35 HOH HOH . G 6 HOH A 14 914 2 HOH HOH . G 6 HOH A 15 915 21 HOH HOH . G 6 HOH A 16 916 33 HOH HOH . G 6 HOH A 17 917 4 HOH HOH . G 6 HOH A 18 918 16 HOH HOH . G 6 HOH A 19 919 10 HOH HOH . G 6 HOH A 20 920 19 HOH HOH . G 6 HOH A 21 921 6 HOH HOH . G 6 HOH A 22 922 13 HOH HOH . G 6 HOH A 23 923 20 HOH HOH . G 6 HOH A 24 924 43 HOH HOH . G 6 HOH A 25 925 37 HOH HOH . G 6 HOH A 26 926 40 HOH HOH . G 6 HOH A 27 927 44 HOH HOH . G 6 HOH A 28 928 22 HOH HOH . G 6 HOH A 29 929 28 HOH HOH . G 6 HOH A 30 930 38 HOH HOH . G 6 HOH A 31 931 27 HOH HOH . G 6 HOH A 32 932 25 HOH HOH . G 6 HOH A 33 933 30 HOH HOH . G 6 HOH A 34 934 26 HOH HOH . G 6 HOH A 35 935 31 HOH HOH . G 6 HOH A 36 936 23 HOH HOH . G 6 HOH A 37 937 34 HOH HOH . G 6 HOH A 38 938 45 HOH HOH . G 6 HOH A 39 939 17 HOH HOH . G 6 HOH A 40 940 36 HOH HOH . G 6 HOH A 41 941 24 HOH HOH . G 6 HOH A 42 942 11 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 . . . E 4 -9.6 -24.135 -39.199 1 62.19 ? C1 GOL 804 A 1 HETATM 2 O O1 GOL . . . E 4 -8.218 -23.948 -39.419 1 54.33 ? O1 GOL 804 A 1 HETATM 3 C C2 GOL . . . E 4 -9.828 -24.677 -37.789 1 66.05 ? C2 GOL 804 A 1 HETATM 4 O O2 GOL . . . E 4 -9.537 -23.661 -36.854 1 63.45 ? O2 GOL 804 A 1 HETATM 5 C C3 GOL . . . E 4 -11.265 -25.189 -37.626 1 56.06 ? C3 GOL 804 A 1 HETATM 6 O O3 GOL . . . E 4 -11.486 -25.706 -36.328 1 57.23 ? O3 GOL 804 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 446 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #