data_3AGN # _model_server_result.job_id x1POWY_xhXljsfPsPbtqRQ _model_server_result.datetime_utc '2024-11-30 19:19:41' _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 3agn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":115}' # _entry.id 3AGN # _exptl.entry_id 3AGN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _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 114.99 _cell.angle_gamma 90 _cell.entry_id 3AGN _cell.length_a 37.88 _cell.length_b 39.789 _cell.length_c 35.884 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 1 A CYS 1 1_555 A SG CYS 54 A CYS 54 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 A SG CYS 1 A CYS 1 1_555 A SG CYS 54 A CYS 54 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.059 ? disulf ? disulf3 A SG CYS 9 A CYS 9 1_555 A SG CYS 113 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 55 A CYS 55 1_555 A SG CYS 96 A CYS 96 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 55 A CYS 55 1_555 A SG CYS 96 A CYS 96 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc1 A O ASP 50 A ASP 50 1_555 C CA CA . A CA 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc2 A OE1 GLN 112 A GLN 112 1_555 C CA CA . A CA 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc3 C CA CA . A CA 116 1_555 D O HOH . A HOH 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc4 C CA CA . A CA 116 1_555 D O HOH . A HOH 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc5 C CA CA . A CA 116 1_555 D O HOH . A HOH 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc6 C CA CA . A CA 116 1_555 D O HOH . A HOH 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc7 C CA CA . A CA 116 1_555 D O HOH . A HOH 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id 3AM _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "3'-AMP" # 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 O1P P 3AM doub 1 n n P O2P 3AM sing 2 n n P O3P 3AM sing 3 n n P O3' 3AM sing 4 n n O2' C2' 3AM sing 5 n n C2' C3' 3AM sing 6 n n C2' C1' 3AM sing 7 n n C3' O3' 3AM sing 8 n n C3' C4' 3AM sing 9 n n C1' O4' 3AM sing 10 n n C1' N9 3AM sing 11 n n O4' C4' 3AM sing 12 n n C4' C5' 3AM sing 13 n n C5' O5' 3AM sing 14 n n N9 C8 3AM sing 15 n y N9 C4 3AM sing 16 n y C8 N7 3AM doub 17 n y N7 C5 3AM sing 18 n y C5 C6 3AM doub 19 n y C5 C4 3AM sing 20 n y C6 N6 3AM sing 21 n n C6 N1 3AM sing 22 n y C4 N3 3AM doub 23 n y N3 C2 3AM sing 24 n y C2 N1 3AM doub 25 n y O2P HO2P 3AM sing 26 n n O3P HO3P 3AM sing 27 n n O2' HO2' 3AM sing 28 n n C2' H2' 3AM sing 29 n n C3' H3' 3AM sing 30 n n C1' H1' 3AM sing 31 n n C4' H4' 3AM sing 32 n n C5' H5' 3AM sing 33 n n C5' "H5'A" 3AM sing 34 n n O5' HO5' 3AM sing 35 n n C8 H8 3AM sing 36 n n N6 HN6 3AM sing 37 n n N6 HN6A 3AM sing 38 n n C2 H2 3AM sing 39 n n # _atom_sites.entry_id 3AGN _atom_sites.fract_transf_matrix[1][1] 0.026399 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.012305 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025133 _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] 0.030746 _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 3AM A 1 115 115 3AM 3AM . C 3 CA A 1 116 116 CA CA . D 4 HOH A 1 117 117 HOH HOH . D 4 HOH A 2 118 118 HOH HOH . D 4 HOH A 3 119 119 HOH HOH . D 4 HOH A 4 120 120 HOH HOH . D 4 HOH A 5 121 121 HOH HOH . D 4 HOH A 6 122 122 HOH HOH . D 4 HOH A 7 123 123 HOH HOH . D 4 HOH A 8 124 124 HOH HOH . D 4 HOH A 9 125 125 HOH HOH . D 4 HOH A 10 126 126 HOH HOH . D 4 HOH A 11 127 127 HOH HOH . D 4 HOH A 12 128 128 HOH HOH . D 4 HOH A 13 129 129 HOH HOH . D 4 HOH A 14 130 130 HOH HOH . D 4 HOH A 15 131 131 HOH HOH . D 4 HOH A 16 132 132 HOH HOH . D 4 HOH A 17 133 133 HOH HOH . D 4 HOH A 18 134 134 HOH HOH . D 4 HOH A 19 135 135 HOH HOH . D 4 HOH A 20 136 136 HOH HOH . D 4 HOH A 21 137 137 HOH HOH . D 4 HOH A 22 138 138 HOH HOH . D 4 HOH A 23 139 139 HOH HOH . D 4 HOH A 24 140 140 HOH HOH . D 4 HOH A 25 141 141 HOH HOH . D 4 HOH A 26 142 142 HOH HOH . D 4 HOH A 27 143 143 HOH HOH . D 4 HOH A 28 144 144 HOH HOH . D 4 HOH A 29 145 145 HOH HOH . D 4 HOH A 30 146 146 HOH HOH . D 4 HOH A 31 147 147 HOH HOH . D 4 HOH A 32 148 148 HOH HOH . D 4 HOH A 33 149 149 HOH HOH . D 4 HOH A 34 150 150 HOH HOH . D 4 HOH A 35 151 151 HOH HOH . D 4 HOH A 36 152 152 HOH HOH . D 4 HOH A 37 153 153 HOH HOH . D 4 HOH A 38 154 154 HOH HOH . D 4 HOH A 39 155 155 HOH HOH . D 4 HOH A 40 156 156 HOH HOH . D 4 HOH A 41 157 157 HOH HOH . D 4 HOH A 42 158 158 HOH HOH . D 4 HOH A 43 159 159 HOH HOH . D 4 HOH A 44 160 160 HOH HOH . D 4 HOH A 45 161 161 HOH HOH . D 4 HOH A 46 162 162 HOH HOH . D 4 HOH A 47 163 163 HOH HOH . D 4 HOH A 48 164 164 HOH HOH . D 4 HOH A 49 165 165 HOH HOH . D 4 HOH A 50 166 166 HOH HOH . D 4 HOH A 51 167 167 HOH HOH . D 4 HOH A 52 168 168 HOH HOH . D 4 HOH A 53 169 169 HOH HOH . D 4 HOH A 54 170 170 HOH HOH . D 4 HOH A 55 171 171 HOH HOH . D 4 HOH A 56 172 172 HOH HOH . D 4 HOH A 57 173 173 HOH HOH . D 4 HOH A 58 174 174 HOH HOH . D 4 HOH A 59 175 175 HOH HOH . D 4 HOH A 60 176 176 HOH HOH . D 4 HOH A 61 177 177 HOH HOH . D 4 HOH A 62 178 178 HOH HOH . D 4 HOH A 63 179 179 HOH HOH . D 4 HOH A 64 180 180 HOH HOH . D 4 HOH A 65 181 181 HOH HOH . D 4 HOH A 66 182 182 HOH HOH . D 4 HOH A 67 183 183 HOH HOH . D 4 HOH A 68 184 184 HOH HOH . D 4 HOH A 69 185 185 HOH HOH . D 4 HOH A 70 186 186 HOH HOH . D 4 HOH A 71 187 187 HOH HOH . D 4 HOH A 72 188 188 HOH HOH . D 4 HOH A 73 189 189 HOH HOH . D 4 HOH A 74 190 190 HOH HOH . D 4 HOH A 75 191 191 HOH HOH . D 4 HOH A 76 192 192 HOH HOH . D 4 HOH A 77 193 193 HOH HOH . D 4 HOH A 78 194 194 HOH HOH . D 4 HOH A 79 195 195 HOH HOH . D 4 HOH A 80 196 196 HOH HOH . D 4 HOH A 81 197 197 HOH HOH . D 4 HOH A 82 198 198 HOH HOH . D 4 HOH A 83 199 199 HOH HOH . D 4 HOH A 84 200 200 HOH HOH . D 4 HOH A 85 201 201 HOH HOH . D 4 HOH A 86 202 202 HOH HOH . D 4 HOH A 87 203 203 HOH HOH . D 4 HOH A 88 204 204 HOH HOH . D 4 HOH A 89 205 205 HOH HOH . D 4 HOH A 90 206 206 HOH HOH . D 4 HOH A 91 207 207 HOH HOH . D 4 HOH A 92 208 208 HOH HOH . D 4 HOH A 93 209 209 HOH HOH . D 4 HOH A 94 210 210 HOH HOH . D 4 HOH A 95 211 211 HOH HOH . D 4 HOH A 96 212 212 HOH HOH . D 4 HOH A 97 213 213 HOH HOH . D 4 HOH A 98 214 214 HOH HOH . D 4 HOH A 99 215 215 HOH HOH . D 4 HOH A 100 216 216 HOH HOH . D 4 HOH A 101 217 217 HOH HOH . D 4 HOH A 102 218 218 HOH HOH . D 4 HOH A 103 219 219 HOH HOH . D 4 HOH A 104 220 220 HOH HOH . D 4 HOH A 105 221 221 HOH HOH . D 4 HOH A 106 222 222 HOH HOH . D 4 HOH A 107 223 223 HOH HOH . D 4 HOH A 108 224 224 HOH HOH . D 4 HOH A 109 225 225 HOH HOH . D 4 HOH A 110 226 226 HOH HOH . D 4 HOH A 111 227 227 HOH HOH . D 4 HOH A 112 228 228 HOH HOH . D 4 HOH A 113 229 229 HOH HOH . D 4 HOH A 114 230 230 HOH HOH . D 4 HOH A 115 231 231 HOH HOH . D 4 HOH A 116 232 232 HOH HOH . D 4 HOH A 117 233 233 HOH HOH . D 4 HOH A 118 234 234 HOH HOH . D 4 HOH A 119 235 235 HOH HOH . D 4 HOH A 120 236 236 HOH HOH . D 4 HOH A 121 237 237 HOH HOH . D 4 HOH A 122 238 238 HOH HOH . D 4 HOH A 123 239 239 HOH HOH . D 4 HOH A 124 240 240 HOH HOH . D 4 HOH A 125 241 241 HOH HOH . D 4 HOH A 126 242 242 HOH HOH . D 4 HOH A 127 243 243 HOH HOH . D 4 HOH A 128 244 244 HOH HOH . D 4 HOH A 129 245 245 HOH HOH . D 4 HOH A 130 246 246 HOH HOH . D 4 HOH A 131 247 247 HOH HOH . D 4 HOH A 132 248 248 HOH HOH . D 4 HOH A 133 249 249 HOH HOH . D 4 HOH A 134 250 250 HOH HOH . D 4 HOH A 135 251 251 HOH HOH . D 4 HOH A 136 252 252 HOH HOH . D 4 HOH A 137 253 253 HOH HOH . D 4 HOH A 138 254 254 HOH HOH . D 4 HOH A 139 255 255 HOH HOH . D 4 HOH A 140 256 256 HOH HOH . D 4 HOH A 141 257 257 HOH HOH . D 4 HOH A 142 258 258 HOH HOH . D 4 HOH A 143 259 259 HOH HOH . D 4 HOH A 144 260 260 HOH HOH . D 4 HOH A 145 261 261 HOH HOH . D 4 HOH A 146 262 262 HOH HOH . D 4 HOH A 147 263 263 HOH HOH . D 4 HOH A 148 264 264 HOH HOH . D 4 HOH A 149 265 265 HOH HOH . D 4 HOH A 150 266 266 HOH HOH . D 4 HOH A 151 267 267 HOH HOH . D 4 HOH A 152 268 268 HOH HOH . D 4 HOH A 153 269 269 HOH HOH . D 4 HOH A 154 270 270 HOH HOH . D 4 HOH A 155 271 271 HOH HOH . D 4 HOH A 156 272 272 HOH HOH . D 4 HOH A 157 273 273 HOH HOH . D 4 HOH A 158 274 274 HOH HOH . D 4 HOH A 159 275 275 HOH HOH . D 4 HOH A 160 276 276 HOH HOH . D 4 HOH A 161 277 277 HOH HOH . D 4 HOH A 162 278 278 HOH HOH . D 4 HOH A 163 279 279 HOH HOH . D 4 HOH A 164 280 280 HOH HOH . D 4 HOH A 165 281 281 HOH HOH . D 4 HOH A 166 282 282 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 O1P 3AM . . . B 2 -1.107 -9.134 7.027 1 5.95 ? O1P 3AM 115 A 1 HETATM 2 P P 3AM . . . B 2 -2.515 -8.612 7.192 1 4.54 ? P 3AM 115 A 1 HETATM 3 O O2P 3AM . . . B 2 -3.331 -8.845 5.942 1 7.39 ? O2P 3AM 115 A 1 HETATM 4 O O3P 3AM . . . B 2 -2.612 -7.223 7.683 1 5.91 ? O3P 3AM 115 A 1 HETATM 5 O O2' 3AM . . . B 2 -4.889 -10.226 10.255 1 4.63 ? O2' 3AM 115 A 1 HETATM 6 C C2' 3AM . . . B 2 -3.557 -9.887 10.639 1 3.93 ? C2' 3AM 115 A 1 HETATM 7 C C3' 3AM . . . B 2 -2.607 -10 9.466 1 4.03 ? C3' 3AM 115 A 1 HETATM 8 O O3' 3AM . . . B 2 -3.252 -9.58 8.269 1 4.18 ? O3' 3AM 115 A 1 HETATM 9 C C1' 3AM . . . B 2 -3.024 -10.913 11.596 1 3.56 ? C1' 3AM 115 A 1 HETATM 10 O O4' 3AM . . . B 2 -2.277 -11.863 10.847 1 3.51 ? O4' 3AM 115 A 1 HETATM 11 C C4' 3AM . . . B 2 -2.259 -11.479 9.464 1 4.05 ? C4' 3AM 115 A 1 HETATM 12 C C5' 3AM . . . B 2 -0.917 -11.826 8.901 1 4.76 ? C5' 3AM 115 A 1 HETATM 13 O O5' 3AM . A . B 2 -0.781 -13.198 8.633 0.5 8.05 ? O5' 3AM 115 A 1 HETATM 14 O O5' 3AM . B . B 2 -0.862 -11.851 7.474 0.5 4.38 ? O5' 3AM 115 A 1 HETATM 15 N N9 3AM . . . B 2 -2.158 -10.34 12.658 1 3.47 ? N9 3AM 115 A 1 HETATM 16 C C8 3AM . . . B 2 -2.654 -9.943 13.853 1 3.85 ? C8 3AM 115 A 1 HETATM 17 N N7 3AM . . . B 2 -1.703 -9.48 14.674 1 3.68 ? N7 3AM 115 A 1 HETATM 18 C C5 3AM . . . B 2 -0.56 -9.602 13.975 1 3.53 ? C5 3AM 115 A 1 HETATM 19 C C6 3AM . . . B 2 0.814 -9.386 14.288 1 3.49 ? C6 3AM 115 A 1 HETATM 20 N N6 3AM . . . B 2 1.208 -8.903 15.459 1 3.7 ? N6 3AM 115 A 1 HETATM 21 C C4 3AM . . . B 2 -0.828 -10.158 12.671 1 3.35 ? C4 3AM 115 A 1 HETATM 22 N N3 3AM . . . B 2 0.105 -10.392 11.735 1 3.9 ? N3 3AM 115 A 1 HETATM 23 C C2 3AM . . . B 2 1.353 -10.154 12.11 1 4.14 ? C2 3AM 115 A 1 HETATM 24 N N1 3AM . . . B 2 1.705 -9.711 13.339 1 3.69 ? N1 3AM 115 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 24 #