data_3K8T # _model_server_result.job_id b1aKKCToQ-vLoGsZgdZyig _model_server_result.datetime_utc '2024-10-14 04:28:35' _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 3k8t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":890}' # _entry.id 3K8T # _exptl.entry_id 3K8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 3K8T _cell.length_a 107.528 _cell.length_b 116.915 _cell.length_c 64.065 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K8T _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 1,2 # 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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 116.915 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 B MG MG . A MG 889 1_555 C O1G DGT . A DGT 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc2 B MG MG . A MG 889 1_555 C O1B DGT . A DGT 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 B MG MG . A MG 889 1_555 C O1A DGT . A DGT 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 B MG MG . A MG 889 1_555 F O HOH . A HOH 942 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc5 B MG MG . A MG 889 1_555 F O HOH . A HOH 948 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id DGT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G DGT sing 133 n n PG O2G DGT sing 134 n n O1G HO1G DGT sing 135 n n O2G HO2G DGT sing 136 n n O3G PG DGT doub 137 n n O3B PG DGT sing 138 n n PB O3B DGT sing 139 n n PB O1B DGT sing 140 n n PB O3A DGT sing 141 n n O1B HO1B DGT sing 142 n n O2B PB DGT doub 143 n n PA O3A DGT sing 144 n n PA O1A DGT sing 145 n n O1A HO1A DGT sing 146 n n O2A PA DGT doub 147 n n O5' PA DGT sing 148 n n O5' C5' DGT sing 149 n n C5' H5' DGT sing 150 n n C5' "H5'A" DGT sing 151 n n C4' C5' DGT sing 152 n n C4' H4' DGT sing 153 n n O4' C4' DGT sing 154 n n C3' C4' DGT sing 155 n n C3' O3' DGT sing 156 n n C3' H3' DGT sing 157 n n O3' HO3' DGT sing 158 n n C2' C3' DGT sing 159 n n C2' C1' DGT sing 160 n n C2' H2' DGT sing 161 n n C2' "H2'A" DGT sing 162 n n C1' O4' DGT sing 163 n n C1' H1' DGT sing 164 n n N9 C1' DGT sing 165 n n N9 C4 DGT sing 166 n y C8 N9 DGT sing 167 n y C8 H8 DGT sing 168 n n N7 C8 DGT doub 169 n y N7 C5 DGT sing 170 n y C5 C6 DGT sing 171 n n C5 C4 DGT doub 172 n y C6 N1 DGT sing 173 n n O6 C6 DGT doub 174 n n N1 C2 DGT sing 175 n n C2 N3 DGT doub 176 n n C2 N2 DGT sing 177 n n N2 HN2 DGT sing 178 n n N2 HN2A DGT sing 179 n n C4 N3 DGT sing 180 n n N1 H16 DGT sing 181 n n # _atom_sites.entry_id 3K8T _atom_sites.fract_transf_matrix[1][1] 0.0093 _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] 0.008553 _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] 0.015609 _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 MG A 1 889 889 MG MG . C 3 DGT A 1 890 890 DGT DGT . D 4 2A5 A 1 891 891 2A5 2A5 . E 5 GOL A 1 892 892 GOL GOL . F 6 HOH A 1 893 893 HOH HOH . F 6 HOH A 2 894 894 HOH HOH . F 6 HOH A 3 895 895 HOH HOH . F 6 HOH A 4 896 896 HOH HOH . F 6 HOH A 5 897 897 HOH HOH . F 6 HOH A 6 898 898 HOH HOH . F 6 HOH A 7 899 899 HOH HOH . F 6 HOH A 8 900 900 HOH HOH . F 6 HOH A 9 901 901 HOH HOH . F 6 HOH A 10 902 902 HOH HOH . F 6 HOH A 11 903 903 HOH HOH . F 6 HOH A 12 904 904 HOH HOH . F 6 HOH A 13 905 905 HOH HOH . F 6 HOH A 14 906 906 HOH HOH . F 6 HOH A 15 907 907 HOH HOH . F 6 HOH A 16 908 908 HOH HOH . F 6 HOH A 17 909 909 HOH HOH . F 6 HOH A 18 910 910 HOH HOH . F 6 HOH A 19 911 911 HOH HOH . F 6 HOH A 20 912 912 HOH HOH . F 6 HOH A 21 913 913 HOH HOH . F 6 HOH A 22 914 914 HOH HOH . F 6 HOH A 23 915 915 HOH HOH . F 6 HOH A 24 916 916 HOH HOH . F 6 HOH A 25 917 917 HOH HOH . F 6 HOH A 26 918 918 HOH HOH . F 6 HOH A 27 919 919 HOH HOH . F 6 HOH A 28 920 920 HOH HOH . F 6 HOH A 29 921 921 HOH HOH . F 6 HOH A 30 922 922 HOH HOH . F 6 HOH A 31 923 923 HOH HOH . F 6 HOH A 32 924 924 HOH HOH . F 6 HOH A 33 925 925 HOH HOH . F 6 HOH A 34 926 926 HOH HOH . F 6 HOH A 35 927 927 HOH HOH . F 6 HOH A 36 928 928 HOH HOH . F 6 HOH A 37 929 929 HOH HOH . F 6 HOH A 38 930 930 HOH HOH . F 6 HOH A 39 931 931 HOH HOH . F 6 HOH A 40 932 932 HOH HOH . F 6 HOH A 41 933 933 HOH HOH . F 6 HOH A 42 934 934 HOH HOH . F 6 HOH A 43 935 935 HOH HOH . F 6 HOH A 44 936 936 HOH HOH . F 6 HOH A 45 937 937 HOH HOH . F 6 HOH A 46 938 938 HOH HOH . F 6 HOH A 47 939 939 HOH HOH . F 6 HOH A 48 940 940 HOH HOH . F 6 HOH A 49 941 941 HOH HOH . F 6 HOH A 50 942 942 HOH HOH . F 6 HOH A 51 943 943 HOH HOH . F 6 HOH A 52 944 944 HOH HOH . F 6 HOH A 53 945 945 HOH HOH . F 6 HOH A 54 946 946 HOH HOH . F 6 HOH A 55 947 947 HOH HOH . F 6 HOH A 56 948 948 HOH HOH . F 6 HOH A 57 949 949 HOH HOH . F 6 HOH A 58 950 950 HOH HOH . F 6 HOH A 59 951 951 HOH HOH . F 6 HOH A 60 952 952 HOH HOH . F 6 HOH A 61 953 953 HOH HOH . F 6 HOH A 62 954 954 HOH HOH . F 6 HOH A 63 955 955 HOH HOH . F 6 HOH A 64 956 956 HOH HOH . F 6 HOH A 65 957 957 HOH HOH . F 6 HOH A 66 958 958 HOH HOH . F 6 HOH A 67 959 959 HOH HOH . F 6 HOH A 68 960 960 HOH HOH . F 6 HOH A 69 961 961 HOH HOH . F 6 HOH A 70 962 962 HOH HOH . F 6 HOH A 71 963 963 HOH HOH . F 6 HOH A 72 964 964 HOH HOH . F 6 HOH A 73 965 965 HOH HOH . F 6 HOH A 74 966 966 HOH HOH . F 6 HOH A 75 967 967 HOH HOH . F 6 HOH A 76 968 968 HOH HOH . F 6 HOH A 77 969 969 HOH HOH . F 6 HOH A 78 970 970 HOH HOH . F 6 HOH A 79 971 971 HOH HOH . F 6 HOH A 80 972 972 HOH HOH . F 6 HOH A 81 973 973 HOH HOH . F 6 HOH A 82 974 974 HOH HOH . F 6 HOH A 83 975 975 HOH HOH . F 6 HOH A 84 976 976 HOH HOH . F 6 HOH A 85 977 977 HOH HOH . F 6 HOH A 86 978 978 HOH HOH . F 6 HOH A 87 979 979 HOH HOH . F 6 HOH A 88 980 980 HOH HOH . F 6 HOH A 89 981 981 HOH HOH . F 6 HOH A 90 982 982 HOH HOH . F 6 HOH A 91 983 983 HOH HOH . F 6 HOH A 92 984 984 HOH HOH . F 6 HOH A 93 985 985 HOH HOH . F 6 HOH A 94 986 986 HOH HOH . F 6 HOH A 95 987 987 HOH HOH . F 6 HOH A 96 988 988 HOH HOH . F 6 HOH A 97 989 989 HOH HOH . F 6 HOH A 98 990 990 HOH HOH . F 6 HOH A 99 991 991 HOH HOH . F 6 HOH A 100 992 992 HOH HOH . F 6 HOH A 101 993 993 HOH HOH . F 6 HOH A 102 994 994 HOH HOH . F 6 HOH A 103 995 995 HOH HOH . F 6 HOH A 104 996 996 HOH HOH . F 6 HOH A 105 997 997 HOH HOH . F 6 HOH A 106 998 998 HOH HOH . F 6 HOH A 107 999 999 HOH HOH . F 6 HOH A 108 1000 1000 HOH HOH . F 6 HOH A 109 1001 1001 HOH HOH . F 6 HOH A 110 1002 1002 HOH HOH . F 6 HOH A 111 1003 1003 HOH HOH . F 6 HOH A 112 1004 1004 HOH HOH . F 6 HOH A 113 1005 1005 HOH HOH . F 6 HOH A 114 1006 1006 HOH HOH . F 6 HOH A 115 1007 1007 HOH HOH . F 6 HOH A 116 1008 1008 HOH HOH . F 6 HOH A 117 1009 1009 HOH HOH . F 6 HOH A 118 1010 1010 HOH HOH . F 6 HOH A 119 1011 1011 HOH HOH . F 6 HOH A 120 1012 1012 HOH HOH . F 6 HOH A 121 1013 1013 HOH HOH . F 6 HOH A 122 1014 1014 HOH HOH . F 6 HOH A 123 1015 1015 HOH HOH . F 6 HOH A 124 1016 1016 HOH HOH . F 6 HOH A 125 1017 1017 HOH HOH . F 6 HOH A 126 1018 1018 HOH HOH . F 6 HOH A 127 1019 1019 HOH HOH . F 6 HOH A 128 1020 1020 HOH HOH . F 6 HOH A 129 1021 1021 HOH HOH . F 6 HOH A 130 1022 1022 HOH HOH . F 6 HOH A 131 1023 1023 HOH HOH . F 6 HOH A 132 1024 1024 HOH HOH . F 6 HOH A 133 1025 1025 HOH HOH . F 6 HOH A 134 1026 1026 HOH HOH . F 6 HOH A 135 1027 1027 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 P PG DGT . . . C 3 -12.364 44.521 26.271 1 49.73 ? PG DGT 890 A 1 HETATM 2 O O1G DGT . . . C 3 -10.895 44.531 26.648 1 48.6 ? O1G DGT 890 A 1 HETATM 3 O O2G DGT . . . C 3 -12.987 44.258 27.622 1 46.79 ? O2G DGT 890 A 1 HETATM 4 O O3G DGT . . . C 3 -12.646 43.543 25.221 1 43.87 ? O3G DGT 890 A 1 HETATM 5 O O3B DGT . . . C 3 -12.96 45.912 25.731 1 45.27 ? O3B DGT 890 A 1 HETATM 6 P PB DGT . . . C 3 -12.382 47.354 26.131 1 47.54 ? PB DGT 890 A 1 HETATM 7 O O1B DGT . . . C 3 -11.647 47.249 27.455 1 39.63 ? O1B DGT 890 A 1 HETATM 8 O O2B DGT . . . C 3 -13.431 48.414 26.275 1 48.47 ? O2B DGT 890 A 1 HETATM 9 O O3A DGT . . . C 3 -11.314 47.659 24.911 1 44.11 ? O3A DGT 890 A 1 HETATM 10 P PA DGT . . . C 3 -9.732 48.069 25.104 1 41.7 ? PA DGT 890 A 1 HETATM 11 O O1A DGT . . . C 3 -9.104 47.316 26.211 1 37.86 ? O1A DGT 890 A 1 HETATM 12 O O2A DGT . . . C 3 -9.441 49.514 25.241 1 37.91 ? O2A DGT 890 A 1 HETATM 13 O O5' DGT . . . C 3 -9.094 47.538 23.719 1 36.75 ? O5' DGT 890 A 1 HETATM 14 C C5' DGT . . . C 3 -8.983 46.166 23.483 1 38.64 ? C5' DGT 890 A 1 HETATM 15 C C4' DGT . . . C 3 -8.345 45.897 22.132 1 40.73 ? C4' DGT 890 A 1 HETATM 16 O O4' DGT . . . C 3 -9.202 46.403 21.15 1 40.89 ? O4' DGT 890 A 1 HETATM 17 C C3' DGT . . . C 3 -7.017 46.56 21.956 1 40.46 ? C3' DGT 890 A 1 HETATM 18 O O3' DGT . . . C 3 -6.134 45.757 21.179 1 40.27 ? O3' DGT 890 A 1 HETATM 19 C C2' DGT . . . C 3 -7.379 47.848 21.251 1 40.56 ? C2' DGT 890 A 1 HETATM 20 C C1' DGT . . . C 3 -8.612 47.463 20.459 1 43.87 ? C1' DGT 890 A 1 HETATM 21 N N9 DGT . . . C 3 -9.577 48.558 20.301 1 44.18 ? N9 DGT 890 A 1 HETATM 22 C C8 DGT . . . C 3 -10.424 49.032 21.294 1 45.78 ? C8 DGT 890 A 1 HETATM 23 N N7 DGT . . . C 3 -11.148 50.054 20.793 1 42.23 ? N7 DGT 890 A 1 HETATM 24 C C5 DGT . . . C 3 -10.788 50.2 19.496 1 45.62 ? C5 DGT 890 A 1 HETATM 25 C C6 DGT . . . C 3 -11.217 51.108 18.548 1 45.08 ? C6 DGT 890 A 1 HETATM 26 O O6 DGT . . . C 3 -12.113 51.913 18.831 1 46.2 ? O6 DGT 890 A 1 HETATM 27 N N1 DGT . . . C 3 -10.688 51.072 17.301 1 45.13 ? N1 DGT 890 A 1 HETATM 28 C C2 DGT . . . C 3 -9.73 50.163 16.993 1 45.01 ? C2 DGT 890 A 1 HETATM 29 N N2 DGT . . . C 3 -9.268 50.177 15.76 1 46.94 ? N2 DGT 890 A 1 HETATM 30 N N3 DGT . . . C 3 -9.277 49.25 17.909 1 45.82 ? N3 DGT 890 A 1 HETATM 31 C C4 DGT . . . C 3 -9.797 49.295 19.17 1 43.81 ? C4 DGT 890 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #