data_7HG8 # _model_server_result.job_id m30y1IubPJjnAOsfZvR62g _model_server_result.datetime_utc '2024-11-21 22:10:10' _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 7hg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":103}' # _entry.id 7HG8 # _exptl.entry_id 7HG8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 234.316 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea" _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 7HG8 _cell.length_a 41.56 _cell.length_b 42.13 _cell.length_c 158.86 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7HG8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,M 1 1 B,H,I,J,N 2 1 C,K,L,O 3 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 4 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H18 N2 O3 S' _chem_comp.formula_weight 234.316 _chem_comp.id VZP _chem_comp.mon_nstd_flag . _chem_comp.name "N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea" _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 O1 S VZP doub 389 n n C4 N1 VZP sing 390 n n S O2 VZP doub 391 n n S C7 VZP sing 392 n n S C8 VZP sing 393 n n C7 C6 VZP sing 394 n n C8 C5 VZP sing 395 n n N1 C5 VZP sing 396 n n N1 C3 VZP sing 397 n n C5 C6 VZP sing 398 n n N C3 VZP sing 399 n n N C1 VZP sing 400 n n C3 O VZP doub 401 n n C C1 VZP sing 402 n n C2 C1 VZP sing 403 n n C4 H1 VZP sing 404 n n C4 H2 VZP sing 405 n n C4 H3 VZP sing 406 n n C5 H4 VZP sing 407 n n C6 H5 VZP sing 408 n n C6 H6 VZP sing 409 n n C7 H7 VZP sing 410 n n C7 H8 VZP sing 411 n n C8 H9 VZP sing 412 n n C8 H10 VZP sing 413 n n N H11 VZP sing 414 n n C1 H12 VZP sing 415 n n C2 H13 VZP sing 416 n n C2 H14 VZP sing 417 n n C2 H15 VZP sing 418 n n C H16 VZP sing 419 n n C H17 VZP sing 420 n n C H18 VZP sing 421 n n # _atom_sites.entry_id 7HG8 _atom_sites.fract_transf_matrix[1][1] 0.024062 _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] 0.023736 _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] 0.006295 _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 D 2 SO4 A 1 101 95 SO4 SO4 . E 2 SO4 A 1 102 96 SO4 SO4 . F 3 EDO A 1 103 97 EDO EDO . G 2 SO4 A 1 104 4 SO4 SO4 . H 2 SO4 B 1 101 1 SO4 SO4 . I 2 SO4 B 1 102 3 SO4 SO4 . J 4 VZP B 1 103 101 VZP LIG . K 3 EDO C 1 101 101 EDO EDO . L 2 SO4 C 1 102 5 SO4 SO4 . M 5 HOH A 1 201 307 HOH HOH . M 5 HOH A 2 202 84 HOH HOH . M 5 HOH A 3 203 336 HOH HOH . M 5 HOH A 4 204 208 HOH HOH . M 5 HOH A 5 205 202 HOH HOH . M 5 HOH A 6 206 304 HOH HOH . M 5 HOH A 7 207 91 HOH HOH . M 5 HOH A 8 208 290 HOH HOH . M 5 HOH A 9 209 66 HOH HOH . M 5 HOH A 10 210 348 HOH HOH . M 5 HOH A 11 211 139 HOH HOH . M 5 HOH A 12 212 97 HOH HOH . M 5 HOH A 13 213 71 HOH HOH . M 5 HOH A 14 214 87 HOH HOH . M 5 HOH A 15 215 349 HOH HOH . M 5 HOH A 16 216 55 HOH HOH . M 5 HOH A 17 217 293 HOH HOH . M 5 HOH A 18 218 95 HOH HOH . M 5 HOH A 19 219 289 HOH HOH . M 5 HOH A 20 220 99 HOH HOH . M 5 HOH A 21 221 26 HOH HOH . M 5 HOH A 22 222 28 HOH HOH . M 5 HOH A 23 223 259 HOH HOH . M 5 HOH A 24 224 142 HOH HOH . M 5 HOH A 25 225 8 HOH HOH . M 5 HOH A 26 226 339 HOH HOH . M 5 HOH A 27 227 27 HOH HOH . M 5 HOH A 28 228 34 HOH HOH . M 5 HOH A 29 229 278 HOH HOH . M 5 HOH A 30 230 167 HOH HOH . M 5 HOH A 31 231 86 HOH HOH . M 5 HOH A 32 232 152 HOH HOH . M 5 HOH A 33 233 32 HOH HOH . M 5 HOH A 34 234 1 HOH HOH . M 5 HOH A 35 235 109 HOH HOH . M 5 HOH A 36 236 292 HOH HOH . M 5 HOH A 37 237 188 HOH HOH . M 5 HOH A 38 238 12 HOH HOH . M 5 HOH A 39 239 37 HOH HOH . M 5 HOH A 40 240 116 HOH HOH . M 5 HOH A 41 241 179 HOH HOH . M 5 HOH A 42 242 23 HOH HOH . M 5 HOH A 43 243 190 HOH HOH . M 5 HOH A 44 244 301 HOH HOH . M 5 HOH A 45 245 7 HOH HOH . M 5 HOH A 46 246 42 HOH HOH . M 5 HOH A 47 247 60 HOH HOH . M 5 HOH A 48 248 111 HOH HOH . M 5 HOH A 49 249 199 HOH HOH . M 5 HOH A 50 250 94 HOH HOH . M 5 HOH A 51 251 267 HOH HOH . M 5 HOH A 52 252 297 HOH HOH . M 5 HOH A 53 253 203 HOH HOH . M 5 HOH A 54 254 342 HOH HOH . M 5 HOH A 55 255 2 HOH HOH . M 5 HOH A 56 256 164 HOH HOH . M 5 HOH A 57 257 274 HOH HOH . M 5 HOH A 58 258 260 HOH HOH . M 5 HOH A 59 259 20 HOH HOH . M 5 HOH A 60 260 93 HOH HOH . M 5 HOH A 61 261 58 HOH HOH . M 5 HOH A 62 262 300 HOH HOH . M 5 HOH A 63 263 38 HOH HOH . M 5 HOH A 64 264 18 HOH HOH . M 5 HOH A 65 265 299 HOH HOH . M 5 HOH A 66 266 288 HOH HOH . M 5 HOH A 67 267 337 HOH HOH . M 5 HOH A 68 268 14 HOH HOH . M 5 HOH A 69 269 78 HOH HOH . M 5 HOH A 70 270 222 HOH HOH . M 5 HOH A 71 271 73 HOH HOH . M 5 HOH A 72 272 165 HOH HOH . M 5 HOH A 73 273 115 HOH HOH . M 5 HOH A 74 274 211 HOH HOH . M 5 HOH A 75 275 21 HOH HOH . M 5 HOH A 76 276 145 HOH HOH . M 5 HOH A 77 277 318 HOH HOH . M 5 HOH A 78 278 47 HOH HOH . M 5 HOH A 79 279 77 HOH HOH . M 5 HOH A 80 280 143 HOH HOH . M 5 HOH A 81 281 9 HOH HOH . M 5 HOH A 82 282 19 HOH HOH . M 5 HOH A 83 283 16 HOH HOH . M 5 HOH A 84 284 64 HOH HOH . M 5 HOH A 85 285 218 HOH HOH . M 5 HOH A 86 286 31 HOH HOH . M 5 HOH A 87 287 281 HOH HOH . M 5 HOH A 88 288 113 HOH HOH . M 5 HOH A 89 289 131 HOH HOH . M 5 HOH A 90 290 22 HOH HOH . M 5 HOH A 91 291 327 HOH HOH . M 5 HOH A 92 292 296 HOH HOH . M 5 HOH A 93 293 340 HOH HOH . M 5 HOH A 94 294 210 HOH HOH . M 5 HOH A 95 295 108 HOH HOH . M 5 HOH A 96 296 83 HOH HOH . M 5 HOH A 97 297 63 HOH HOH . M 5 HOH A 98 298 185 HOH HOH . M 5 HOH A 99 299 219 HOH HOH . M 5 HOH A 100 300 75 HOH HOH . M 5 HOH A 101 301 156 HOH HOH . M 5 HOH A 102 302 283 HOH HOH . M 5 HOH A 103 303 35 HOH HOH . M 5 HOH A 104 304 205 HOH HOH . M 5 HOH A 105 305 57 HOH HOH . M 5 HOH A 106 306 313 HOH HOH . M 5 HOH A 107 307 206 HOH HOH . M 5 HOH A 108 308 125 HOH HOH . M 5 HOH A 109 309 332 HOH HOH . N 5 HOH B 1 201 247 HOH HOH . N 5 HOH B 2 202 184 HOH HOH . N 5 HOH B 3 203 258 HOH HOH . N 5 HOH B 4 204 279 HOH HOH . N 5 HOH B 5 205 345 HOH HOH . N 5 HOH B 6 206 123 HOH HOH . N 5 HOH B 7 207 98 HOH HOH . N 5 HOH B 8 208 89 HOH HOH . N 5 HOH B 9 209 69 HOH HOH . N 5 HOH B 10 210 272 HOH HOH . N 5 HOH B 11 211 172 HOH HOH . N 5 HOH B 12 212 249 HOH HOH . N 5 HOH B 13 213 54 HOH HOH . N 5 HOH B 14 214 119 HOH HOH . N 5 HOH B 15 215 157 HOH HOH . N 5 HOH B 16 216 329 HOH HOH . N 5 HOH B 17 217 215 HOH HOH . N 5 HOH B 18 218 333 HOH HOH . N 5 HOH B 19 219 242 HOH HOH . N 5 HOH B 20 220 59 HOH HOH . N 5 HOH B 21 221 101 HOH HOH . N 5 HOH B 22 222 17 HOH HOH . N 5 HOH B 23 223 150 HOH HOH . N 5 HOH B 24 224 117 HOH HOH . N 5 HOH B 25 225 341 HOH HOH . N 5 HOH B 26 226 224 HOH HOH . N 5 HOH B 27 227 261 HOH HOH . N 5 HOH B 28 228 96 HOH HOH . N 5 HOH B 29 229 5 HOH HOH . N 5 HOH B 30 230 10 HOH HOH . N 5 HOH B 31 231 6 HOH HOH . N 5 HOH B 32 232 175 HOH HOH . N 5 HOH B 33 233 137 HOH HOH . N 5 HOH B 34 234 320 HOH HOH . N 5 HOH B 35 235 24 HOH HOH . N 5 HOH B 36 236 331 HOH HOH . N 5 HOH B 37 237 280 HOH HOH . N 5 HOH B 38 238 153 HOH HOH . N 5 HOH B 39 239 61 HOH HOH . N 5 HOH B 40 240 169 HOH HOH . N 5 HOH B 41 241 334 HOH HOH . N 5 HOH B 42 242 25 HOH HOH . N 5 HOH B 43 243 315 HOH HOH . N 5 HOH B 44 244 46 HOH HOH . N 5 HOH B 45 245 36 HOH HOH . N 5 HOH B 46 246 223 HOH HOH . N 5 HOH B 47 247 197 HOH HOH . N 5 HOH B 48 248 68 HOH HOH . N 5 HOH B 49 249 214 HOH HOH . N 5 HOH B 50 250 13 HOH HOH . N 5 HOH B 51 251 76 HOH HOH . N 5 HOH B 52 252 168 HOH HOH . N 5 HOH B 53 253 74 HOH HOH . N 5 HOH B 54 254 217 HOH HOH . N 5 HOH B 55 255 79 HOH HOH . N 5 HOH B 56 256 72 HOH HOH . N 5 HOH B 57 257 303 HOH HOH . N 5 HOH B 58 258 346 HOH HOH . N 5 HOH B 59 259 104 HOH HOH . N 5 HOH B 60 260 44 HOH HOH . N 5 HOH B 61 261 120 HOH HOH . N 5 HOH B 62 262 177 HOH HOH . N 5 HOH B 63 263 182 HOH HOH . N 5 HOH B 64 264 170 HOH HOH . N 5 HOH B 65 265 160 HOH HOH . N 5 HOH B 66 266 316 HOH HOH . N 5 HOH B 67 267 201 HOH HOH . N 5 HOH B 68 268 291 HOH HOH . N 5 HOH B 69 269 163 HOH HOH . N 5 HOH B 70 270 322 HOH HOH . N 5 HOH B 71 271 338 HOH HOH . N 5 HOH B 72 272 314 HOH HOH . N 5 HOH B 73 273 107 HOH HOH . N 5 HOH B 74 274 312 HOH HOH . O 5 HOH C 1 201 321 HOH HOH . O 5 HOH C 2 202 323 HOH HOH . O 5 HOH C 3 203 161 HOH HOH . O 5 HOH C 4 204 226 HOH HOH . O 5 HOH C 5 205 254 HOH HOH . O 5 HOH C 6 206 209 HOH HOH . O 5 HOH C 7 207 317 HOH HOH . O 5 HOH C 8 208 173 HOH HOH . O 5 HOH C 9 209 284 HOH HOH . O 5 HOH C 10 210 134 HOH HOH . O 5 HOH C 11 211 90 HOH HOH . O 5 HOH C 12 212 271 HOH HOH . O 5 HOH C 13 213 49 HOH HOH . O 5 HOH C 14 214 15 HOH HOH . O 5 HOH C 15 215 85 HOH HOH . O 5 HOH C 16 216 118 HOH HOH . O 5 HOH C 17 217 82 HOH HOH . O 5 HOH C 18 218 335 HOH HOH . O 5 HOH C 19 219 269 HOH HOH . O 5 HOH C 20 220 4 HOH HOH . O 5 HOH C 21 221 48 HOH HOH . O 5 HOH C 22 222 347 HOH HOH . O 5 HOH C 23 223 189 HOH HOH . O 5 HOH C 24 224 56 HOH HOH . O 5 HOH C 25 225 343 HOH HOH . O 5 HOH C 26 226 41 HOH HOH . O 5 HOH C 27 227 43 HOH HOH . O 5 HOH C 28 228 302 HOH HOH . O 5 HOH C 29 229 45 HOH HOH . O 5 HOH C 30 230 275 HOH HOH . O 5 HOH C 31 231 122 HOH HOH . O 5 HOH C 32 232 40 HOH HOH . O 5 HOH C 33 233 126 HOH HOH . O 5 HOH C 34 234 309 HOH HOH . O 5 HOH C 35 235 102 HOH HOH . O 5 HOH C 36 236 298 HOH HOH . O 5 HOH C 37 237 132 HOH HOH . O 5 HOH C 38 238 295 HOH HOH . O 5 HOH C 39 239 325 HOH HOH . O 5 HOH C 40 240 62 HOH HOH . O 5 HOH C 41 241 149 HOH HOH . O 5 HOH C 42 242 148 HOH HOH . O 5 HOH C 43 243 294 HOH HOH . O 5 HOH C 44 244 67 HOH HOH . O 5 HOH C 45 245 287 HOH HOH . O 5 HOH C 46 246 130 HOH HOH . O 5 HOH C 47 247 53 HOH HOH . O 5 HOH C 48 248 198 HOH HOH . O 5 HOH C 49 249 326 HOH HOH . O 5 HOH C 50 250 135 HOH HOH . O 5 HOH C 51 251 328 HOH HOH . O 5 HOH C 52 252 246 HOH HOH . O 5 HOH C 53 253 65 HOH HOH . O 5 HOH C 54 254 330 HOH HOH . O 5 HOH C 55 255 241 HOH HOH . O 5 HOH C 56 256 171 HOH HOH . O 5 HOH C 57 257 305 HOH HOH . O 5 HOH C 58 258 151 HOH HOH . O 5 HOH C 59 259 146 HOH HOH . O 5 HOH C 60 260 270 HOH HOH . O 5 HOH C 61 261 344 HOH HOH . O 5 HOH C 62 262 324 HOH HOH . O 5 HOH C 63 263 70 HOH HOH . O 5 HOH C 64 264 103 HOH HOH . O 5 HOH C 65 265 319 HOH HOH . O 5 HOH C 66 266 92 HOH HOH . O 5 HOH C 67 267 310 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 VZP . . . J 4 20.339 -16.871 -23.784 0.7 37.59 ? N1 VZP 103 B 1 HETATM 2 C C4 VZP . . . J 4 20.988 -15.59 -24.064 0.7 39.17 ? C4 VZP 103 B 1 HETATM 3 C C5 VZP . . . J 4 18.854 -16.867 -23.953 0.7 33.66 ? C5 VZP 103 B 1 HETATM 4 C C6 VZP . . . J 4 18.416 -16.659 -25.406 0.7 32.98 ? C6 VZP 103 B 1 HETATM 5 C C7 VZP . . . J 4 17.018 -16.06 -25.355 0.7 32.54 ? C7 VZP 103 B 1 HETATM 6 C C8 VZP . . . J 4 18.143 -15.837 -23.053 0.7 34.67 ? C8 VZP 103 B 1 HETATM 7 O O2 VZP . . . J 4 17.79 -13.727 -24.648 0.7 29.94 ? O2 VZP 103 B 1 HETATM 8 S S VZP . . . J 4 17.102 -14.889 -24.151 0.7 33.76 ? S VZP 103 B 1 HETATM 9 O O1 VZP . . . J 4 15.796 -14.686 -23.588 0.7 32.67 ? O1 VZP 103 B 1 HETATM 10 C C3 VZP . . . J 4 20.914 -17.771 -22.924 0.7 44.48 ? C3 VZP 103 B 1 HETATM 11 O O VZP . . . J 4 20.339 -18.797 -22.585 0.7 40.4 ? O VZP 103 B 1 HETATM 12 N N VZP . . . J 4 22.174 -17.49 -22.501 0.7 52.74 ? N VZP 103 B 1 HETATM 13 C C1 VZP . . . J 4 22.899 -18.379 -21.583 0.7 58.06 ? C1 VZP 103 B 1 HETATM 14 C C2 VZP . . . J 4 23.049 -17.721 -20.225 0.7 61.49 ? C2 VZP 103 B 1 HETATM 15 C C VZP . . . J 4 24.238 -18.782 -22.174 0.7 56.87 ? C VZP 103 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 15 #