data_4R3U # _model_server_result.job_id nCu2nc8CvnDvZiPJXsI-hA _model_server_result.datetime_utc '2024-10-12 09:19:03' _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 4r3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":803}' # _entry.id 4R3U # _exptl.entry_id 4R3U _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 91.23 _cell.angle_gamma 90 _cell.entry_id 4R3U _cell.length_a 69.03 _cell.length_b 119.56 _cell.length_c 173.94 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R3U _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,J,L,N 1 1,2 B,D,H,I,K,M,O 2 1,3 # 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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 65.296221 0 173.899921 3 'crystal symmetry operation' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 69.03 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 C NE2 HIS 29 C HIS 18 1_555 J CO B12 . C B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc2 D NE2 HIS 29 D HIS 18 1_555 K CO B12 . D B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? # _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 197 n y N1 C6 5AD sing 198 n y C2 N3 5AD sing 199 n y C2 H2 5AD sing 200 n n N3 C4 5AD doub 201 n y C4 N9 5AD sing 202 n y C4 C5 5AD sing 203 n y N9 C8 5AD sing 204 n y N9 C1' 5AD sing 205 n n C8 N7 5AD doub 206 n y C8 H8 5AD sing 207 n n N7 C5 5AD sing 208 n y C5 C6 5AD doub 209 n y C6 N6 5AD sing 210 n n N6 HN61 5AD sing 211 n n N6 HN62 5AD sing 212 n n C1' C2' 5AD sing 213 n n C1' O4' 5AD sing 214 n n C1' H1' 5AD sing 215 n n C2' C3' 5AD sing 216 n n C2' O2' 5AD sing 217 n n C2' H2' 5AD sing 218 n n C3' C4' 5AD sing 219 n n C3' O3' 5AD sing 220 n n C3' H3' 5AD sing 221 n n C4' C5' 5AD sing 222 n n C4' O4' 5AD sing 223 n n C4' H4' 5AD sing 224 n n C5' "H5'1" 5AD sing 225 n n C5' "H5'2" 5AD sing 226 n n C5' "H5'3" 5AD sing 227 n n O2' HO2' 5AD sing 228 n n O3' HO3' 5AD sing 229 n n # _atom_sites.entry_id 4R3U _atom_sites.fract_transf_matrix[1][1] 0.014486 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000311 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008364 _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] 0.00575 _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 E 3 3HC A 1 801 801 3HC 3HB . F 4 3KK A 1 802 802 3KK HIB . G 5 5AD A 1 803 803 5AD 5AD . H 3 3HC B 1 801 801 3HC 3HB . I 4 3KK B 1 802 802 3KK HIB . J 6 B12 C 1 800 800 B12 B12 . K 6 B12 D 1 800 800 B12 B12 . L 7 HOH A 1 901 2 HOH HOH . L 7 HOH A 2 902 6 HOH HOH . L 7 HOH A 3 903 7 HOH HOH . L 7 HOH A 4 904 8 HOH HOH . L 7 HOH A 5 905 9 HOH HOH . L 7 HOH A 6 906 11 HOH HOH . L 7 HOH A 7 907 12 HOH HOH . L 7 HOH A 8 908 13 HOH HOH . L 7 HOH A 9 909 14 HOH HOH . L 7 HOH A 10 910 16 HOH HOH . L 7 HOH A 11 911 17 HOH HOH . L 7 HOH A 12 912 18 HOH HOH . L 7 HOH A 13 913 21 HOH HOH . L 7 HOH A 14 914 23 HOH HOH . L 7 HOH A 15 915 24 HOH HOH . L 7 HOH A 16 916 26 HOH HOH . L 7 HOH A 17 917 27 HOH HOH . L 7 HOH A 18 918 28 HOH HOH . L 7 HOH A 19 919 30 HOH HOH . L 7 HOH A 20 920 31 HOH HOH . L 7 HOH A 21 921 33 HOH HOH . L 7 HOH A 22 922 36 HOH HOH . L 7 HOH A 23 923 38 HOH HOH . L 7 HOH A 24 924 40 HOH HOH . L 7 HOH A 25 925 42 HOH HOH . L 7 HOH A 26 926 45 HOH HOH . L 7 HOH A 27 927 46 HOH HOH . L 7 HOH A 28 928 47 HOH HOH . L 7 HOH A 29 929 49 HOH HOH . L 7 HOH A 30 930 52 HOH HOH . L 7 HOH A 31 931 54 HOH HOH . L 7 HOH A 32 932 55 HOH HOH . L 7 HOH A 33 933 56 HOH HOH . L 7 HOH A 34 934 58 HOH HOH . L 7 HOH A 35 935 59 HOH HOH . L 7 HOH A 36 936 61 HOH HOH . L 7 HOH A 37 937 62 HOH HOH . L 7 HOH A 38 938 63 HOH HOH . L 7 HOH A 39 939 64 HOH HOH . L 7 HOH A 40 940 66 HOH HOH . L 7 HOH A 41 941 67 HOH HOH . L 7 HOH A 42 942 71 HOH HOH . L 7 HOH A 43 943 72 HOH HOH . L 7 HOH A 44 944 73 HOH HOH . L 7 HOH A 45 945 75 HOH HOH . L 7 HOH A 46 946 77 HOH HOH . L 7 HOH A 47 947 78 HOH HOH . L 7 HOH A 48 948 79 HOH HOH . L 7 HOH A 49 949 80 HOH HOH . L 7 HOH A 50 950 83 HOH HOH . L 7 HOH A 51 951 84 HOH HOH . L 7 HOH A 52 952 85 HOH HOH . L 7 HOH A 53 953 86 HOH HOH . L 7 HOH A 54 954 87 HOH HOH . L 7 HOH A 55 955 88 HOH HOH . L 7 HOH A 56 956 89 HOH HOH . L 7 HOH A 57 957 90 HOH HOH . L 7 HOH A 58 958 92 HOH HOH . L 7 HOH A 59 959 95 HOH HOH . L 7 HOH A 60 960 97 HOH HOH . L 7 HOH A 61 961 99 HOH HOH . L 7 HOH A 62 962 106 HOH HOH . L 7 HOH A 63 963 111 HOH HOH . L 7 HOH A 64 964 112 HOH HOH . L 7 HOH A 65 965 113 HOH HOH . L 7 HOH A 66 966 116 HOH HOH . L 7 HOH A 67 967 118 HOH HOH . L 7 HOH A 68 968 125 HOH HOH . L 7 HOH A 69 969 127 HOH HOH . L 7 HOH A 70 970 128 HOH HOH . L 7 HOH A 71 971 131 HOH HOH . L 7 HOH A 72 972 132 HOH HOH . L 7 HOH A 73 973 135 HOH HOH . L 7 HOH A 74 974 139 HOH HOH . L 7 HOH A 75 975 142 HOH HOH . L 7 HOH A 76 976 143 HOH HOH . L 7 HOH A 77 977 145 HOH HOH . L 7 HOH A 78 978 155 HOH HOH . L 7 HOH A 79 979 157 HOH HOH . L 7 HOH A 80 980 161 HOH HOH . L 7 HOH A 81 981 163 HOH HOH . L 7 HOH A 82 982 169 HOH HOH . L 7 HOH A 83 983 172 HOH HOH . L 7 HOH A 84 984 176 HOH HOH . L 7 HOH A 85 985 177 HOH HOH . L 7 HOH A 86 986 179 HOH HOH . L 7 HOH A 87 987 205 HOH HOH . L 7 HOH A 88 988 208 HOH HOH . L 7 HOH A 89 989 209 HOH HOH . L 7 HOH A 90 990 210 HOH HOH . L 7 HOH A 91 991 221 HOH HOH . L 7 HOH A 92 992 236 HOH HOH . L 7 HOH A 93 993 237 HOH HOH . L 7 HOH A 94 994 240 HOH HOH . L 7 HOH A 95 995 241 HOH HOH . L 7 HOH A 96 996 257 HOH HOH . L 7 HOH A 97 997 261 HOH HOH . L 7 HOH A 98 998 263 HOH HOH . L 7 HOH A 99 999 264 HOH HOH . L 7 HOH A 100 1000 265 HOH HOH . L 7 HOH A 101 1001 268 HOH HOH . L 7 HOH A 102 1002 269 HOH HOH . L 7 HOH A 103 1003 270 HOH HOH . L 7 HOH A 104 1004 271 HOH HOH . L 7 HOH A 105 1005 272 HOH HOH . L 7 HOH A 106 1006 273 HOH HOH . L 7 HOH A 107 1007 274 HOH HOH . L 7 HOH A 108 1008 275 HOH HOH . L 7 HOH A 109 1009 278 HOH HOH . L 7 HOH A 110 1010 285 HOH HOH . L 7 HOH A 111 1011 286 HOH HOH . L 7 HOH A 112 1012 287 HOH HOH . L 7 HOH A 113 1013 288 HOH HOH . L 7 HOH A 114 1014 294 HOH HOH . L 7 HOH A 115 1015 295 HOH HOH . L 7 HOH A 116 1016 296 HOH HOH . L 7 HOH A 117 1017 297 HOH HOH . L 7 HOH A 118 1018 298 HOH HOH . L 7 HOH A 119 1019 299 HOH HOH . L 7 HOH A 120 1020 300 HOH HOH . L 7 HOH A 121 1021 301 HOH HOH . L 7 HOH A 122 1022 302 HOH HOH . L 7 HOH A 123 1023 303 HOH HOH . L 7 HOH A 124 1024 304 HOH HOH . L 7 HOH A 125 1025 306 HOH HOH . L 7 HOH A 126 1026 307 HOH HOH . L 7 HOH A 127 1027 308 HOH HOH . L 7 HOH A 128 1028 309 HOH HOH . L 7 HOH A 129 1029 310 HOH HOH . L 7 HOH A 130 1030 312 HOH HOH . L 7 HOH A 131 1031 313 HOH HOH . L 7 HOH A 132 1032 314 HOH HOH . L 7 HOH A 133 1033 315 HOH HOH . L 7 HOH A 134 1034 316 HOH HOH . L 7 HOH A 135 1035 317 HOH HOH . L 7 HOH A 136 1036 323 HOH HOH . L 7 HOH A 137 1037 324 HOH HOH . L 7 HOH A 138 1038 326 HOH HOH . L 7 HOH A 139 1039 327 HOH HOH . L 7 HOH A 140 1040 329 HOH HOH . L 7 HOH A 141 1041 331 HOH HOH . L 7 HOH A 142 1042 332 HOH HOH . L 7 HOH A 143 1043 333 HOH HOH . L 7 HOH A 144 1044 334 HOH HOH . L 7 HOH A 145 1045 337 HOH HOH . L 7 HOH A 146 1046 338 HOH HOH . L 7 HOH A 147 1047 339 HOH HOH . L 7 HOH A 148 1048 340 HOH HOH . L 7 HOH A 149 1049 341 HOH HOH . L 7 HOH A 150 1050 342 HOH HOH . L 7 HOH A 151 1051 343 HOH HOH . L 7 HOH A 152 1052 345 HOH HOH . L 7 HOH A 153 1053 347 HOH HOH . L 7 HOH A 154 1054 348 HOH HOH . L 7 HOH A 155 1055 349 HOH HOH . L 7 HOH A 156 1056 350 HOH HOH . L 7 HOH A 157 1057 351 HOH HOH . L 7 HOH A 158 1058 311 HOH HOH . M 7 HOH B 1 901 3 HOH HOH . M 7 HOH B 2 902 32 HOH HOH . M 7 HOH B 3 903 39 HOH HOH . M 7 HOH B 4 904 121 HOH HOH . M 7 HOH B 5 905 164 HOH HOH . M 7 HOH B 6 906 167 HOH HOH . M 7 HOH B 7 907 171 HOH HOH . M 7 HOH B 8 908 204 HOH HOH . M 7 HOH B 9 909 226 HOH HOH . M 7 HOH B 10 910 229 HOH HOH . M 7 HOH B 11 911 244 HOH HOH . M 7 HOH B 12 912 282 HOH HOH . M 7 HOH B 13 913 289 HOH HOH . M 7 HOH B 14 914 291 HOH HOH . M 7 HOH B 15 915 318 HOH HOH . M 7 HOH B 16 916 330 HOH HOH . N 7 HOH C 1 901 4 HOH HOH . N 7 HOH C 2 902 15 HOH HOH . N 7 HOH C 3 903 19 HOH HOH . N 7 HOH C 4 904 20 HOH HOH . N 7 HOH C 5 905 29 HOH HOH . N 7 HOH C 6 906 34 HOH HOH . N 7 HOH C 7 907 41 HOH HOH . N 7 HOH C 8 908 43 HOH HOH . N 7 HOH C 9 909 48 HOH HOH . N 7 HOH C 10 910 74 HOH HOH . N 7 HOH C 11 911 76 HOH HOH . N 7 HOH C 12 912 101 HOH HOH . N 7 HOH C 13 913 104 HOH HOH . N 7 HOH C 14 914 105 HOH HOH . N 7 HOH C 15 915 126 HOH HOH . N 7 HOH C 16 916 138 HOH HOH . N 7 HOH C 17 917 165 HOH HOH . N 7 HOH C 18 918 166 HOH HOH . N 7 HOH C 19 919 217 HOH HOH . N 7 HOH C 20 920 250 HOH HOH . N 7 HOH C 21 921 254 HOH HOH . N 7 HOH C 22 922 255 HOH HOH . N 7 HOH C 23 923 262 HOH HOH . N 7 HOH C 24 924 276 HOH HOH . N 7 HOH C 25 925 277 HOH HOH . N 7 HOH C 26 926 280 HOH HOH . N 7 HOH C 27 927 281 HOH HOH . N 7 HOH C 28 928 284 HOH HOH . N 7 HOH C 29 929 292 HOH HOH . N 7 HOH C 30 930 293 HOH HOH . N 7 HOH C 31 931 319 HOH HOH . N 7 HOH C 32 932 320 HOH HOH . N 7 HOH C 33 933 321 HOH HOH . N 7 HOH C 34 934 322 HOH HOH . N 7 HOH C 35 935 325 HOH HOH . N 7 HOH C 36 936 328 HOH HOH . N 7 HOH C 37 937 335 HOH HOH . N 7 HOH C 38 938 346 HOH HOH . O 7 HOH D 1 901 91 HOH HOH . O 7 HOH D 2 902 159 HOH HOH . O 7 HOH D 3 903 344 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 . C . G 5 36.572 10.476 68.084 0.5 17.93 ? N1 5AD 803 A 1 HETATM 2 C C2 5AD . C . G 5 36.34 9.523 69.075 0.5 20.21 ? C2 5AD 803 A 1 HETATM 3 N N3 5AD . C . G 5 35.23 8.651 68.942 0.5 23.69 ? N3 5AD 803 A 1 HETATM 4 C C4 5AD . C . G 5 34.479 8.705 67.821 0.5 26.69 ? C4 5AD 803 A 1 HETATM 5 N N9 5AD . C . G 5 33.397 8.028 67.428 0.5 27.68 ? N9 5AD 803 A 1 HETATM 6 C C8 5AD . C . G 5 33.106 8.422 66.185 0.5 27.15 ? C8 5AD 803 A 1 HETATM 7 N N7 5AD . C . G 5 33.929 9.393 65.827 0.5 26.55 ? N7 5AD 803 A 1 HETATM 8 C C5 5AD . C . G 5 34.799 9.563 66.829 0.5 26.02 ? C5 5AD 803 A 1 HETATM 9 C C6 5AD . C . G 5 35.829 10.412 66.968 0.5 21.43 ? C6 5AD 803 A 1 HETATM 10 N N6 5AD . C . G 5 36.011 11.253 65.964 0.5 21.65 ? N6 5AD 803 A 1 HETATM 11 C C1' 5AD . C . G 5 32.776 6.812 67.98 0.5 27.53 ? C1' 5AD 803 A 1 HETATM 12 C C2' 5AD . C . G 5 32.068 6.963 69.281 0.5 28.76 ? C2' 5AD 803 A 1 HETATM 13 C C3' 5AD . C . G 5 30.955 5.938 69.143 0.5 31.13 ? C3' 5AD 803 A 1 HETATM 14 C C4' 5AD . C . G 5 31.111 5.317 67.754 0.5 30.21 ? C4' 5AD 803 A 1 HETATM 15 C C5' 5AD . C . G 5 29.745 5.187 67.091 0.5 30.69 ? C5' 5AD 803 A 1 HETATM 16 O O4' 5AD . C . G 5 31.793 6.325 67.053 0.5 28.07 ? O4' 5AD 803 A 1 HETATM 17 O O2' 5AD . C . G 5 32.947 6.544 70.334 0.5 27.47 ? O2' 5AD 803 A 1 HETATM 18 O O3' 5AD . C . G 5 31.09 4.95 70.182 0.5 32.43 ? O3' 5AD 803 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 18 #