data_3UDV # _model_server_result.job_id GYkthy0ViSyGKNkH3zLJfg _model_server_result.datetime_utc '2025-03-09 04:12:03' _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 3udv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":171}' # _entry.id 3UDV # _exptl.entry_id 3UDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 628.706 _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)carbonyl]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 3UDV _cell.length_a 53 _cell.length_b 70.64 _cell.length_c 36.25 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UDV _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 H36 N12 O5 S' _chem_comp.formula_weight 628.706 _chem_comp.id J1C _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)carbonyl]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 J1C sing 166 n n C1 C2 J1C sing 167 n n C1 C10 J1C sing 168 n n N1 C4 J1C sing 169 n n N1 C5 J1C sing 170 n y N1 C9 J1C sing 171 n y O1 C4 J1C sing 172 n n S1 C10 J1C sing 173 n n S1 C11 J1C sing 174 n n C2 O2 J1C sing 175 n n C2 C3 J1C sing 176 n n N2 C5 J1C doub 177 n y N2 C6 J1C sing 178 n y C3 O3 J1C sing 179 n n C3 C4 J1C sing 180 n n N3 C7 J1C sing 181 n n N4 C7 J1C doub 182 n y N4 C8 J1C sing 183 n y O4 C18 J1C doub 184 n n N5 C8 J1C doub 185 n y N5 C9 J1C sing 186 n y O5 C20 J1C doub 187 n n C6 C7 J1C sing 188 n y C6 C9 J1C doub 189 n y N6 C13 J1C sing 190 n n N6 C14 J1C sing 191 n n N6 C16 J1C sing 192 n n N8 C19 J1C doub 193 n n N8 C25 J1C sing 194 n n N9 C19 J1C sing 195 n n N10 C19 J1C sing 196 n n N10 C20 J1C sing 197 n n C11 C12 J1C sing 198 n n C11 C15 J1C sing 199 n n N11 C21 J1C doub 200 n n N11 C26 J1C sing 201 n n C12 C13 J1C sing 202 n n N12 C22 J1C sing 203 n n N12 C25 J1C sing 204 n n C14 C15 J1C sing 205 n n C16 C27 J1C sing 206 n n C18 C21 J1C sing 207 n n C18 N28 J1C sing 208 n n C20 C26 J1C sing 209 n n C21 C22 J1C sing 210 n n C22 C23 J1C sing 211 n n C22 C24 J1C sing 212 n n C25 C26 J1C doub 213 n n C27 N28 J1C sing 214 n n C1 H1 J1C sing 215 n n C2 H2 J1C sing 216 n n O2 HO2 J1C sing 217 n n C3 H3 J1C sing 218 n n N3 HN3 J1C sing 219 n n N3 HN3A J1C sing 220 n n O3 HO3 J1C sing 221 n n C4 H4 J1C sing 222 n n C5 H5 J1C sing 223 n n C8 H8 J1C sing 224 n n N9 HN9 J1C sing 225 n n N9 HN9A J1C sing 226 n n C10 H10 J1C sing 227 n n C10 H10A J1C sing 228 n n N10 HN10 J1C sing 229 n n C11 H11 J1C sing 230 n n C12 H12 J1C sing 231 n n C12 H12A J1C sing 232 n n N12 HN12 J1C sing 233 n n C13 H13 J1C sing 234 n n C13 H13A J1C sing 235 n n C14 H14 J1C sing 236 n n C14 H14A J1C sing 237 n n C15 H15 J1C sing 238 n n C15 H15A J1C sing 239 n n C16 H16 J1C sing 240 n n C16 H16A J1C sing 241 n n C23 H23 J1C sing 242 n n C23 H23A J1C sing 243 n n C23 H23B J1C sing 244 n n C24 H24 J1C sing 245 n n C24 H24A J1C sing 246 n n C24 H24B J1C sing 247 n n C27 H27 J1C sing 248 n n C27 H27A J1C sing 249 n n N28 HN28 J1C sing 250 n n # _atom_sites.entry_id 3UDV _atom_sites.fract_transf_matrix[1][1] 0.018867 _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] 0.014156 _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] 0.027587 _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 J1C A 1 171 171 J1C J1C . 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 . D 4 HOH A 89 289 289 HOH HOH . D 4 HOH A 90 290 290 HOH HOH . D 4 HOH A 91 291 291 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 J1C . . . B 2 1.921 17.243 15.588 1 61.74 ? C1 J1C 171 A 1 HETATM 2 N N1 J1C . . . B 2 2.629 14.362 13.483 1 41.71 ? N1 J1C 171 A 1 HETATM 3 O O1 J1C . . . B 2 1.964 16.456 14.402 1 46.43 ? O1 J1C 171 A 1 HETATM 4 S S1 J1C . . . B 2 3.931 19.384 15.145 1 76.08 ? S1 J1C 171 A 1 HETATM 5 C C2 J1C . . . B 2 2.917 16.54 16.568 1 49.97 ? C2 J1C 171 A 1 HETATM 6 N N2 J1C . . . B 2 2.303 12.985 11.646 1 32.19 ? N2 J1C 171 A 1 HETATM 7 O O2 J1C . . . B 2 2.267 16.391 17.793 1 60.4 ? O2 J1C 171 A 1 HETATM 8 C C3 J1C . . . B 2 3.205 15.124 15.883 1 43.76 ? C3 J1C 171 A 1 HETATM 9 N N3 J1C . . . B 2 4.639 12.439 9.655 1 17.33 ? N3 J1C 171 A 1 HETATM 10 O O3 J1C . . . B 2 2.964 14.052 16.765 1 52.36 ? O3 J1C 171 A 1 HETATM 11 C C4 J1C . . . B 2 2.201 15.101 14.714 1 27.41 ? C4 J1C 171 A 1 HETATM 12 N N4 J1C . . . B 2 5.922 13.83 11.03 1 26.79 ? N4 J1C 171 A 1 HETATM 13 O O4 J1C . . . B 2 4.812 25.488 11.104 1 49.12 ? O4 J1C 171 A 1 HETATM 14 C C5 J1C . . . B 2 1.739 13.533 12.726 1 30.52 ? C5 J1C 171 A 1 HETATM 15 N N5 J1C . . . B 2 5.02 14.919 13.035 1 42.57 ? N5 J1C 171 A 1 HETATM 16 O O5 J1C . . . B 2 9.362 24.901 7.068 1 24.01 ? O5 J1C 171 A 1 HETATM 17 C C6 J1C . . . B 2 3.624 13.457 11.649 1 44.05 ? C6 J1C 171 A 1 HETATM 18 N N6 J1C . . . B 2 5.294 19.996 11.416 1 73.48 ? N6 J1C 171 A 1 HETATM 19 C C7 J1C . . . B 2 4.716 13.23 10.76 1 32.91 ? C7 J1C 171 A 1 HETATM 20 C C8 J1C . . . B 2 5.974 14.614 12.13 1 42.62 ? C8 J1C 171 A 1 HETATM 21 N N8 J1C . . . B 2 7.29 28.217 5.846 1 37.88 ? N8 J1C 171 A 1 HETATM 22 C C9 J1C . . . B 2 3.836 14.31 12.771 1 40.44 ? C9 J1C 171 A 1 HETATM 23 N N9 J1C . . . B 2 8.997 28.429 4.217 1 25.21 ? N9 J1C 171 A 1 HETATM 24 C C10 J1C . . . B 2 2.162 18.779 15.301 1 34.12 ? C10 J1C 171 A 1 HETATM 25 N N10 J1C . . . B 2 9.126 26.635 5.694 1 18.22 ? N10 J1C 171 A 1 HETATM 26 C C11 J1C . . . B 2 4.979 18.306 13.936 1 61.4 ? C11 J1C 171 A 1 HETATM 27 N N11 J1C . . . B 2 6.993 25.589 8.47 1 37.55 ? N11 J1C 171 A 1 HETATM 28 C C12 J1C . . . B 2 4.235 18.03 12.643 1 59.53 ? C12 J1C 171 A 1 HETATM 29 N N12 J1C . . . B 2 5.679 27.889 7.554 1 28.77 ? N12 J1C 171 A 1 HETATM 30 C C13 J1C . . . B 2 4.017 19.347 11.882 1 71.43 ? C13 J1C 171 A 1 HETATM 31 C C14 J1C . . . B 2 6.387 20.033 12.495 1 31.91 ? C14 J1C 171 A 1 HETATM 32 C C15 J1C . . . B 2 6.367 18.88 13.556 1 43.36 ? C15 J1C 171 A 1 HETATM 33 C C16 J1C . . . B 2 4.981 21.279 10.616 1 41.41 ? C16 J1C 171 A 1 HETATM 34 C C18 J1C . . . B 2 5.448 25.006 10.166 1 45.95 ? C18 J1C 171 A 1 HETATM 35 C C19 J1C . . . B 2 8.443 27.756 5.285 1 26.36 ? C19 J1C 171 A 1 HETATM 36 C C20 J1C . . . B 2 8.67 25.873 6.797 1 24.91 ? C20 J1C 171 A 1 HETATM 37 C C21 J1C . . . B 2 5.896 25.937 9.06 1 43.39 ? C21 J1C 171 A 1 HETATM 38 C C22 J1C . . . B 2 5.087 27.19 8.734 1 41.48 ? C22 J1C 171 A 1 HETATM 39 C C23 J1C . . . B 2 4.988 28.245 9.833 1 33.25 ? C23 J1C 171 A 1 HETATM 40 C C24 J1C . . . B 2 3.645 26.773 8.387 1 41.01 ? C24 J1C 171 A 1 HETATM 41 C C25 J1C . . . B 2 6.818 27.481 6.923 1 30.02 ? C25 J1C 171 A 1 HETATM 42 C C26 J1C . . . B 2 7.447 26.34 7.401 1 26.38 ? C26 J1C 171 A 1 HETATM 43 C C27 J1C . . . B 2 5.297 22.686 11.185 1 45.36 ? C27 J1C 171 A 1 HETATM 44 N N28 J1C . . . B 2 5.725 23.637 10.121 1 37.65 ? N28 J1C 171 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 44 #