data_3UDE # _model_server_result.job_id q104cV0BDsj80aMPTSg9Zg _model_server_result.datetime_utc '2024-11-16 08:41:50' _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 3ude # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":171}' # _entry.id 3UDE # _exptl.entry_id 3UDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 614.723 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[1-(2-{[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-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 90 _cell.angle_gamma 90 _cell.entry_id 3UDE _cell.length_a 52.91 _cell.length_b 70.98 _cell.length_c 36.38 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 # _chem_comp.formula 'C26 H38 N12 O4 S' _chem_comp.formula_weight 614.723 _chem_comp.id J1B _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[1-(2-{[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-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 C1 O1 J1B sing 166 n n C1 C2 J1B sing 167 n n C1 C10 J1B sing 168 n n N1 C4 J1B sing 169 n n N1 C5 J1B sing 170 n y N1 C9 J1B sing 171 n y O1 C4 J1B sing 172 n n S1 C10 J1B sing 173 n n S1 C11 J1B sing 174 n n C2 O2 J1B sing 175 n n C2 C3 J1B sing 176 n n N2 C5 J1B doub 177 n y N2 C6 J1B sing 178 n y C3 O3 J1B sing 179 n n C3 C4 J1B sing 180 n n N3 C7 J1B sing 181 n n N4 C7 J1B doub 182 n y N4 C8 J1B sing 183 n y N5 C8 J1B doub 184 n y N5 C9 J1B sing 185 n y O5 C20 J1B doub 186 n n C6 C7 J1B sing 187 n y C6 C9 J1B doub 188 n y N6 C13 J1B sing 189 n n N6 C14 J1B sing 190 n n N6 C16 J1B sing 191 n n N8 C19 J1B doub 192 n n N8 C25 J1B sing 193 n n N9 C19 J1B sing 194 n n N10 C19 J1B sing 195 n n N10 C20 J1B sing 196 n n C11 C12 J1B sing 197 n n C11 C15 J1B sing 198 n n N11 C21 J1B doub 199 n n N11 C26 J1B sing 200 n n C12 C13 J1B sing 201 n n N12 C22 J1B sing 202 n n N12 C25 J1B sing 203 n n C14 C15 J1B sing 204 n n C16 C27 J1B sing 205 n n C18 C21 J1B sing 206 n n C18 N28 J1B sing 207 n n C20 C26 J1B sing 208 n n C21 C22 J1B sing 209 n n C22 C23 J1B sing 210 n n C22 C24 J1B sing 211 n n C25 C26 J1B doub 212 n n C27 N28 J1B sing 213 n n C1 H1 J1B sing 214 n n C2 H2 J1B sing 215 n n O2 HO2 J1B sing 216 n n C3 H3 J1B sing 217 n n N3 HN3 J1B sing 218 n n N3 HN3A J1B sing 219 n n O3 HO3 J1B sing 220 n n C4 H4 J1B sing 221 n n C5 H5 J1B sing 222 n n C8 H8 J1B sing 223 n n N9 HN9 J1B sing 224 n n N9 HN9A J1B sing 225 n n C10 H10 J1B sing 226 n n C10 H10A J1B sing 227 n n N10 HN10 J1B sing 228 n n C11 H11 J1B sing 229 n n C12 H12 J1B sing 230 n n C12 H12A J1B sing 231 n n N12 HN12 J1B sing 232 n n C13 H13 J1B sing 233 n n C13 H13A J1B sing 234 n n C14 H14 J1B sing 235 n n C14 H14A J1B sing 236 n n C15 H15 J1B sing 237 n n C15 H15A J1B sing 238 n n C16 H16 J1B sing 239 n n C16 H16A J1B sing 240 n n C18 H18 J1B sing 241 n n C18 H18A J1B sing 242 n n C23 H23 J1B sing 243 n n C23 H23A J1B sing 244 n n C23 H23B J1B sing 245 n n C24 H24 J1B sing 246 n n C24 H24A J1B sing 247 n n C24 H24B J1B sing 248 n n C27 H27 J1B sing 249 n n C27 H27A J1B sing 250 n n N28 HN28 J1B sing 251 n n # _atom_sites.entry_id 3UDE _atom_sites.fract_transf_matrix[1][1] 0.0189 _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] 0.014089 _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] 0.027491 _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 J1B A 1 171 171 J1B J1B . C 3 ACT A 1 191 191 ACT ACT . D 4 HOH A 1 201 201 HOH HOH . D 4 HOH A 2 202 202 HOH HOH . D 4 HOH A 3 203 203 HOH HOH . D 4 HOH A 4 204 204 HOH HOH . D 4 HOH A 5 205 205 HOH HOH . D 4 HOH A 6 206 206 HOH HOH . D 4 HOH A 7 207 207 HOH HOH . D 4 HOH A 8 208 208 HOH HOH . D 4 HOH A 9 209 209 HOH HOH . D 4 HOH A 10 210 210 HOH HOH . D 4 HOH A 11 211 211 HOH HOH . D 4 HOH A 12 212 212 HOH HOH . D 4 HOH A 13 213 213 HOH HOH . D 4 HOH A 14 214 214 HOH HOH . D 4 HOH A 15 215 215 HOH HOH . D 4 HOH A 16 216 216 HOH HOH . D 4 HOH A 17 217 217 HOH HOH . D 4 HOH A 18 218 218 HOH HOH . D 4 HOH A 19 219 219 HOH HOH . D 4 HOH A 20 220 220 HOH HOH . D 4 HOH A 21 221 221 HOH HOH . D 4 HOH A 22 222 222 HOH HOH . D 4 HOH A 23 223 223 HOH HOH . D 4 HOH A 24 224 224 HOH HOH . D 4 HOH A 25 225 225 HOH HOH . D 4 HOH A 26 226 226 HOH HOH . D 4 HOH A 27 227 227 HOH HOH . D 4 HOH A 28 228 228 HOH HOH . D 4 HOH A 29 229 229 HOH HOH . D 4 HOH A 30 230 230 HOH HOH . D 4 HOH A 31 231 231 HOH HOH . D 4 HOH A 32 232 232 HOH HOH . D 4 HOH A 33 233 233 HOH HOH . D 4 HOH A 34 234 234 HOH HOH . D 4 HOH A 35 235 235 HOH HOH . D 4 HOH A 36 236 236 HOH HOH . D 4 HOH A 37 237 237 HOH HOH . D 4 HOH A 38 238 238 HOH HOH . D 4 HOH A 39 239 239 HOH HOH . D 4 HOH A 40 240 240 HOH HOH . D 4 HOH A 41 241 241 HOH HOH . D 4 HOH A 42 242 242 HOH HOH . D 4 HOH A 43 243 243 HOH HOH . D 4 HOH A 44 244 244 HOH HOH . D 4 HOH A 45 245 245 HOH HOH . D 4 HOH A 46 246 246 HOH HOH . D 4 HOH A 47 247 247 HOH HOH . D 4 HOH A 48 248 248 HOH HOH . D 4 HOH A 49 249 249 HOH HOH . D 4 HOH A 50 250 250 HOH HOH . D 4 HOH A 51 251 251 HOH HOH . D 4 HOH A 52 252 252 HOH HOH . D 4 HOH A 53 253 253 HOH HOH . D 4 HOH A 54 254 254 HOH HOH . D 4 HOH A 55 255 255 HOH HOH . D 4 HOH A 56 256 256 HOH HOH . D 4 HOH A 57 257 257 HOH HOH . D 4 HOH A 58 258 258 HOH HOH . D 4 HOH A 59 259 259 HOH HOH . D 4 HOH A 60 260 260 HOH HOH . D 4 HOH A 61 261 261 HOH HOH . D 4 HOH A 62 262 262 HOH HOH . D 4 HOH A 63 263 263 HOH HOH . D 4 HOH A 64 264 264 HOH HOH . D 4 HOH A 65 265 265 HOH HOH . D 4 HOH A 66 266 266 HOH HOH . D 4 HOH A 67 267 267 HOH HOH . D 4 HOH A 68 268 268 HOH HOH . D 4 HOH A 69 269 269 HOH HOH . D 4 HOH A 70 270 270 HOH HOH . D 4 HOH A 71 271 271 HOH HOH . D 4 HOH A 72 272 272 HOH HOH . D 4 HOH A 73 273 273 HOH HOH . D 4 HOH A 74 274 274 HOH HOH . D 4 HOH A 75 275 275 HOH HOH . D 4 HOH A 76 276 276 HOH HOH . D 4 HOH A 77 277 277 HOH HOH . D 4 HOH A 78 278 278 HOH HOH . D 4 HOH A 79 279 279 HOH HOH . D 4 HOH A 80 280 280 HOH HOH . D 4 HOH A 81 281 281 HOH HOH . D 4 HOH A 82 282 282 HOH HOH . D 4 HOH A 83 283 283 HOH HOH . D 4 HOH A 84 284 284 HOH HOH . D 4 HOH A 85 285 285 HOH HOH . D 4 HOH A 86 286 286 HOH HOH . D 4 HOH A 87 287 287 HOH HOH . D 4 HOH A 88 288 288 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 J1B . . . B 2 2.156 17.073 15.706 1 39.02 ? C1 J1B 171 A 1 HETATM 2 N N1 J1B . . . B 2 2.748 14.373 13.534 1 28.54 ? N1 J1B 171 A 1 HETATM 3 O O1 J1B . . . B 2 2.269 16.433 14.454 1 36.04 ? O1 J1B 171 A 1 HETATM 4 S S1 J1B . . . B 2 4.119 19.061 15.418 1 41.23 ? S1 J1B 171 A 1 HETATM 5 C C2 J1B . . . B 2 3.154 16.327 16.593 1 37.78 ? C2 J1B 171 A 1 HETATM 6 N N2 J1B . . . B 2 2.591 13.189 11.577 1 26.01 ? N2 J1B 171 A 1 HETATM 7 O O2 J1B . . . B 2 2.683 16.268 17.909 1 43.13 ? O2 J1B 171 A 1 HETATM 8 C C3 J1B . . . B 2 3.208 14.885 15.959 1 35.98 ? C3 J1B 171 A 1 HETATM 9 N N3 J1B . . . B 2 4.87 12.77 9.799 1 12.96 ? N3 J1B 171 A 1 HETATM 10 O O3 J1B . . . B 2 2.659 13.914 16.824 1 33.49 ? O3 J1B 171 A 1 HETATM 11 C C4 J1B . . . B 2 2.29 15.026 14.741 1 27.98 ? C4 J1B 171 A 1 HETATM 12 N N4 J1B . . . B 2 6.162 14.048 11.352 1 19.89 ? N4 J1B 171 A 1 HETATM 13 C C5 J1B . . . B 2 1.917 13.631 12.645 1 26.6 ? C5 J1B 171 A 1 HETATM 14 N N5 J1B . . . B 2 5.15 14.991 13.392 1 22.96 ? N5 J1B 171 A 1 HETATM 15 O O5 J1B . . . B 2 9.579 24.929 7.16 1 18.25 ? O5 J1B 171 A 1 HETATM 16 C C6 J1B . . . B 2 3.883 13.654 11.773 1 24.04 ? C6 J1B 171 A 1 HETATM 17 N N6 J1B . . . B 2 5.496 20.189 11.742 1 37.99 ? N6 J1B 171 A 1 HETATM 18 C C7 J1B . . . B 2 4.998 13.491 10.97 1 21.56 ? C7 J1B 171 A 1 HETATM 19 C C8 J1B . . . B 2 6.174 14.754 12.524 1 21.82 ? C8 J1B 171 A 1 HETATM 20 N N8 J1B . . . B 2 7.398 28.199 6.062 1 29.18 ? N8 J1B 171 A 1 HETATM 21 C C9 J1B . . . B 2 4.005 14.397 12.969 1 27.07 ? C9 J1B 171 A 1 HETATM 22 N N9 J1B . . . B 2 9.005 28.503 4.432 1 22.67 ? N9 J1B 171 A 1 HETATM 23 C C10 J1B . . . B 2 2.411 18.562 15.62 1 32.48 ? C10 J1B 171 A 1 HETATM 24 N N10 J1B . . . B 2 9.259 26.677 5.857 1 19.46 ? N10 J1B 171 A 1 HETATM 25 C C11 J1B . . . B 2 4.835 18.368 13.894 1 31.48 ? C11 J1B 171 A 1 HETATM 26 N N11 J1B . . . B 2 7.191 25.539 8.62 1 27.68 ? N11 J1B 171 A 1 HETATM 27 C C12 J1B . . . B 2 3.938 18.691 12.733 1 33.23 ? C12 J1B 171 A 1 HETATM 28 N N12 J1B . . . B 2 5.816 27.834 7.745 1 35.51 ? N12 J1B 171 A 1 HETATM 29 C C13 J1B . . . B 2 4.135 20.124 12.315 1 41.34 ? C13 J1B 171 A 1 HETATM 30 C C14 J1B . . . B 2 6.483 20.152 12.825 1 31.28 ? C14 J1B 171 A 1 HETATM 31 C C15 J1B . . . B 2 6.277 18.86 13.701 1 29.23 ? C15 J1B 171 A 1 HETATM 32 C C16 J1B . . . B 2 5.572 21.304 10.727 1 47.89 ? C16 J1B 171 A 1 HETATM 33 C C18 J1B . . . B 2 5.664 24.981 10.336 1 35.98 ? C18 J1B 171 A 1 HETATM 34 C C19 J1B . . . B 2 8.534 27.773 5.48 1 26.26 ? C19 J1B 171 A 1 HETATM 35 C C20 J1B . . . B 2 8.847 25.875 6.923 1 25.75 ? C20 J1B 171 A 1 HETATM 36 C C21 J1B . . . B 2 6.062 25.852 9.174 1 40.6 ? C21 J1B 171 A 1 HETATM 37 C C22 J1B . . . B 2 5.191 27.064 8.83 1 34.46 ? C22 J1B 171 A 1 HETATM 38 C C23 J1B . . . B 2 4.977 27.992 10.016 1 35.46 ? C23 J1B 171 A 1 HETATM 39 C C24 J1B . . . B 2 3.82 26.623 8.335 1 34.07 ? C24 J1B 171 A 1 HETATM 40 C C25 J1B . . . B 2 6.968 27.429 7.116 1 28.3 ? C25 J1B 171 A 1 HETATM 41 C C26 J1B . . . B 2 7.642 26.31 7.558 1 22.56 ? C26 J1B 171 A 1 HETATM 42 C C27 J1B . . . B 2 5.837 22.72 11.246 1 45.67 ? C27 J1B 171 A 1 HETATM 43 N N28 J1B . . . B 2 6.027 23.582 10.088 1 37.57 ? N28 J1B 171 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #