data_3K8T # _model_server_result.job_id dT_dLlw_C9B-UGZqwgWEZQ _model_server_result.datetime_utc '2024-12-03 20:22:14' _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":"D","auth_seq_id":891}' # _entry.id 3K8T # _exptl.entry_id 3K8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.254 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-2'-(2-hydroxyethyl)adenosine 5'-(trihydrogen 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 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 4 _struct_asym.id D _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 'C12 H19 N5 O10 P2' _chem_comp.formula_weight 455.254 _chem_comp.id 2A5 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-2'-(2-hydroxyethyl)adenosine 5'-(trihydrogen 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 PA O2A 2A5 sing 1 n n O2A HO2A 2A5 sing 2 n n O1A PA 2A5 doub 3 n n PA O3A 2A5 sing 4 n n PA O5' 2A5 sing 5 n n PB O3A 2A5 sing 6 n n O3B PB 2A5 doub 7 n n O2B PB 2A5 sing 8 n n PB O1B 2A5 sing 9 n n O2B HO2B 2A5 sing 10 n n O1B HO1B 2A5 sing 11 n n O5' C5' 2A5 sing 12 n n C5' C4' 2A5 sing 13 n n C5' H5' 2A5 sing 14 n n C5' "H5'A" 2A5 sing 15 n n O4' C4' 2A5 sing 16 n n C3' C4' 2A5 sing 17 n n C4' H4' 2A5 sing 18 n n C1' O4' 2A5 sing 19 n n N9 C1' 2A5 sing 20 n n C1' C2' 2A5 sing 21 n n C1' H1' 2A5 sing 22 n n C2' C3' 2A5 sing 23 n n C2' C01 2A5 sing 24 n n C2' H2' 2A5 sing 25 n n C01 C02 2A5 sing 26 n n C01 H01 2A5 sing 27 n n C01 H01A 2A5 sing 28 n n C02 O01 2A5 sing 29 n n C02 H02 2A5 sing 30 n n C02 H02A 2A5 sing 31 n n O01 HO01 2A5 sing 32 n n C3' O3' 2A5 sing 33 n n C3' H3' 2A5 sing 34 n n O3' HO3' 2A5 sing 35 n n C8 N9 2A5 sing 36 n y C4 N9 2A5 sing 37 n y N7 C8 2A5 doub 38 n y C8 H8 2A5 sing 39 n n N7 C5 2A5 sing 40 n y C6 C5 2A5 doub 41 n y C5 C4 2A5 sing 42 n y C4 N3 2A5 doub 43 n y N6 C6 2A5 sing 44 n n C6 N1 2A5 sing 45 n y N6 HN6 2A5 sing 46 n n N6 HN6A 2A5 sing 47 n n N1 C2 2A5 doub 48 n y C2 N3 2A5 sing 49 n y C2 H2 2A5 sing 50 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 O O2A 2A5 . . . D 4 26.744 49.364 16.273 1 80 ? O2A 2A5 891 A 1 HETATM 2 P PA 2A5 . . . D 4 25.663 50.249 15.689 1 82.36 ? PA 2A5 891 A 1 HETATM 3 O O1A 2A5 . . . D 4 25.396 50.249 14.192 1 84.03 ? O1A 2A5 891 A 1 HETATM 4 O O3A 2A5 . . . D 4 25.813 51.774 16.242 1 80.24 ? O3A 2A5 891 A 1 HETATM 5 P PB 2A5 . . . D 4 27.086 52.796 16.207 1 79.35 ? PB 2A5 891 A 1 HETATM 6 O O2B 2A5 . . . D 4 26.497 54.029 15.537 1 80.56 ? O2B 2A5 891 A 1 HETATM 7 O O1B 2A5 . . . D 4 27.409 52.963 17.675 1 76.75 ? O1B 2A5 891 A 1 HETATM 8 O O3B 2A5 . . . D 4 28.204 52.204 15.365 1 79.74 ? O3B 2A5 891 A 1 HETATM 9 O O5' 2A5 . . . D 4 24.26 49.824 16.329 1 82.17 ? O5' 2A5 891 A 1 HETATM 10 C C5' 2A5 . . . D 4 24.231 49.612 17.729 1 81.84 ? C5' 2A5 891 A 1 HETATM 11 C C4' 2A5 . . . D 4 22.901 50.065 18.308 1 81.82 ? C4' 2A5 891 A 1 HETATM 12 O O4' 2A5 . . . D 4 22.437 51.308 17.77 1 82.26 ? O4' 2A5 891 A 1 HETATM 13 C C1' 2A5 . . . D 4 20.993 51.317 17.746 1 82.5 ? C1' 2A5 891 A 1 HETATM 14 C C2' 2A5 . . . D 4 20.521 49.872 17.942 1 79.32 ? C2' 2A5 891 A 1 HETATM 15 C C01 2A5 . . . D 4 19.595 49.835 19.147 1 77.25 ? C01 2A5 891 A 1 HETATM 16 C C02 2A5 . . . D 4 18.851 48.536 19.394 1 75.65 ? C02 2A5 891 A 1 HETATM 17 O O01 2A5 . . . D 4 17.534 48.754 19.92 1 71.86 ? O01 2A5 891 A 1 HETATM 18 C C3' 2A5 . . . D 4 21.813 49.046 18.045 1 81.06 ? C3' 2A5 891 A 1 HETATM 19 O O3' 2A5 . . . D 4 21.898 48.06 19.084 1 80.64 ? O3' 2A5 891 A 1 HETATM 20 N N9 2A5 . . . D 4 20.525 51.935 16.468 1 83.13 ? N9 2A5 891 A 1 HETATM 21 C C8 2A5 . . . D 4 20.954 51.581 15.235 1 83.24 ? C8 2A5 891 A 1 HETATM 22 N N7 2A5 . . . D 4 20.369 52.34 14.278 1 83.41 ? N7 2A5 891 A 1 HETATM 23 C C5 2A5 . . . D 4 19.548 53.207 14.901 1 83.01 ? C5 2A5 891 A 1 HETATM 24 C C4 2A5 . . . D 4 19.654 52.947 16.346 1 83.54 ? C4 2A5 891 A 1 HETATM 25 C C6 2A5 . . . D 4 18.622 54.28 14.478 1 83.72 ? C6 2A5 891 A 1 HETATM 26 N N6 2A5 . . . D 4 18.487 54.557 13.16 1 83.26 ? N6 2A5 891 A 1 HETATM 27 N N1 2A5 . . . D 4 17.934 54.968 15.435 1 83.37 ? N1 2A5 891 A 1 HETATM 28 C C2 2A5 . . . D 4 18.081 54.684 16.744 1 83.08 ? C2 2A5 891 A 1 HETATM 29 N N3 2A5 . . . D 4 18.907 53.708 17.189 1 83.24 ? N3 2A5 891 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 77 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #