data_3ELC # _model_server_result.job_id RclQwBZTc-5BSUyau66LWA _model_server_result.datetime_utc '2024-11-24 20:33:28' _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 3elc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":904}' # _entry.id 3ELC # _exptl.entry_id 3ELC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL DIPHOSPHATE' _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 99.66 _cell.angle_gamma 90 _cell.entry_id 3ELC _cell.length_a 104.676 _cell.length_b 54.833 _cell.length_c 88.506 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ELC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J,K,L,M _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 4 _struct_asym.id J _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 OD2 ASP 14 A ASP 8 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc2 A NE2 HIS 16 A HIS 10 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc3 A ND1 HIS 48 A HIS 42 1_555 D ZN ZN . A ZN 801 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc4 A ND1 HIS 48 A HIS 42 1_555 D ZN ZN . A ZN 801 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 B NE2 HIS 16 B HIS 10 1_555 F ZN ZN . B ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 B ND1 HIS 48 B HIS 42 1_555 F ZN ZN . B ZN 802 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc7 B ND1 HIS 48 B HIS 42 1_555 F ZN ZN . B ZN 802 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 C NE2 HIS 16 C HIS 10 1_555 H ZN ZN . C ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc9 C ND1 HIS 48 C HIS 42 1_555 H ZN ZN . C ZN 803 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc10 C ND1 HIS 48 C HIS 42 1_555 H ZN ZN . C ZN 803 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.222 ? # _chem_comp.formula 'C10 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 GPP sing 160 n n C1 C2 GPP sing 161 n n C1 H11 GPP sing 162 n n C1 H12 GPP sing 163 n n O1 PA GPP sing 164 n n C2 C3 GPP doub 165 e n C2 H2 GPP sing 166 n n C3 C4 GPP sing 167 n n C3 C5 GPP sing 168 n n C4 H41 GPP sing 169 n n C4 H42 GPP sing 170 n n C4 H43 GPP sing 171 n n C5 C6 GPP sing 172 n n C5 H51 GPP sing 173 n n C5 H52 GPP sing 174 n n C6 C7 GPP sing 175 n n C6 H61 GPP sing 176 n n C6 H62 GPP sing 177 n n C7 C8 GPP doub 178 n n C7 H7 GPP sing 179 n n C8 C9 GPP sing 180 n n C8 C10 GPP sing 181 n n C9 H91 GPP sing 182 n n C9 H92 GPP sing 183 n n C9 H93 GPP sing 184 n n C10 H101 GPP sing 185 n n C10 H102 GPP sing 186 n n C10 H103 GPP sing 187 n n PA O1A GPP doub 188 n n PA O2A GPP sing 189 n n PA O3A GPP sing 190 n n O2A HOA2 GPP sing 191 n n O3A PB GPP sing 192 n n PB O1B GPP doub 193 n n PB O2B GPP sing 194 n n PB O3B GPP sing 195 n n O2B HOB2 GPP sing 196 n n O3B HOB3 GPP sing 197 n n # _atom_sites.entry_id 3ELC _atom_sites.fract_transf_matrix[1][1] 0.009553 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001626 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018237 _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] 0.011461 _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 D 2 ZN A 1 801 801 ZN ZN . E 3 F01 A 1 901 901 F01 F01 . F 2 ZN B 1 802 802 ZN ZN . G 3 F01 B 1 902 902 F01 F01 . H 2 ZN C 1 803 803 ZN ZN . I 3 F01 C 1 903 903 F01 F01 . J 4 GPP C 1 904 0 GPP GPP . K 5 HOH A 1 902 902 HOH HOH . K 5 HOH A 2 903 903 HOH HOH . K 5 HOH A 3 904 904 HOH HOH . K 5 HOH A 4 905 905 HOH HOH . K 5 HOH A 5 906 906 HOH HOH . K 5 HOH A 6 907 907 HOH HOH . K 5 HOH A 7 908 908 HOH HOH . K 5 HOH A 8 909 909 HOH HOH . K 5 HOH A 9 910 910 HOH HOH . K 5 HOH A 10 911 911 HOH HOH . K 5 HOH A 11 912 912 HOH HOH . K 5 HOH A 12 913 913 HOH HOH . K 5 HOH A 13 914 914 HOH HOH . K 5 HOH A 14 915 915 HOH HOH . K 5 HOH A 15 916 916 HOH HOH . K 5 HOH A 16 917 917 HOH HOH . K 5 HOH A 17 918 918 HOH HOH . K 5 HOH A 18 919 919 HOH HOH . K 5 HOH A 19 920 920 HOH HOH . K 5 HOH A 20 921 921 HOH HOH . K 5 HOH A 21 922 922 HOH HOH . K 5 HOH A 22 923 923 HOH HOH . K 5 HOH A 23 924 924 HOH HOH . K 5 HOH A 24 925 925 HOH HOH . K 5 HOH A 25 926 926 HOH HOH . K 5 HOH A 26 927 927 HOH HOH . K 5 HOH A 27 928 928 HOH HOH . K 5 HOH A 28 929 929 HOH HOH . K 5 HOH A 29 930 930 HOH HOH . K 5 HOH A 30 931 931 HOH HOH . K 5 HOH A 31 932 932 HOH HOH . K 5 HOH A 32 933 933 HOH HOH . K 5 HOH A 33 934 934 HOH HOH . K 5 HOH A 34 935 935 HOH HOH . K 5 HOH A 35 936 936 HOH HOH . K 5 HOH A 36 937 937 HOH HOH . K 5 HOH A 37 938 938 HOH HOH . L 5 HOH B 1 903 903 HOH HOH . L 5 HOH B 2 904 904 HOH HOH . L 5 HOH B 3 905 905 HOH HOH . L 5 HOH B 4 906 906 HOH HOH . L 5 HOH B 5 907 907 HOH HOH . L 5 HOH B 6 908 908 HOH HOH . L 5 HOH B 7 909 909 HOH HOH . L 5 HOH B 8 910 910 HOH HOH . L 5 HOH B 9 911 911 HOH HOH . L 5 HOH B 10 912 912 HOH HOH . L 5 HOH B 11 913 913 HOH HOH . L 5 HOH B 12 914 914 HOH HOH . L 5 HOH B 13 915 915 HOH HOH . L 5 HOH B 14 916 916 HOH HOH . L 5 HOH B 15 917 917 HOH HOH . L 5 HOH B 16 918 918 HOH HOH . L 5 HOH B 17 919 919 HOH HOH . L 5 HOH B 18 920 920 HOH HOH . L 5 HOH B 19 921 921 HOH HOH . L 5 HOH B 20 922 922 HOH HOH . L 5 HOH B 21 923 923 HOH HOH . L 5 HOH B 22 924 924 HOH HOH . L 5 HOH B 23 925 925 HOH HOH . L 5 HOH B 24 926 926 HOH HOH . L 5 HOH B 25 927 927 HOH HOH . L 5 HOH B 26 928 928 HOH HOH . L 5 HOH B 27 929 929 HOH HOH . L 5 HOH B 28 930 930 HOH HOH . L 5 HOH B 29 931 931 HOH HOH . L 5 HOH B 30 932 932 HOH HOH . L 5 HOH B 31 933 933 HOH HOH . L 5 HOH B 32 934 934 HOH HOH . L 5 HOH B 33 935 935 HOH HOH . L 5 HOH B 34 936 936 HOH HOH . L 5 HOH B 35 937 937 HOH HOH . L 5 HOH B 36 938 938 HOH HOH . M 5 HOH C 1 905 904 HOH HOH . M 5 HOH C 2 906 905 HOH HOH . M 5 HOH C 3 907 906 HOH HOH . M 5 HOH C 4 908 907 HOH HOH . M 5 HOH C 5 909 908 HOH HOH . M 5 HOH C 6 910 909 HOH HOH . M 5 HOH C 7 911 910 HOH HOH . M 5 HOH C 8 912 911 HOH HOH . M 5 HOH C 9 913 912 HOH HOH . M 5 HOH C 10 914 913 HOH HOH . M 5 HOH C 11 915 914 HOH HOH . M 5 HOH C 12 916 915 HOH HOH . M 5 HOH C 13 917 916 HOH HOH . M 5 HOH C 14 918 917 HOH HOH . M 5 HOH C 15 919 918 HOH HOH . M 5 HOH C 16 920 919 HOH HOH . M 5 HOH C 17 921 920 HOH HOH . M 5 HOH C 18 922 921 HOH HOH . M 5 HOH C 19 923 922 HOH HOH . M 5 HOH C 20 924 923 HOH HOH . M 5 HOH C 21 925 924 HOH HOH . M 5 HOH C 22 926 925 HOH HOH . M 5 HOH C 23 927 926 HOH HOH . M 5 HOH C 24 928 927 HOH HOH . M 5 HOH C 25 929 928 HOH HOH . M 5 HOH C 26 930 929 HOH HOH . M 5 HOH C 27 931 930 HOH HOH . M 5 HOH C 28 932 931 HOH HOH . M 5 HOH C 29 933 932 HOH HOH . M 5 HOH C 30 934 933 HOH HOH . M 5 HOH C 31 935 934 HOH HOH . M 5 HOH C 32 936 935 HOH HOH . M 5 HOH C 33 937 936 HOH HOH . M 5 HOH C 34 938 937 HOH HOH . M 5 HOH C 35 939 938 HOH HOH . M 5 HOH C 36 940 939 HOH HOH . M 5 HOH C 37 941 940 HOH HOH . M 5 HOH C 38 942 941 HOH HOH . M 5 HOH C 39 943 942 HOH HOH . M 5 HOH C 40 944 943 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 GPP . . . J 4 42.531 -0.764 27.439 1 73.14 ? C1 GPP 904 C 1 HETATM 2 O O1 GPP . . . J 4 43.641 -1.619 26.916 1 73.32 ? O1 GPP 904 C 1 HETATM 3 C C2 GPP . . . J 4 41.587 -0.438 26.453 1 73.34 ? C2 GPP 904 C 1 HETATM 4 C C3 GPP . . . J 4 40.327 0.168 26.587 1 73.52 ? C3 GPP 904 C 1 HETATM 5 C C4 GPP . . . J 4 39.822 0.603 27.97 1 72.43 ? C4 GPP 904 C 1 HETATM 6 C C5 GPP . . . J 4 39.435 0.451 25.338 1 73.57 ? C5 GPP 904 C 1 HETATM 7 C C6 GPP . . . J 4 38.625 -0.753 24.784 1 73.15 ? C6 GPP 904 C 1 HETATM 8 C C7 GPP . . . J 4 39.501 -1.646 24.165 1 73.68 ? C7 GPP 904 C 1 HETATM 9 C C8 GPP . . . J 4 40.001 -2.839 24.689 1 73.6 ? C8 GPP 904 C 1 HETATM 10 C C9 GPP . . . J 4 40.982 -3.67 23.876 1 73.18 ? C9 GPP 904 C 1 HETATM 11 C C10 GPP . . . J 4 39.582 -3.355 26.072 1 73.7 ? C10 GPP 904 C 1 HETATM 12 P PA GPP . . . J 4 45.083 -0.946 26.466 1 71.29 ? PA GPP 904 C 1 HETATM 13 O O1A GPP . . . J 4 45.022 -0.716 25 1 72.11 ? O1A GPP 904 C 1 HETATM 14 O O2A GPP . . . J 4 45.347 0.168 27.411 1 71.68 ? O2A GPP 904 C 1 HETATM 15 O O3A GPP . . . J 4 46.295 -2.016 26.693 1 66.28 ? O3A GPP 904 C 1 HETATM 16 P PB GPP . . . J 4 47.876 -1.585 26.909 1 61.7 ? PB GPP 904 C 1 HETATM 17 O O1B GPP . . . J 4 48.196 -2.28 28.314 1 60.24 ? O1B GPP 904 C 1 HETATM 18 O O2B GPP . . . J 4 48.692 -2.405 25.794 1 60.92 ? O2B GPP 904 C 1 HETATM 19 O O3B GPP . . . J 4 48.254 -0.146 26.94 1 59.64 ? O3B GPP 904 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 471 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 19 #