data_3PD3
#
_model_server_result.job_id            Gdile6FjbBBaQiq9w3J7bA 
_model_server_result.datetime_utc      '2024-11-15 18:52:25' 
_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          3pd3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":148}' 
#
_entry.id    3PD3 
#
_exptl.entry_id    3PD3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              367.36 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3'-deoxy-3'-(L-threonylamino)adenosine" 
_entity.pdbx_number_of_molecules    2 
_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            3PD3 
_cell.length_a            38.295 
_cell.length_b            65.914 
_cell.length_c            93.698 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PD3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
#
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C14 H21 N7 O5' 
_chem_comp.formula_weight    367.36 
_chem_comp.id                A3T 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3'-deoxy-3'-(L-threonylamino)adenosine" 
_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
C O A3T doub 1 n n 
C N8 A3T sing 2 n n 
C CA A3T sing 3 n n 
N CA A3T sing 4 n n 
N1 C2 A3T doub 5 n y 
N1 C6 A3T sing 6 n y 
C2 N3 A3T sing 7 n y 
N3 C4 A3T doub 8 n y 
C4 C5 A3T sing 9 n y 
C4 N9 A3T sing 10 n y 
C5 C6 A3T doub 11 n y 
C5 N7 A3T sing 12 n y 
C6 N6 A3T sing 13 n n 
N7 C8 A3T doub 14 n y 
C8 N9 A3T sing 15 n y 
N8 C3' A3T sing 16 n n 
N9 C1' A3T sing 17 n n 
CA CB A3T sing 18 n n 
CB OG A3T sing 19 n n 
CB CG2 A3T sing 20 n n 
C1' C2' A3T sing 21 n n 
C1' O4' A3T sing 22 n n 
C2' O2' A3T sing 23 n n 
C2' C3' A3T sing 24 n n 
C3' C4' A3T sing 25 n n 
C4' O4' A3T sing 26 n n 
C4' C5' A3T sing 27 n n 
C5' O5' A3T sing 28 n n 
N HN A3T sing 29 n n 
N HNA A3T sing 30 n n 
C2 H2 A3T sing 31 n n 
N6 HN6 A3T sing 32 n n 
N6 HN6A A3T sing 33 n n 
C8 H8 A3T sing 34 n n 
N8 HN8 A3T sing 35 n n 
CA HA A3T sing 36 n n 
CB HB A3T sing 37 n n 
OG HOG A3T sing 38 n n 
C1' H1' A3T sing 39 n n 
C2' H2' A3T sing 40 n n 
O2' HO2' A3T sing 41 n n 
C3' H3' A3T sing 42 n n 
C4' H4' A3T sing 43 n n 
C5' H5' A3T sing 44 n n 
C5' "H5'A" A3T sing 45 n n 
O5' HO5' A3T sing 46 n n 
CG2 HG2 A3T sing 47 n n 
CG2 HG2A A3T sing 48 n n 
CG2 HG2B A3T sing 49 n n 
#
_atom_sites.entry_id                     3PD3 
_atom_sites.fract_transf_matrix[1][1]    0.026113 
_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]    0.015171 
_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]    0.010673 
_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
C 2 A3T A 1 148 1 A3T A3T . 
D 2 A3T B 1 148 2 A3T A3T . 
E 3 HOH A 1 1002 1002 HOH HOH . 
E 3 HOH A 2 1003 1003 HOH HOH . 
E 3 HOH A 3 1004 1004 HOH HOH . 
E 3 HOH A 4 1005 1005 HOH HOH . 
E 3 HOH A 5 1006 1006 HOH HOH . 
E 3 HOH A 6 1007 1007 HOH HOH . 
E 3 HOH A 7 1008 1008 HOH HOH . 
E 3 HOH A 8 1009 1009 HOH HOH . 
E 3 HOH A 9 1012 1012 HOH HOH . 
E 3 HOH A 10 1014 1014 HOH HOH . 
E 3 HOH A 11 1015 1015 HOH HOH . 
E 3 HOH A 12 1016 1016 HOH HOH . 
E 3 HOH A 13 1017 1017 HOH HOH . 
E 3 HOH A 14 1018 1018 HOH HOH . 
E 3 HOH A 15 1020 1020 HOH HOH . 
E 3 HOH A 16 1023 1023 HOH HOH . 
E 3 HOH A 17 1025 1025 HOH HOH . 
E 3 HOH A 18 1026 1026 HOH HOH . 
E 3 HOH A 19 1027 1027 HOH HOH . 
E 3 HOH A 20 1028 1028 HOH HOH . 
E 3 HOH A 21 1031 1031 HOH HOH . 
E 3 HOH A 22 1034 1034 HOH HOH . 
E 3 HOH A 23 1037 1037 HOH HOH . 
E 3 HOH A 24 1039 1039 HOH HOH . 
E 3 HOH A 25 1040 1040 HOH HOH . 
E 3 HOH A 26 1041 1041 HOH HOH . 
E 3 HOH A 27 1042 1042 HOH HOH . 
E 3 HOH A 28 1045 1045 HOH HOH . 
E 3 HOH A 29 1046 1046 HOH HOH . 
E 3 HOH A 30 1047 1047 HOH HOH . 
E 3 HOH A 31 1048 1048 HOH HOH . 
E 3 HOH A 32 1052 1052 HOH HOH . 
E 3 HOH A 33 1053 1053 HOH HOH . 
E 3 HOH A 34 1054 1054 HOH HOH . 
E 3 HOH A 35 1055 1055 HOH HOH . 
E 3 HOH A 36 1056 1056 HOH HOH . 
E 3 HOH A 37 1058 1058 HOH HOH . 
E 3 HOH A 38 1059 1059 HOH HOH . 
E 3 HOH A 39 1062 1062 HOH HOH . 
E 3 HOH A 40 1063 1063 HOH HOH . 
E 3 HOH A 41 1064 1064 HOH HOH . 
E 3 HOH A 42 1068 1068 HOH HOH . 
E 3 HOH A 43 1070 1070 HOH HOH . 
E 3 HOH A 44 1071 1071 HOH HOH . 
E 3 HOH A 45 1073 1073 HOH HOH . 
E 3 HOH A 46 1074 1074 HOH HOH . 
E 3 HOH A 47 1075 1075 HOH HOH . 
E 3 HOH A 48 1077 1077 HOH HOH . 
E 3 HOH A 49 1078 1078 HOH HOH . 
E 3 HOH A 50 1079 1079 HOH HOH . 
E 3 HOH A 51 1080 1080 HOH HOH . 
E 3 HOH A 52 1081 1081 HOH HOH . 
E 3 HOH A 53 1082 1082 HOH HOH . 
E 3 HOH A 54 1084 1084 HOH HOH . 
E 3 HOH A 55 1086 1086 HOH HOH . 
E 3 HOH A 56 1090 1090 HOH HOH . 
E 3 HOH A 57 1091 1091 HOH HOH . 
E 3 HOH A 58 1092 1092 HOH HOH . 
E 3 HOH A 59 1096 1096 HOH HOH . 
E 3 HOH A 60 1098 1098 HOH HOH . 
E 3 HOH A 61 1100 1100 HOH HOH . 
E 3 HOH A 62 1102 1102 HOH HOH . 
E 3 HOH A 63 1103 1103 HOH HOH . 
E 3 HOH A 64 1104 1104 HOH HOH . 
E 3 HOH A 65 1105 1105 HOH HOH . 
E 3 HOH A 66 1107 1107 HOH HOH . 
E 3 HOH A 67 1109 1109 HOH HOH . 
E 3 HOH A 68 1110 1110 HOH HOH . 
E 3 HOH A 69 1111 1111 HOH HOH . 
E 3 HOH A 70 1116 1116 HOH HOH . 
E 3 HOH A 71 1119 1119 HOH HOH . 
E 3 HOH A 72 1120 1120 HOH HOH . 
E 3 HOH A 73 1122 1122 HOH HOH . 
E 3 HOH A 74 1125 1125 HOH HOH . 
E 3 HOH A 75 1126 1126 HOH HOH . 
E 3 HOH A 76 1130 1130 HOH HOH . 
E 3 HOH A 77 1131 1131 HOH HOH . 
E 3 HOH A 78 1133 1133 HOH HOH . 
E 3 HOH A 79 1135 1135 HOH HOH . 
E 3 HOH A 80 1139 1139 HOH HOH . 
E 3 HOH A 81 1141 1141 HOH HOH . 
E 3 HOH A 82 1144 1144 HOH HOH . 
E 3 HOH A 83 1148 1148 HOH HOH . 
E 3 HOH A 84 1149 1149 HOH HOH . 
E 3 HOH A 85 1150 1150 HOH HOH . 
E 3 HOH A 86 1152 1152 HOH HOH . 
E 3 HOH A 87 1153 1153 HOH HOH . 
E 3 HOH A 88 1157 1157 HOH HOH . 
E 3 HOH A 89 1159 1159 HOH HOH . 
E 3 HOH A 90 1161 1161 HOH HOH . 
E 3 HOH A 91 1162 1162 HOH HOH . 
E 3 HOH A 92 1166 1166 HOH HOH . 
E 3 HOH A 93 1168 1168 HOH HOH . 
E 3 HOH A 94 1170 1170 HOH HOH . 
E 3 HOH A 95 1173 1173 HOH HOH . 
E 3 HOH A 96 1175 1175 HOH HOH . 
E 3 HOH A 97 1176 1176 HOH HOH . 
E 3 HOH A 98 1177 1177 HOH HOH . 
E 3 HOH A 99 1181 1181 HOH HOH . 
E 3 HOH A 100 1183 1183 HOH HOH . 
E 3 HOH A 101 1186 1186 HOH HOH . 
E 3 HOH A 102 1190 1190 HOH HOH . 
E 3 HOH A 103 1193 1193 HOH HOH . 
E 3 HOH A 104 1194 1194 HOH HOH . 
E 3 HOH A 105 1195 1195 HOH HOH . 
E 3 HOH A 106 1196 1196 HOH HOH . 
E 3 HOH A 107 1197 1197 HOH HOH . 
E 3 HOH A 108 1199 1199 HOH HOH . 
E 3 HOH A 109 1200 1200 HOH HOH . 
E 3 HOH A 110 1201 1201 HOH HOH . 
F 3 HOH B 1 1001 1001 HOH HOH . 
F 3 HOH B 2 1010 1010 HOH HOH . 
F 3 HOH B 3 1011 1011 HOH HOH . 
F 3 HOH B 4 1013 1013 HOH HOH . 
F 3 HOH B 5 1019 1019 HOH HOH . 
F 3 HOH B 6 1021 1021 HOH HOH . 
F 3 HOH B 7 1022 1022 HOH HOH . 
F 3 HOH B 8 1024 1024 HOH HOH . 
F 3 HOH B 9 1029 1029 HOH HOH . 
F 3 HOH B 10 1030 1030 HOH HOH . 
F 3 HOH B 11 1032 1032 HOH HOH . 
F 3 HOH B 12 1033 1033 HOH HOH . 
F 3 HOH B 13 1035 1035 HOH HOH . 
F 3 HOH B 14 1036 1036 HOH HOH . 
F 3 HOH B 15 1038 1038 HOH HOH . 
F 3 HOH B 16 1043 1043 HOH HOH . 
F 3 HOH B 17 1044 1044 HOH HOH . 
F 3 HOH B 18 1049 1049 HOH HOH . 
F 3 HOH B 19 1050 1050 HOH HOH . 
F 3 HOH B 20 1051 1051 HOH HOH . 
F 3 HOH B 21 1057 1057 HOH HOH . 
F 3 HOH B 22 1060 1060 HOH HOH . 
F 3 HOH B 23 1061 1061 HOH HOH . 
F 3 HOH B 24 1065 1065 HOH HOH . 
F 3 HOH B 25 1066 1066 HOH HOH . 
F 3 HOH B 26 1067 1067 HOH HOH . 
F 3 HOH B 27 1069 1069 HOH HOH . 
F 3 HOH B 28 1072 1072 HOH HOH . 
F 3 HOH B 29 1076 1076 HOH HOH . 
F 3 HOH B 30 1083 1083 HOH HOH . 
F 3 HOH B 31 1085 1085 HOH HOH . 
F 3 HOH B 32 1087 1087 HOH HOH . 
F 3 HOH B 33 1088 1088 HOH HOH . 
F 3 HOH B 34 1089 1089 HOH HOH . 
F 3 HOH B 35 1093 1093 HOH HOH . 
F 3 HOH B 36 1094 1094 HOH HOH . 
F 3 HOH B 37 1095 1095 HOH HOH . 
F 3 HOH B 38 1097 1097 HOH HOH . 
F 3 HOH B 39 1099 1099 HOH HOH . 
F 3 HOH B 40 1101 1101 HOH HOH . 
F 3 HOH B 41 1106 1106 HOH HOH . 
F 3 HOH B 42 1112 1112 HOH HOH . 
F 3 HOH B 43 1113 1113 HOH HOH . 
F 3 HOH B 44 1114 1114 HOH HOH . 
F 3 HOH B 45 1117 1117 HOH HOH . 
F 3 HOH B 46 1118 1118 HOH HOH . 
F 3 HOH B 47 1121 1121 HOH HOH . 
F 3 HOH B 48 1123 1123 HOH HOH . 
F 3 HOH B 49 1124 1124 HOH HOH . 
F 3 HOH B 50 1127 1127 HOH HOH . 
F 3 HOH B 51 1128 1128 HOH HOH . 
F 3 HOH B 52 1129 1129 HOH HOH . 
F 3 HOH B 53 1134 1134 HOH HOH . 
F 3 HOH B 54 1136 1136 HOH HOH . 
F 3 HOH B 55 1137 1137 HOH HOH . 
F 3 HOH B 56 1138 1138 HOH HOH . 
F 3 HOH B 57 1140 1140 HOH HOH . 
F 3 HOH B 58 1142 1142 HOH HOH . 
F 3 HOH B 59 1143 1143 HOH HOH . 
F 3 HOH B 60 1145 1145 HOH HOH . 
F 3 HOH B 61 1146 1146 HOH HOH . 
F 3 HOH B 62 1147 1147 HOH HOH . 
F 3 HOH B 63 1151 1151 HOH HOH . 
F 3 HOH B 64 1154 1154 HOH HOH . 
F 3 HOH B 65 1155 1155 HOH HOH . 
F 3 HOH B 66 1156 1156 HOH HOH . 
F 3 HOH B 67 1158 1158 HOH HOH . 
F 3 HOH B 68 1160 1160 HOH HOH . 
F 3 HOH B 69 1163 1163 HOH HOH . 
F 3 HOH B 70 1164 1164 HOH HOH . 
F 3 HOH B 71 1165 1165 HOH HOH . 
F 3 HOH B 72 1167 1167 HOH HOH . 
F 3 HOH B 73 1169 1169 HOH HOH . 
F 3 HOH B 74 1171 1171 HOH HOH . 
F 3 HOH B 75 1172 1172 HOH HOH . 
F 3 HOH B 76 1174 1174 HOH HOH . 
F 3 HOH B 77 1178 1178 HOH HOH . 
F 3 HOH B 78 1179 1179 HOH HOH . 
F 3 HOH B 79 1180 1180 HOH HOH . 
F 3 HOH B 80 1182 1182 HOH HOH . 
F 3 HOH B 81 1184 1184 HOH HOH . 
F 3 HOH B 82 1185 1185 HOH HOH . 
F 3 HOH B 83 1187 1187 HOH HOH . 
F 3 HOH B 84 1188 1188 HOH HOH . 
F 3 HOH B 85 1189 1189 HOH HOH . 
F 3 HOH B 86 1191 1191 HOH HOH . 
F 3 HOH B 87 1192 1192 HOH HOH . 
F 3 HOH B 88 1198 1198 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 C A3T . . . D 2 22.01 -5.926 2.919 1 24.53 ? C A3T 148 B 1 
HETATM 2 N N A3T . . . D 2 19.896 -6.567 1.851 1 23.34 ? N A3T 148 B 1 
HETATM 3 O O A3T . . . D 2 21.98 -4.715 2.302 1 25.08 ? O A3T 148 B 1 
HETATM 4 N N1 A3T . . . D 2 23.254 0.967 5.121 1 24.5 ? N1 A3T 148 B 1 
HETATM 5 C C2 A3T . . . D 2 22.332 0.034 5.284 1 24.4 ? C2 A3T 148 B 1 
HETATM 6 N N3 A3T . . . D 2 22.646 -1.2 5.639 1 25 ? N3 A3T 148 B 1 
HETATM 7 C C4 A3T . . . D 2 23.925 -1.545 5.846 1 25.66 ? C4 A3T 148 B 1 
HETATM 8 C C5 A3T . . . D 2 24.92 -0.593 5.68 1 26.28 ? C5 A3T 148 B 1 
HETATM 9 C C6 A3T . . . D 2 24.552 0.694 5.312 1 26.12 ? C6 A3T 148 B 1 
HETATM 10 N N6 A3T . . . D 2 25.476 1.643 5.18 1 27.81 ? N6 A3T 148 B 1 
HETATM 11 N N7 A3T . . . D 2 26.086 -1.176 5.94 1 27.36 ? N7 A3T 148 B 1 
HETATM 12 C C8 A3T . . . D 2 25.839 -2.443 6.264 1 27.15 ? C8 A3T 148 B 1 
HETATM 13 N N8 A3T . . . D 2 22.698 -6.178 4.028 1 24.3 ? N8 A3T 148 B 1 
HETATM 14 N N9 A3T . . . D 2 24.528 -2.67 6.22 1 25.36 ? N9 A3T 148 B 1 
HETATM 15 C CA A3T . . . D 2 21.195 -7.074 2.32 1 24.7 ? CA A3T 148 B 1 
HETATM 16 C CB A3T . . . D 2 21.95 -7.696 1.143 1 23.81 ? CB A3T 148 B 1 
HETATM 17 O OG A3T . . . D 2 21.252 -8.87 0.717 1 24.18 ? OG A3T 148 B 1 
HETATM 18 C C1' A3T . . . D 2 23.885 -3.926 6.669 1 24.94 ? C1' A3T 148 B 1 
HETATM 19 C C2' A3T . . . D 2 22.741 -4.397 5.767 1 24.66 ? C2' A3T 148 B 1 
HETATM 20 O O2' A3T . . . D 2 21.897 -5.292 6.496 1 24.22 ? O2' A3T 148 B 1 
HETATM 21 C C3' A3T . . . D 2 23.525 -5.176 4.716 1 25.16 ? C3' A3T 148 B 1 
HETATM 22 C C4' A3T . . . D 2 24.564 -5.885 5.585 1 24.67 ? C4' A3T 148 B 1 
HETATM 23 O O4' A3T . . . D 2 24.896 -4.948 6.624 1 25.55 ? O4' A3T 148 B 1 
HETATM 24 C C5' A3T . . . D 2 25.792 -6.166 4.717 1 24.41 ? C5' A3T 148 B 1 
HETATM 25 O O5' A3T . . . D 2 26.237 -4.945 4.119 1 25.16 ? O5' A3T 148 B 1 
HETATM 26 C CG2 A3T . . . D 2 23.398 -8.018 1.516 1 24.36 ? CG2 A3T 148 B 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           26 
#