data_3ESJ # _model_server_result.job_id 5-f55RtHrzWJFQnyXILhQA _model_server_result.datetime_utc '2024-11-22 10:58:45' _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 3esj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":904}' # _entry.id 3ESJ # _exptl.entry_id 3ESJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 3ESJ _cell.length_a 144.498 _cell.length_b 144.498 _cell.length_c 144.498 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ESJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 A NE2 HIS 16 A HIS 10 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc3 A ND1 HIS 48 A HIS 42 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 A OE1 GLU 155 A GLU 149 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc5 A OE2 GLU 155 A GLU 149 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc6 B ZN ZN . A ZN 900 1_555 F O HOH . A HOH 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? # _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 163 n n C1 C2 GPP sing 164 n n C1 H11 GPP sing 165 n n C1 H12 GPP sing 166 n n O1 PA GPP sing 167 n n C2 C3 GPP doub 168 e n C2 H2 GPP sing 169 n n C3 C4 GPP sing 170 n n C3 C5 GPP sing 171 n n C4 H41 GPP sing 172 n n C4 H42 GPP sing 173 n n C4 H43 GPP sing 174 n n C5 C6 GPP sing 175 n n C5 H51 GPP sing 176 n n C5 H52 GPP sing 177 n n C6 C7 GPP sing 178 n n C6 H61 GPP sing 179 n n C6 H62 GPP sing 180 n n C7 C8 GPP doub 181 n n C7 H7 GPP sing 182 n n C8 C9 GPP sing 183 n n C8 C10 GPP sing 184 n n C9 H91 GPP sing 185 n n C9 H92 GPP sing 186 n n C9 H93 GPP sing 187 n n C10 H101 GPP sing 188 n n C10 H102 GPP sing 189 n n C10 H103 GPP sing 190 n n PA O1A GPP doub 191 n n PA O2A GPP sing 192 n n PA O3A GPP sing 193 n n O2A HOA2 GPP sing 194 n n O3A PB GPP sing 195 n n PB O1B GPP doub 196 n n PB O2B GPP sing 197 n n PB O3B GPP sing 198 n n O2B HOB2 GPP sing 199 n n O3B HOB3 GPP sing 200 n n # _atom_sites.entry_id 3ESJ _atom_sites.fract_transf_matrix[1][1] 0.006921 _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] 0.006921 _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] 0.006921 _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 1 900 900 ZN ZN . C 3 CC7 A 1 901 901 CC7 CC7 . D 4 MG A 1 903 903 MG MG . E 5 GPP A 1 904 904 GPP GPP . F 6 HOH A 1 905 905 HOH HOH . F 6 HOH A 2 906 906 HOH HOH . F 6 HOH A 3 907 907 HOH HOH . F 6 HOH A 4 908 908 HOH HOH . F 6 HOH A 5 909 909 HOH HOH . F 6 HOH A 6 910 910 HOH HOH . F 6 HOH A 7 911 911 HOH HOH . F 6 HOH A 8 912 912 HOH HOH . F 6 HOH A 9 913 913 HOH HOH . F 6 HOH A 10 914 914 HOH HOH . F 6 HOH A 11 915 915 HOH HOH . F 6 HOH A 12 916 916 HOH HOH . F 6 HOH A 13 917 917 HOH HOH . F 6 HOH A 14 918 918 HOH HOH . F 6 HOH A 15 919 919 HOH HOH . F 6 HOH A 16 920 920 HOH HOH . F 6 HOH A 17 921 921 HOH HOH . F 6 HOH A 18 922 922 HOH HOH . F 6 HOH A 19 923 923 HOH HOH . F 6 HOH A 20 924 924 HOH HOH . F 6 HOH A 21 925 925 HOH HOH . F 6 HOH A 22 926 926 HOH HOH . F 6 HOH A 23 927 927 HOH HOH . F 6 HOH A 24 928 928 HOH HOH . F 6 HOH A 25 929 929 HOH HOH . F 6 HOH A 26 930 930 HOH HOH . F 6 HOH A 27 931 931 HOH HOH . F 6 HOH A 28 932 932 HOH HOH . F 6 HOH A 29 933 933 HOH HOH . F 6 HOH A 30 934 934 HOH HOH . F 6 HOH A 31 935 935 HOH HOH . F 6 HOH A 32 936 936 HOH HOH . F 6 HOH A 33 937 937 HOH HOH . F 6 HOH A 34 938 938 HOH HOH . F 6 HOH A 35 939 939 HOH HOH . F 6 HOH A 36 940 940 HOH HOH . F 6 HOH A 37 941 941 HOH HOH . F 6 HOH A 38 942 942 HOH HOH . F 6 HOH A 39 943 943 HOH HOH . F 6 HOH A 40 944 944 HOH HOH . F 6 HOH A 41 945 945 HOH HOH . F 6 HOH A 42 946 946 HOH HOH . F 6 HOH A 43 947 947 HOH HOH . F 6 HOH A 44 948 948 HOH HOH . F 6 HOH A 45 949 949 HOH HOH . F 6 HOH A 46 950 950 HOH HOH . F 6 HOH A 47 951 951 HOH HOH . F 6 HOH A 48 952 952 HOH HOH . F 6 HOH A 49 953 953 HOH HOH . F 6 HOH A 50 954 954 HOH HOH . F 6 HOH A 51 955 955 HOH HOH . F 6 HOH A 52 956 956 HOH HOH . F 6 HOH A 53 957 957 HOH HOH . F 6 HOH A 54 958 958 HOH HOH . F 6 HOH A 55 959 959 HOH HOH . F 6 HOH A 56 960 960 HOH HOH . F 6 HOH A 57 961 961 HOH HOH . F 6 HOH A 58 962 962 HOH HOH . F 6 HOH A 59 963 963 HOH HOH . F 6 HOH A 60 964 964 HOH HOH . F 6 HOH A 61 965 965 HOH HOH . F 6 HOH A 62 966 966 HOH HOH . F 6 HOH A 63 967 967 HOH HOH . F 6 HOH A 64 968 968 HOH HOH . F 6 HOH A 65 969 969 HOH HOH . F 6 HOH A 66 970 970 HOH HOH . F 6 HOH A 67 971 971 HOH HOH . F 6 HOH A 68 972 972 HOH HOH . F 6 HOH A 69 973 973 HOH HOH . F 6 HOH A 70 974 974 HOH HOH . F 6 HOH A 71 975 975 HOH HOH . F 6 HOH A 72 976 976 HOH HOH . F 6 HOH A 73 977 977 HOH HOH . F 6 HOH A 74 978 978 HOH HOH . F 6 HOH A 75 979 979 HOH HOH . F 6 HOH A 76 980 980 HOH HOH . F 6 HOH A 77 981 981 HOH HOH . F 6 HOH A 78 982 982 HOH HOH . F 6 HOH A 79 983 983 HOH HOH . F 6 HOH A 80 984 984 HOH HOH . F 6 HOH A 81 985 985 HOH HOH . F 6 HOH A 82 986 986 HOH HOH . F 6 HOH A 83 987 987 HOH HOH . F 6 HOH A 84 988 988 HOH HOH . F 6 HOH A 85 989 989 HOH HOH . F 6 HOH A 86 990 990 HOH HOH . F 6 HOH A 87 991 991 HOH HOH . F 6 HOH A 88 992 992 HOH HOH . F 6 HOH A 89 993 993 HOH HOH . F 6 HOH A 90 994 994 HOH HOH . F 6 HOH A 91 995 995 HOH HOH . F 6 HOH A 92 996 996 HOH HOH . F 6 HOH A 93 997 997 HOH HOH . F 6 HOH A 94 998 998 HOH HOH . F 6 HOH A 95 999 999 HOH HOH . F 6 HOH A 96 1000 1000 HOH HOH . F 6 HOH A 97 1001 1001 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 . . . E 5 11.296 14.145 13.1 0.33 51.09 ? C1 GPP 904 A 1 HETATM 2 O O1 GPP . . . E 5 11.765 13.51 11.93 0.33 49.86 ? O1 GPP 904 A 1 HETATM 3 C C2 GPP . . . E 5 12.322 15.115 13.608 0.33 52.81 ? C2 GPP 904 A 1 HETATM 4 C C3 GPP . . . E 5 12.233 16.409 13.298 1 54.67 ? C3 GPP 904 A 1 HETATM 5 C C4 GPP . . . E 5 11.118 16.873 12.4 1 55.95 ? C4 GPP 904 A 1 HETATM 6 C C5 GPP . . . E 5 12.553 17.401 14.378 1 56.93 ? C5 GPP 904 A 1 HETATM 7 C C6 GPP . . . E 5 13.718 16.96 15.214 1 60.18 ? C6 GPP 904 A 1 HETATM 8 C C7 GPP . . . E 5 13.73 17.978 16.31 1 65.64 ? C7 GPP 904 A 1 HETATM 9 C C8 GPP . . . E 5 14.88 18.603 16.621 1 69.99 ? C8 GPP 904 A 1 HETATM 10 C C9 GPP . . . E 5 16.138 18.281 15.89 1 71.32 ? C9 GPP 904 A 1 HETATM 11 C C10 GPP . . . E 5 14.98 19.636 17.706 1 71.53 ? C10 GPP 904 A 1 HETATM 12 P PA GPP . . . E 5 12.58 12.133 12.037 0.33 48.91 ? PA GPP 904 A 1 HETATM 13 O O1A GPP . . . E 5 13.64 12.131 10.859 0.33 48.71 ? O1A GPP 904 A 1 HETATM 14 O O2A GPP . . . E 5 13.313 12.005 13.446 0.33 49.06 ? O2A GPP 904 A 1 HETATM 15 O O3A GPP . . . E 5 11.443 10.988 11.921 0.33 47.51 ? O3A GPP 904 A 1 HETATM 16 P PB GPP . . . E 5 10.66 10.557 10.582 0.33 45.51 ? PB GPP 904 A 1 HETATM 17 O O1B GPP . . . E 5 11.67 10.338 9.386 0.33 45.58 ? O1B GPP 904 A 1 HETATM 18 O O2B GPP . . . E 5 9.924 9.194 10.892 0.33 45.62 ? O2B GPP 904 A 1 HETATM 19 O O3B GPP . . . E 5 9.577 11.635 10.162 0.33 45.34 ? O3B GPP 904 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #