data_3CI3 # _model_server_result.job_id mryLoEMOoOltbwRcmqvbFQ _model_server_result.datetime_utc '2024-10-14 07:28:35' _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 3ci3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":902}' # _entry.id 3CI3 # _exptl.entry_id 3CI3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXYADENOSINE" _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 120 _cell.entry_id 3CI3 _cell.length_a 67.965 _cell.length_b 67.965 _cell.length_c 110.941 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 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,G _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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 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 O ILE 9 A ILE 3 1_555 B NA NA . A NA 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc2 B NA NA . A NA 189 1_555 D O1G 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc3 B NA NA . A NA 189 1_555 D O2A 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc4 B NA NA . A NA 189 1_555 D O1A 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc5 C MG MG . A MG 190 1_555 D O3G 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 C MG MG . A MG 190 1_555 D O1B 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc7 C MG MG . A MG 190 1_555 D O1A 3PO . A 3PO 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc8 C MG MG . A MG 190 1_555 G O HOH . A HOH 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc9 C MG MG . A MG 190 1_555 G O HOH . A HOH 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc10 F CO B12 . A B12 800 1_555 E C5' 5AD . A 5AD 902 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.05 ? metalc ? metalc11 F CO B12 . A B12 800 1_555 G O HOH . A HOH 1073 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.645 ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 5AD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXYADENOSINE" _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 N1 C2 5AD doub 18 n y N1 C6 5AD sing 19 n y C2 N3 5AD sing 20 n y C2 H2 5AD sing 21 n n N3 C4 5AD doub 22 n y C4 N9 5AD sing 23 n y C4 C5 5AD sing 24 n y N9 C8 5AD sing 25 n y N9 C1' 5AD sing 26 n n C8 N7 5AD doub 27 n y C8 H8 5AD sing 28 n n N7 C5 5AD sing 29 n y C5 C6 5AD doub 30 n y C6 N6 5AD sing 31 n n N6 HN61 5AD sing 32 n n N6 HN62 5AD sing 33 n n C1' C2' 5AD sing 34 n n C1' O4' 5AD sing 35 n n C1' H1' 5AD sing 36 n n C2' C3' 5AD sing 37 n n C2' O2' 5AD sing 38 n n C2' H2' 5AD sing 39 n n C3' C4' 5AD sing 40 n n C3' O3' 5AD sing 41 n n C3' H3' 5AD sing 42 n n C4' C5' 5AD sing 43 n n C4' O4' 5AD sing 44 n n C4' H4' 5AD sing 45 n n C5' "H5'1" 5AD sing 46 n n C5' "H5'2" 5AD sing 47 n n C5' "H5'3" 5AD sing 48 n n O2' HO2' 5AD sing 49 n n O3' HO3' 5AD sing 50 n n # _atom_sites.entry_id 3CI3 _atom_sites.fract_transf_matrix[1][1] 0.014713 _atom_sites.fract_transf_matrix[1][2] 0.008495 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01699 _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] 0.009014 _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 NA A 1 189 189 NA NA . C 3 MG A 1 190 190 MG MG . D 4 3PO A 1 901 901 3PO 3PO . E 5 5AD A 1 902 902 5AD 5AD . F 6 B12 A 1 800 800 B12 B12 . G 7 HOH A 1 903 903 HOH HOH . G 7 HOH A 2 904 904 HOH HOH . G 7 HOH A 3 905 905 HOH HOH . G 7 HOH A 4 906 906 HOH HOH . G 7 HOH A 5 907 907 HOH HOH . G 7 HOH A 6 908 908 HOH HOH . G 7 HOH A 7 909 909 HOH HOH . G 7 HOH A 8 910 910 HOH HOH . G 7 HOH A 9 911 911 HOH HOH . G 7 HOH A 10 912 912 HOH HOH . G 7 HOH A 11 913 913 HOH HOH . G 7 HOH A 12 914 914 HOH HOH . G 7 HOH A 13 915 915 HOH HOH . G 7 HOH A 14 916 916 HOH HOH . G 7 HOH A 15 917 917 HOH HOH . G 7 HOH A 16 918 918 HOH HOH . G 7 HOH A 17 919 919 HOH HOH . G 7 HOH A 18 920 920 HOH HOH . G 7 HOH A 19 921 921 HOH HOH . G 7 HOH A 20 922 922 HOH HOH . G 7 HOH A 21 923 923 HOH HOH . G 7 HOH A 22 924 924 HOH HOH . G 7 HOH A 23 925 925 HOH HOH . G 7 HOH A 24 926 926 HOH HOH . G 7 HOH A 25 927 927 HOH HOH . G 7 HOH A 26 928 928 HOH HOH . G 7 HOH A 27 929 929 HOH HOH . G 7 HOH A 28 930 930 HOH HOH . G 7 HOH A 29 931 931 HOH HOH . G 7 HOH A 30 932 932 HOH HOH . G 7 HOH A 31 933 933 HOH HOH . G 7 HOH A 32 934 934 HOH HOH . G 7 HOH A 33 935 935 HOH HOH . G 7 HOH A 34 936 936 HOH HOH . G 7 HOH A 35 937 937 HOH HOH . G 7 HOH A 36 938 938 HOH HOH . G 7 HOH A 37 939 939 HOH HOH . G 7 HOH A 38 940 940 HOH HOH . G 7 HOH A 39 941 941 HOH HOH . G 7 HOH A 40 942 942 HOH HOH . G 7 HOH A 41 943 943 HOH HOH . G 7 HOH A 42 944 944 HOH HOH . G 7 HOH A 43 945 945 HOH HOH . G 7 HOH A 44 946 946 HOH HOH . G 7 HOH A 45 947 947 HOH HOH . G 7 HOH A 46 948 948 HOH HOH . G 7 HOH A 47 949 949 HOH HOH . G 7 HOH A 48 950 950 HOH HOH . G 7 HOH A 49 951 951 HOH HOH . G 7 HOH A 50 952 952 HOH HOH . G 7 HOH A 51 953 953 HOH HOH . G 7 HOH A 52 954 954 HOH HOH . G 7 HOH A 53 955 955 HOH HOH . G 7 HOH A 54 956 956 HOH HOH . G 7 HOH A 55 957 957 HOH HOH . G 7 HOH A 56 958 958 HOH HOH . G 7 HOH A 57 959 959 HOH HOH . G 7 HOH A 58 960 960 HOH HOH . G 7 HOH A 59 961 961 HOH HOH . G 7 HOH A 60 962 962 HOH HOH . G 7 HOH A 61 963 963 HOH HOH . G 7 HOH A 62 964 964 HOH HOH . G 7 HOH A 63 965 965 HOH HOH . G 7 HOH A 64 966 966 HOH HOH . G 7 HOH A 65 967 967 HOH HOH . G 7 HOH A 66 968 968 HOH HOH . G 7 HOH A 67 969 969 HOH HOH . G 7 HOH A 68 970 970 HOH HOH . G 7 HOH A 69 971 971 HOH HOH . G 7 HOH A 70 972 972 HOH HOH . G 7 HOH A 71 973 973 HOH HOH . G 7 HOH A 72 974 974 HOH HOH . G 7 HOH A 73 975 975 HOH HOH . G 7 HOH A 74 976 976 HOH HOH . G 7 HOH A 75 977 977 HOH HOH . G 7 HOH A 76 978 978 HOH HOH . G 7 HOH A 77 979 979 HOH HOH . G 7 HOH A 78 980 980 HOH HOH . G 7 HOH A 79 981 981 HOH HOH . G 7 HOH A 80 982 982 HOH HOH . G 7 HOH A 81 983 983 HOH HOH . G 7 HOH A 82 984 984 HOH HOH . G 7 HOH A 83 985 985 HOH HOH . G 7 HOH A 84 986 986 HOH HOH . G 7 HOH A 85 987 987 HOH HOH . G 7 HOH A 86 988 988 HOH HOH . G 7 HOH A 87 989 989 HOH HOH . G 7 HOH A 88 990 990 HOH HOH . G 7 HOH A 89 991 991 HOH HOH . G 7 HOH A 90 992 992 HOH HOH . G 7 HOH A 91 993 993 HOH HOH . G 7 HOH A 92 994 994 HOH HOH . G 7 HOH A 93 995 995 HOH HOH . G 7 HOH A 94 996 996 HOH HOH . G 7 HOH A 95 997 997 HOH HOH . G 7 HOH A 96 998 998 HOH HOH . G 7 HOH A 97 999 999 HOH HOH . G 7 HOH A 98 1000 1000 HOH HOH . G 7 HOH A 99 1001 1001 HOH HOH . G 7 HOH A 100 1002 1002 HOH HOH . G 7 HOH A 101 1003 1003 HOH HOH . G 7 HOH A 102 1004 1004 HOH HOH . G 7 HOH A 103 1005 1005 HOH HOH . G 7 HOH A 104 1006 1006 HOH HOH . G 7 HOH A 105 1007 1007 HOH HOH . G 7 HOH A 106 1008 1008 HOH HOH . G 7 HOH A 107 1009 1009 HOH HOH . G 7 HOH A 108 1010 1010 HOH HOH . G 7 HOH A 109 1011 1011 HOH HOH . G 7 HOH A 110 1012 1012 HOH HOH . G 7 HOH A 111 1013 1013 HOH HOH . G 7 HOH A 112 1014 1014 HOH HOH . G 7 HOH A 113 1015 1015 HOH HOH . G 7 HOH A 114 1016 1016 HOH HOH . G 7 HOH A 115 1017 1017 HOH HOH . G 7 HOH A 116 1018 1018 HOH HOH . G 7 HOH A 117 1019 1019 HOH HOH . G 7 HOH A 118 1020 1020 HOH HOH . G 7 HOH A 119 1021 1021 HOH HOH . G 7 HOH A 120 1022 1022 HOH HOH . G 7 HOH A 121 1023 1023 HOH HOH . G 7 HOH A 122 1024 1024 HOH HOH . G 7 HOH A 123 1025 1025 HOH HOH . G 7 HOH A 124 1026 1026 HOH HOH . G 7 HOH A 125 1027 1027 HOH HOH . G 7 HOH A 126 1028 1028 HOH HOH . G 7 HOH A 127 1029 1029 HOH HOH . G 7 HOH A 128 1030 1030 HOH HOH . G 7 HOH A 129 1031 1031 HOH HOH . G 7 HOH A 130 1032 1032 HOH HOH . G 7 HOH A 131 1033 1033 HOH HOH . G 7 HOH A 132 1034 1034 HOH HOH . G 7 HOH A 133 1035 1035 HOH HOH . G 7 HOH A 134 1036 1036 HOH HOH . G 7 HOH A 135 1037 1037 HOH HOH . G 7 HOH A 136 1038 1038 HOH HOH . G 7 HOH A 137 1039 1039 HOH HOH . G 7 HOH A 138 1040 1040 HOH HOH . G 7 HOH A 139 1041 1041 HOH HOH . G 7 HOH A 140 1042 1042 HOH HOH . G 7 HOH A 141 1043 1043 HOH HOH . G 7 HOH A 142 1044 1044 HOH HOH . G 7 HOH A 143 1045 1045 HOH HOH . G 7 HOH A 144 1046 1046 HOH HOH . G 7 HOH A 145 1047 1047 HOH HOH . G 7 HOH A 146 1048 1048 HOH HOH . G 7 HOH A 147 1049 1049 HOH HOH . G 7 HOH A 148 1050 1050 HOH HOH . G 7 HOH A 149 1051 1051 HOH HOH . G 7 HOH A 150 1052 1052 HOH HOH . G 7 HOH A 151 1053 1053 HOH HOH . G 7 HOH A 152 1054 1054 HOH HOH . G 7 HOH A 153 1055 1055 HOH HOH . G 7 HOH A 154 1056 1056 HOH HOH . G 7 HOH A 155 1057 1057 HOH HOH . G 7 HOH A 156 1058 1058 HOH HOH . G 7 HOH A 157 1059 1059 HOH HOH . G 7 HOH A 158 1060 1060 HOH HOH . G 7 HOH A 159 1061 1061 HOH HOH . G 7 HOH A 160 1062 1062 HOH HOH . G 7 HOH A 161 1063 1063 HOH HOH . G 7 HOH A 162 1064 1064 HOH HOH . G 7 HOH A 163 1065 1065 HOH HOH . G 7 HOH A 164 1066 1066 HOH HOH . G 7 HOH A 165 1067 1067 HOH HOH . G 7 HOH A 166 1068 1068 HOH HOH . G 7 HOH A 167 1069 1069 HOH HOH . G 7 HOH A 168 1070 1070 HOH HOH . G 7 HOH A 169 1071 1071 HOH HOH . G 7 HOH A 170 1072 1072 HOH HOH . G 7 HOH A 171 1073 1073 HOH HOH . G 7 HOH A 172 1074 1074 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 N N1 5AD . A . E 5 5.79 -9.953 -8.023 0.4 8.09 ? N1 5AD 902 A 1 HETATM 2 C C2 5AD . A . E 5 4.866 -10.919 -7.961 0.4 10.97 ? C2 5AD 902 A 1 HETATM 3 N N3 5AD . A . E 5 5.09 -12.241 -8.08 0.4 9.96 ? N3 5AD 902 A 1 HETATM 4 C C4 5AD . A . E 5 6.377 -12.618 -8.238 0.4 9.85 ? C4 5AD 902 A 1 HETATM 5 N N9 5AD . A . E 5 6.952 -13.799 -8.356 0.4 11.4 ? N9 5AD 902 A 1 HETATM 6 C C8 5AD . A . E 5 8.295 -13.637 -8.445 0.4 9.32 ? C8 5AD 902 A 1 HETATM 7 N N7 5AD . A . E 5 8.624 -12.318 -8.36 0.4 8.09 ? N7 5AD 902 A 1 HETATM 8 C C5 5AD . A . E 5 7.468 -11.662 -8.203 0.4 11.34 ? C5 5AD 902 A 1 HETATM 9 C C6 5AD . A . E 5 7.111 -10.261 -8.097 0.4 9.79 ? C6 5AD 902 A 1 HETATM 10 N N6 5AD . A . E 5 8.114 -9.328 -8.063 0.4 8.67 ? N6 5AD 902 A 1 HETATM 11 C C1' 5AD . A . E 5 6.12 -15.033 -8.354 0.4 11.29 ? C1' 5AD 902 A 1 HETATM 12 C C2' 5AD . A . E 5 6.614 -16.172 -9.248 0.4 12.85 ? C2' 5AD 902 A 1 HETATM 13 C C3' 5AD . A . E 5 7.516 -16.982 -8.324 0.4 12.14 ? C3' 5AD 902 A 1 HETATM 14 C C4' 5AD . A . E 5 6.484 -16.933 -7.227 0.4 14.35 ? C4' 5AD 902 A 1 HETATM 15 C C5' 5AD . A . E 5 6.862 -17.284 -5.847 0.4 13.22 ? C5' 5AD 902 A 1 HETATM 16 O O4' 5AD . A . E 5 6.073 -15.59 -7.028 0.4 10.99 ? O4' 5AD 902 A 1 HETATM 17 O O2' 5AD . A . E 5 5.436 -16.94 -9.609 0.4 11.6 ? O2' 5AD 902 A 1 HETATM 18 O O3' 5AD . A . E 5 7.707 -18.334 -8.765 0.4 12.36 ? O3' 5AD 902 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #