data_3UD5 # _model_server_result.job_id UNYKonn1l8xeg9QR77rA6g _model_server_result.datetime_utc '2025-03-09 04:53:34' _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 3ud5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":171}' # _entry.id 3UD5 # _exptl.entry_id 3UD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 584.654 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[1-(2-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine" _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 102.57 _cell.angle_gamma 90 _cell.entry_id 3UD5 _cell.length_a 79.92 _cell.length_b 52.84 _cell.length_c 36.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,E _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 # _chem_comp.formula 'C24 H32 N12 O4 S' _chem_comp.formula_weight 584.654 _chem_comp.id J1A _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[1-(2-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine" _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 C2 C1 J1A sing 169 n n C10 C1 J1A sing 170 n n C1 O1 J1A sing 171 n n C1 H1 J1A sing 172 n n C4 N1 J1A sing 173 n n N1 C9 J1A sing 174 n y N1 C5 J1A sing 175 n y O1 C4 J1A sing 176 n n C10 S1 J1A sing 177 n n S1 C11 J1A sing 178 n n O2 C2 J1A sing 179 n n C2 C3 J1A sing 180 n n C2 H2 J1A sing 181 n n C5 N2 J1A doub 182 n y C6 N2 J1A sing 183 n y O2 HO2 J1A sing 184 n n O3 C3 J1A sing 185 n n C3 C4 J1A sing 186 n n C3 H3 J1A sing 187 n n C7 N3 J1A sing 188 n n N3 HN3 J1A sing 189 n n N3 HN3A J1A sing 190 n n O3 HO3 J1A sing 191 n n C4 H4 J1A sing 192 n n C8 N4 J1A doub 193 n y N4 C7 J1A sing 194 n y O4 C20 J1A doub 195 n n C5 H5 J1A sing 196 n n N5 C9 J1A doub 197 n y N5 C8 J1A sing 198 n y C9 C6 J1A sing 199 n y C6 C7 J1A doub 200 n y C13 N6 J1A sing 201 n n N6 C14 J1A sing 202 n n N6 C16 J1A sing 203 n n C8 H8 J1A sing 204 n n C25 N8 J1A sing 205 n n N8 C19 J1A doub 206 n n C19 N9 J1A sing 207 n n N9 HN9 J1A sing 208 n n N9 HN9A J1A sing 209 n n C10 H10 J1A sing 210 n n C10 H10A J1A sing 211 n n C20 N10 J1A sing 212 n n N10 C19 J1A sing 213 n n N10 HN10 J1A sing 214 n n C12 C11 J1A sing 215 n n C11 C15 J1A sing 216 n n C11 H11 J1A sing 217 n n C21 N11 J1A doub 218 n y N11 C26 J1A sing 219 n y C12 C13 J1A sing 220 n n C12 H12 J1A sing 221 n n C12 H12A J1A sing 222 n n C22 N12 J1A doub 223 n y N12 C25 J1A sing 224 n y C13 H13 J1A sing 225 n n C13 H13A J1A sing 226 n n C15 C14 J1A sing 227 n n C14 H14 J1A sing 228 n n C14 H14A J1A sing 229 n n C15 H15 J1A sing 230 n n C15 H15A J1A sing 231 n n C16 C27 J1A sing 232 n n C16 H16 J1A sing 233 n n C16 H16A J1A sing 234 n n N28 C18 J1A sing 235 n n C18 C21 J1A sing 236 n n C18 H18 J1A sing 237 n n C18 H18A J1A sing 238 n n C26 C20 J1A sing 239 n n C21 C22 J1A sing 240 n y C22 H22 J1A sing 241 n n C26 C25 J1A doub 242 n y N28 C27 J1A sing 243 n n C27 H27 J1A sing 244 n n C27 H27A J1A sing 245 n n N28 HN28 J1A sing 246 n n # _atom_sites.entry_id 3UD5 _atom_sites.fract_transf_matrix[1][1] 0.012513 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00279 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018926 _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] 0.027869 _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 J1A A 1 171 171 J1A J1A . C 3 EDO A 1 191 191 EDO EDO . D 3 EDO A 1 192 192 EDO EDO . E 4 HOH A 1 201 201 HOH HOH . E 4 HOH A 2 202 202 HOH HOH . E 4 HOH A 3 203 203 HOH HOH . E 4 HOH A 4 204 204 HOH HOH . E 4 HOH A 5 205 205 HOH HOH . E 4 HOH A 6 206 206 HOH HOH . E 4 HOH A 7 207 207 HOH HOH . E 4 HOH A 8 208 208 HOH HOH . E 4 HOH A 9 209 209 HOH HOH . E 4 HOH A 10 210 210 HOH HOH . E 4 HOH A 11 211 211 HOH HOH . E 4 HOH A 12 212 212 HOH HOH . E 4 HOH A 13 213 213 HOH HOH . E 4 HOH A 14 214 214 HOH HOH . E 4 HOH A 15 215 215 HOH HOH . E 4 HOH A 16 216 216 HOH HOH . E 4 HOH A 17 217 217 HOH HOH . E 4 HOH A 18 218 218 HOH HOH . E 4 HOH A 19 219 219 HOH HOH . E 4 HOH A 20 220 220 HOH HOH . E 4 HOH A 21 221 221 HOH HOH . E 4 HOH A 22 222 222 HOH HOH . E 4 HOH A 23 223 223 HOH HOH . E 4 HOH A 24 224 224 HOH HOH . E 4 HOH A 25 225 225 HOH HOH . E 4 HOH A 26 226 226 HOH HOH . E 4 HOH A 27 227 227 HOH HOH . E 4 HOH A 28 228 228 HOH HOH . E 4 HOH A 29 229 229 HOH HOH . E 4 HOH A 30 230 230 HOH HOH . E 4 HOH A 31 231 231 HOH HOH . E 4 HOH A 32 232 232 HOH HOH . E 4 HOH A 33 233 233 HOH HOH . E 4 HOH A 34 234 234 HOH HOH . E 4 HOH A 35 235 235 HOH HOH . E 4 HOH A 36 236 236 HOH HOH . E 4 HOH A 37 237 237 HOH HOH . E 4 HOH A 38 238 238 HOH HOH . E 4 HOH A 39 239 239 HOH HOH . E 4 HOH A 40 240 240 HOH HOH . E 4 HOH A 41 241 241 HOH HOH . E 4 HOH A 42 242 242 HOH HOH . E 4 HOH A 43 243 243 HOH HOH . E 4 HOH A 44 244 244 HOH HOH . E 4 HOH A 45 245 245 HOH HOH . E 4 HOH A 46 246 246 HOH HOH . E 4 HOH A 47 247 247 HOH HOH . E 4 HOH A 48 248 248 HOH HOH . E 4 HOH A 49 249 249 HOH HOH . E 4 HOH A 50 250 250 HOH HOH . E 4 HOH A 51 251 251 HOH HOH . E 4 HOH A 52 252 252 HOH HOH . E 4 HOH A 53 253 253 HOH HOH . E 4 HOH A 54 254 254 HOH HOH . E 4 HOH A 55 255 255 HOH HOH . E 4 HOH A 56 256 256 HOH HOH . E 4 HOH A 57 257 257 HOH HOH . E 4 HOH A 58 258 258 HOH HOH . E 4 HOH A 59 259 259 HOH HOH . E 4 HOH A 60 260 260 HOH HOH . E 4 HOH A 61 261 261 HOH HOH . E 4 HOH A 62 262 262 HOH HOH . E 4 HOH A 63 263 263 HOH HOH . E 4 HOH A 64 264 264 HOH HOH . E 4 HOH A 65 265 265 HOH HOH . E 4 HOH A 66 266 266 HOH HOH . E 4 HOH A 67 267 267 HOH HOH . E 4 HOH A 68 268 268 HOH HOH . E 4 HOH A 69 269 269 HOH HOH . E 4 HOH A 70 270 270 HOH HOH . E 4 HOH A 71 271 271 HOH HOH . E 4 HOH A 72 272 272 HOH HOH . E 4 HOH A 73 273 273 HOH HOH . E 4 HOH A 74 274 274 HOH HOH . E 4 HOH A 75 275 275 HOH HOH . E 4 HOH A 76 276 276 HOH HOH . E 4 HOH A 77 277 277 HOH HOH . E 4 HOH A 78 278 278 HOH HOH . E 4 HOH A 79 279 279 HOH HOH . E 4 HOH A 80 280 280 HOH HOH . E 4 HOH A 81 281 281 HOH HOH . E 4 HOH A 82 282 282 HOH HOH . E 4 HOH A 83 283 283 HOH HOH . E 4 HOH A 84 284 284 HOH HOH . E 4 HOH A 85 285 285 HOH HOH . E 4 HOH A 86 286 286 HOH HOH . E 4 HOH A 87 287 287 HOH HOH . E 4 HOH A 88 288 288 HOH HOH . E 4 HOH A 89 289 289 HOH HOH . E 4 HOH A 90 290 290 HOH HOH . E 4 HOH A 91 291 291 HOH HOH . E 4 HOH A 92 292 292 HOH HOH . E 4 HOH A 93 293 293 HOH HOH . E 4 HOH A 94 294 294 HOH HOH . E 4 HOH A 95 295 295 HOH HOH . E 4 HOH A 96 296 296 HOH HOH . E 4 HOH A 97 297 297 HOH HOH . E 4 HOH A 98 298 298 HOH HOH . E 4 HOH A 99 299 299 HOH HOH . E 4 HOH A 100 300 300 HOH HOH . E 4 HOH A 101 301 301 HOH HOH . E 4 HOH A 102 302 302 HOH HOH . E 4 HOH A 103 303 303 HOH HOH . E 4 HOH A 104 304 304 HOH HOH . E 4 HOH A 105 305 305 HOH HOH . E 4 HOH A 106 306 306 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 C1 J1A . . . B 2 20.703 5.866 2.485 1 50.05 ? C1 J1A 171 A 1 HETATM 2 N N1 J1A . . . B 2 22.682 5.295 5.271 1 36.09 ? N1 J1A 171 A 1 HETATM 3 O O1 J1A . . . B 2 20.962 5.696 3.864 1 31.8 ? O1 J1A 171 A 1 HETATM 4 S S1 J1A . . . B 2 18.316 4.201 2.415 1 74.76 ? S1 J1A 171 A 1 HETATM 5 C C2 J1A . . . B 2 21.721 4.929 1.776 1 40.04 ? C2 J1A 171 A 1 HETATM 6 N N2 J1A . . . B 2 23.374 5.47 7.397 1 24.2 ? N2 J1A 171 A 1 HETATM 7 O O2 J1A . . . B 2 22.195 5.436 0.582 1 46.27 ? O2 J1A 171 A 1 HETATM 8 C C3 J1A . . . B 2 22.924 4.87 2.781 1 37.08 ? C3 J1A 171 A 1 HETATM 9 N N3 J1A . . . B 2 23.333 3.254 9.281 1 24.82 ? N3 J1A 171 A 1 HETATM 10 O O3 J1A . . . B 2 24.123 5.352 2.28 1 34.65 ? O3 J1A 171 A 1 HETATM 11 C C4 J1A . . . B 2 22.372 5.74 3.959 1 41.47 ? C4 J1A 171 A 1 HETATM 12 N N4 J1A . . . B 2 22.401 1.892 7.519 1 27.43 ? N4 J1A 171 A 1 HETATM 13 O O4 J1A . . . B 2 11.071 -1.191 9.57 1 26.8 ? O4 J1A 171 A 1 HETATM 14 C C5 J1A . . . B 2 23.202 6.11 6.258 1 30.52 ? C5 J1A 171 A 1 HETATM 15 N N5 J1A . . . B 2 22.005 2.881 5.299 1 30.37 ? N5 J1A 171 A 1 HETATM 16 C C6 J1A . . . B 2 22.939 4.199 7.165 1 38.04 ? C6 J1A 171 A 1 HETATM 17 N N6 J1A . . . B 2 15.14 3.743 5.812 1 95.19 ? N6 J1A 171 A 1 HETATM 18 C C7 J1A . . . B 2 22.883 3.098 8.016 1 34.03 ? C7 J1A 171 A 1 HETATM 19 C C8 J1A . . . B 2 21.996 1.878 6.21 1 33.5 ? C8 J1A 171 A 1 HETATM 20 N N8 J1A . . . B 2 7.557 0.937 10.051 1 31.87 ? N8 J1A 171 A 1 HETATM 21 C C9 J1A . . . B 2 22.492 4.032 5.83 1 34.44 ? C9 J1A 171 A 1 HETATM 22 N N9 J1A . . . B 2 6.852 -0.758 11.498 1 23.63 ? N9 J1A 171 A 1 HETATM 23 C C10 J1A . . . B 2 19.2 5.758 2.158 1 58.84 ? C10 J1A 171 A 1 HETATM 24 N N10 J1A . . . B 2 9.023 -0.982 10.518 1 21.91 ? N10 J1A 171 A 1 HETATM 25 C C11 J1A . . . B 2 17.063 4.525 3.732 1 82.49 ? C11 J1A 171 A 1 HETATM 26 N N11 J1A . . . B 2 10.766 1.271 8.145 1 35.97 ? N11 J1A 171 A 1 HETATM 27 C C12 J1A . . . B 2 15.705 3.959 3.303 1 50.1 ? C12 J1A 171 A 1 HETATM 28 N N12 J1A . . . B 2 8.254 2.647 8.587 1 38.8 ? N12 J1A 171 A 1 HETATM 29 C C13 J1A . . . B 2 14.687 4.159 4.445 1 78.32 ? C13 J1A 171 A 1 HETATM 30 C C14 J1A . . . B 2 16.538 4.146 6.143 1 77.49 ? C14 J1A 171 A 1 HETATM 31 C C15 J1A . . . B 2 17.54 3.858 5.033 1 64.69 ? C15 J1A 171 A 1 HETATM 32 C C16 J1A . . . B 2 14.857 2.325 6.151 1 73.79 ? C16 J1A 171 A 1 HETATM 33 C C18 J1A . . . B 2 11.359 3.213 6.613 1 57.76 ? C18 J1A 171 A 1 HETATM 34 C C19 J1A . . . B 2 7.833 -0.255 10.669 1 29.11 ? C19 J1A 171 A 1 HETATM 35 C C20 J1A . . . B 2 10.072 -0.512 9.663 1 26.72 ? C20 J1A 171 A 1 HETATM 36 C C21 J1A . . . B 2 10.439 2.471 7.564 1 50.73 ? C21 J1A 171 A 1 HETATM 37 C C22 J1A . . . B 2 9.196 3.124 7.784 1 35.75 ? C22 J1A 171 A 1 HETATM 38 C C25 J1A . . . B 2 8.555 1.428 9.214 1 31.48 ? C25 J1A 171 A 1 HETATM 39 C C26 J1A . . . B 2 9.796 0.761 8.985 1 28.08 ? C26 J1A 171 A 1 HETATM 40 C C27 J1A . . . B 2 13.591 2.344 7.03 1 78.33 ? C27 J1A 171 A 1 HETATM 41 N N28 J1A . . . B 2 12.452 2.425 6.077 1 64.59 ? N28 J1A 171 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 41 #