data_5SBT # _model_server_result.job_id AsZU2LeUqka8dR7TdOkCUw _model_server_result.datetime_utc '2024-11-07 10:12:10' _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 5sbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5SBT # _exptl.entry_id 5SBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 234.316 _entity.id 2 _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 117.89 _cell.angle_gamma 90 _cell.entry_id 5SBT _cell.length_a 31.02 _cell.length_b 82.04 _cell.length_c 32.12 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SBT _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,E,F,G,H,I _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 10 A CYS 32 1_555 A SG CYS 112 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 A SG CYS 35 A CYS 57 1_555 A SG CYS 101 A CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf3 A SG CYS 59 A CYS 81 1_555 A SG CYS 79 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _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 ? # _atom_sites.entry_id 5SBT _atom_sites.fract_transf_matrix[1][1] 0.032237 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.017062 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012189 _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] 0.035225 _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 VZP A 1 201 201 VZP LIG . C 3 DMS A 1 202 1 DMS DMS . D 3 DMS A 1 203 2 DMS DMS . E 3 DMS A 1 204 3 DMS DMS . F 4 EDO A 1 205 1 EDO EDO . G 4 EDO A 1 206 2 EDO EDO . H 4 EDO A 1 207 3 EDO EDO . I 5 HOH A 1 301 278 HOH HOH . I 5 HOH A 2 302 32 HOH HOH . I 5 HOH A 3 303 192 HOH HOH . I 5 HOH A 4 304 268 HOH HOH . I 5 HOH A 5 305 250 HOH HOH . I 5 HOH A 6 306 115 HOH HOH . I 5 HOH A 7 307 103 HOH HOH . I 5 HOH A 8 308 21 HOH HOH . I 5 HOH A 9 309 71 HOH HOH . I 5 HOH A 10 310 85 HOH HOH . I 5 HOH A 11 311 50 HOH HOH . I 5 HOH A 12 312 60 HOH HOH . I 5 HOH A 13 313 68 HOH HOH . I 5 HOH A 14 314 49 HOH HOH . I 5 HOH A 15 315 120 HOH HOH . I 5 HOH A 16 316 180 HOH HOH . I 5 HOH A 17 317 290 HOH HOH . I 5 HOH A 18 318 114 HOH HOH . I 5 HOH A 19 319 255 HOH HOH . I 5 HOH A 20 320 81 HOH HOH . I 5 HOH A 21 321 62 HOH HOH . I 5 HOH A 22 322 144 HOH HOH . I 5 HOH A 23 323 125 HOH HOH . I 5 HOH A 24 324 1 HOH HOH . I 5 HOH A 25 325 91 HOH HOH . I 5 HOH A 26 326 41 HOH HOH . I 5 HOH A 27 327 51 HOH HOH . I 5 HOH A 28 328 126 HOH HOH . I 5 HOH A 29 329 2 HOH HOH . I 5 HOH A 30 330 4 HOH HOH . I 5 HOH A 31 331 63 HOH HOH . I 5 HOH A 32 332 182 HOH HOH . I 5 HOH A 33 333 112 HOH HOH . I 5 HOH A 34 334 34 HOH HOH . I 5 HOH A 35 335 109 HOH HOH . I 5 HOH A 36 336 174 HOH HOH . I 5 HOH A 37 337 13 HOH HOH . I 5 HOH A 38 338 10 HOH HOH . I 5 HOH A 39 339 33 HOH HOH . I 5 HOH A 40 340 292 HOH HOH . I 5 HOH A 41 341 18 HOH HOH . I 5 HOH A 42 342 254 HOH HOH . I 5 HOH A 43 343 210 HOH HOH . I 5 HOH A 44 344 117 HOH HOH . I 5 HOH A 45 345 137 HOH HOH . I 5 HOH A 46 346 76 HOH HOH . I 5 HOH A 47 347 154 HOH HOH . I 5 HOH A 48 348 3 HOH HOH . I 5 HOH A 49 349 55 HOH HOH . I 5 HOH A 50 350 161 HOH HOH . I 5 HOH A 51 351 28 HOH HOH . I 5 HOH A 52 352 46 HOH HOH . I 5 HOH A 53 353 38 HOH HOH . I 5 HOH A 54 354 101 HOH HOH . I 5 HOH A 55 355 79 HOH HOH . I 5 HOH A 56 356 215 HOH HOH . I 5 HOH A 57 357 27 HOH HOH . I 5 HOH A 58 358 31 HOH HOH . I 5 HOH A 59 359 102 HOH HOH . I 5 HOH A 60 360 195 HOH HOH . I 5 HOH A 61 361 5 HOH HOH . I 5 HOH A 62 362 45 HOH HOH . I 5 HOH A 63 363 26 HOH HOH . I 5 HOH A 64 364 9 HOH HOH . I 5 HOH A 65 365 11 HOH HOH . I 5 HOH A 66 366 14 HOH HOH . I 5 HOH A 67 367 205 HOH HOH . I 5 HOH A 68 368 44 HOH HOH . I 5 HOH A 69 369 7 HOH HOH . I 5 HOH A 70 370 178 HOH HOH . I 5 HOH A 71 371 54 HOH HOH . I 5 HOH A 72 372 57 HOH HOH . I 5 HOH A 73 373 66 HOH HOH . I 5 HOH A 74 374 35 HOH HOH . I 5 HOH A 75 375 100 HOH HOH . I 5 HOH A 76 376 19 HOH HOH . I 5 HOH A 77 377 95 HOH HOH . I 5 HOH A 78 378 16 HOH HOH . I 5 HOH A 79 379 193 HOH HOH . I 5 HOH A 80 380 160 HOH HOH . I 5 HOH A 81 381 212 HOH HOH . I 5 HOH A 82 382 82 HOH HOH . I 5 HOH A 83 383 110 HOH HOH . I 5 HOH A 84 384 15 HOH HOH . I 5 HOH A 85 385 171 HOH HOH . I 5 HOH A 86 386 111 HOH HOH . I 5 HOH A 87 387 223 HOH HOH . I 5 HOH A 88 388 86 HOH HOH . I 5 HOH A 89 389 36 HOH HOH . I 5 HOH A 90 390 238 HOH HOH . I 5 HOH A 91 391 121 HOH HOH . I 5 HOH A 92 392 127 HOH HOH . I 5 HOH A 93 393 78 HOH HOH . I 5 HOH A 94 394 201 HOH HOH . I 5 HOH A 95 395 73 HOH HOH . I 5 HOH A 96 396 228 HOH HOH . I 5 HOH A 97 397 75 HOH HOH . I 5 HOH A 98 398 48 HOH HOH . I 5 HOH A 99 399 47 HOH HOH . I 5 HOH A 100 400 25 HOH HOH . I 5 HOH A 101 401 158 HOH HOH . I 5 HOH A 102 402 43 HOH HOH . I 5 HOH A 103 403 130 HOH HOH . I 5 HOH A 104 404 227 HOH HOH . I 5 HOH A 105 405 163 HOH HOH . I 5 HOH A 106 406 139 HOH HOH . I 5 HOH A 107 407 124 HOH HOH . I 5 HOH A 108 408 155 HOH HOH . I 5 HOH A 109 409 39 HOH HOH . I 5 HOH A 110 410 153 HOH HOH . I 5 HOH A 111 411 20 HOH HOH . I 5 HOH A 112 412 279 HOH HOH . I 5 HOH A 113 413 128 HOH HOH . I 5 HOH A 114 414 156 HOH HOH . I 5 HOH A 115 415 123 HOH HOH . I 5 HOH A 116 416 64 HOH HOH . I 5 HOH A 117 417 40 HOH HOH . I 5 HOH A 118 418 169 HOH HOH . I 5 HOH A 119 419 107 HOH HOH . I 5 HOH A 120 420 6 HOH HOH . I 5 HOH A 121 421 116 HOH HOH . I 5 HOH A 122 422 17 HOH HOH . I 5 HOH A 123 423 87 HOH HOH . I 5 HOH A 124 424 106 HOH HOH . I 5 HOH A 125 425 200 HOH HOH . I 5 HOH A 126 426 92 HOH HOH . I 5 HOH A 127 427 42 HOH HOH . I 5 HOH A 128 428 189 HOH HOH . I 5 HOH A 129 429 259 HOH HOH . I 5 HOH A 130 430 72 HOH HOH . I 5 HOH A 131 431 167 HOH HOH . I 5 HOH A 132 432 159 HOH HOH . I 5 HOH A 133 433 67 HOH HOH . I 5 HOH A 134 434 24 HOH HOH . I 5 HOH A 135 435 177 HOH HOH . I 5 HOH A 136 436 149 HOH HOH . I 5 HOH A 137 437 197 HOH HOH . I 5 HOH A 138 438 218 HOH HOH . I 5 HOH A 139 439 89 HOH HOH . I 5 HOH A 140 440 239 HOH HOH . I 5 HOH A 141 441 12 HOH HOH . I 5 HOH A 142 442 270 HOH HOH . I 5 HOH A 143 443 98 HOH HOH . I 5 HOH A 144 444 146 HOH HOH . I 5 HOH A 145 445 258 HOH HOH . I 5 HOH A 146 446 108 HOH HOH . I 5 HOH A 147 447 252 HOH HOH . I 5 HOH A 148 448 70 HOH HOH . I 5 HOH A 149 449 23 HOH HOH . I 5 HOH A 150 450 221 HOH HOH . I 5 HOH A 151 451 166 HOH HOH . I 5 HOH A 152 452 264 HOH HOH . I 5 HOH A 153 453 281 HOH HOH . I 5 HOH A 154 454 237 HOH HOH . I 5 HOH A 155 455 256 HOH HOH . I 5 HOH A 156 456 96 HOH HOH . I 5 HOH A 157 457 105 HOH HOH . I 5 HOH A 158 458 272 HOH HOH . I 5 HOH A 159 459 151 HOH HOH . I 5 HOH A 160 460 222 HOH HOH . I 5 HOH A 161 461 183 HOH HOH . I 5 HOH A 162 462 77 HOH HOH . I 5 HOH A 163 463 58 HOH HOH . I 5 HOH A 164 464 266 HOH HOH . I 5 HOH A 165 465 131 HOH HOH . I 5 HOH A 166 466 80 HOH HOH . I 5 HOH A 167 467 179 HOH HOH . I 5 HOH A 168 468 94 HOH HOH . I 5 HOH A 169 469 53 HOH HOH . I 5 HOH A 170 470 226 HOH HOH . I 5 HOH A 171 471 284 HOH HOH . I 5 HOH A 172 472 113 HOH HOH . I 5 HOH A 173 473 84 HOH HOH . I 5 HOH A 174 474 56 HOH HOH . I 5 HOH A 175 475 122 HOH HOH . I 5 HOH A 176 476 291 HOH HOH . I 5 HOH A 177 477 69 HOH HOH . I 5 HOH A 178 478 249 HOH HOH . I 5 HOH A 179 479 134 HOH HOH . I 5 HOH A 180 480 214 HOH HOH . I 5 HOH A 181 481 230 HOH HOH . I 5 HOH A 182 482 52 HOH HOH . I 5 HOH A 183 483 97 HOH HOH . I 5 HOH A 184 484 165 HOH HOH . I 5 HOH A 185 485 129 HOH HOH . I 5 HOH A 186 486 283 HOH HOH . I 5 HOH A 187 487 185 HOH HOH . I 5 HOH A 188 488 282 HOH HOH . I 5 HOH A 189 489 267 HOH HOH . I 5 HOH A 190 490 136 HOH HOH . I 5 HOH A 191 491 173 HOH HOH . I 5 HOH A 192 492 241 HOH HOH . I 5 HOH A 193 493 274 HOH HOH . I 5 HOH A 194 494 83 HOH HOH . I 5 HOH A 195 495 243 HOH HOH . I 5 HOH A 196 496 135 HOH HOH . I 5 HOH A 197 497 194 HOH HOH . I 5 HOH A 198 498 187 HOH HOH . I 5 HOH A 199 499 138 HOH HOH . I 5 HOH A 200 500 37 HOH HOH . I 5 HOH A 201 501 61 HOH HOH . I 5 HOH A 202 502 168 HOH HOH . I 5 HOH A 203 503 119 HOH HOH . I 5 HOH A 204 504 104 HOH HOH . I 5 HOH A 205 505 220 HOH HOH . I 5 HOH A 206 506 181 HOH HOH . I 5 HOH A 207 507 59 HOH HOH . I 5 HOH A 208 508 8 HOH HOH . I 5 HOH A 209 509 172 HOH HOH . I 5 HOH A 210 510 209 HOH HOH . I 5 HOH A 211 511 247 HOH HOH . I 5 HOH A 212 512 148 HOH HOH . I 5 HOH A 213 513 236 HOH HOH . I 5 HOH A 214 514 184 HOH HOH . I 5 HOH A 215 515 213 HOH HOH . I 5 HOH A 216 516 206 HOH HOH . I 5 HOH A 217 517 118 HOH HOH . I 5 HOH A 218 518 145 HOH HOH . I 5 HOH A 219 519 132 HOH HOH . I 5 HOH A 220 520 142 HOH HOH . I 5 HOH A 221 521 143 HOH HOH . I 5 HOH A 222 522 242 HOH HOH . I 5 HOH A 223 523 253 HOH HOH . I 5 HOH A 224 524 234 HOH HOH . I 5 HOH A 225 525 30 HOH HOH . I 5 HOH A 226 526 202 HOH HOH . I 5 HOH A 227 527 186 HOH HOH . I 5 HOH A 228 528 287 HOH HOH . I 5 HOH A 229 529 164 HOH HOH . I 5 HOH A 230 530 285 HOH HOH . I 5 HOH A 231 531 211 HOH HOH . I 5 HOH A 232 532 90 HOH HOH . I 5 HOH A 233 533 251 HOH HOH . I 5 HOH A 234 534 265 HOH HOH . I 5 HOH A 235 535 141 HOH HOH . I 5 HOH A 236 536 190 HOH HOH . I 5 HOH A 237 537 65 HOH HOH . I 5 HOH A 238 538 208 HOH HOH . I 5 HOH A 239 539 244 HOH HOH . I 5 HOH A 240 540 99 HOH HOH . I 5 HOH A 241 541 93 HOH HOH . I 5 HOH A 242 542 88 HOH HOH . I 5 HOH A 243 543 133 HOH HOH . I 5 HOH A 244 544 150 HOH HOH . I 5 HOH A 245 545 198 HOH HOH . I 5 HOH A 246 546 162 HOH HOH . I 5 HOH A 247 547 199 HOH HOH . I 5 HOH A 248 548 74 HOH HOH . I 5 HOH A 249 549 289 HOH HOH . I 5 HOH A 250 550 170 HOH HOH . I 5 HOH A 251 551 257 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 . . . B 2 15.274 -6.288 -1.719 0.3 10.52 ? N1 VZP 201 A 1 HETATM 2 C C4 VZP . . . B 2 16.597 -6.87 -1.907 0.3 10.65 ? C4 VZP 201 A 1 HETATM 3 C C5 VZP . . . B 2 15.024 -4.877 -1.987 0.3 10.3 ? C5 VZP 201 A 1 HETATM 4 C C6 VZP . . . B 2 14.823 -4.468 -3.726 0.3 10.27 ? C6 VZP 201 A 1 HETATM 5 C C7 VZP . . . B 2 14.893 -3.03 -3.808 0.3 10.23 ? C7 VZP 201 A 1 HETATM 6 C C8 VZP . . . B 2 16.074 -3.982 -1.539 0.3 10.25 ? C8 VZP 201 A 1 HETATM 7 O O2 VZP . . . B 2 14.721 -1.826 -1.653 0.3 10.21 ? O2 VZP 201 A 1 HETATM 8 S S VZP . . . B 2 15.736 -2.481 -2.367 0.3 10.28 ? S VZP 201 A 1 HETATM 9 O O1 VZP . . . B 2 16.965 -1.683 -2.72 0.3 9.91 ? O1 VZP 201 A 1 HETATM 10 C C3 VZP . . . B 2 14.18 -7.102 -1.225 0.3 10.73 ? C3 VZP 201 A 1 HETATM 11 O O VZP . . . B 2 13.092 -6.612 -1.103 0.3 11.15 ? O VZP 201 A 1 HETATM 12 N N VZP . . . B 2 14.425 -8.496 -0.872 0.3 10.99 ? N VZP 201 A 1 HETATM 13 C C1 VZP . . . B 2 13.382 -9.368 -0.358 0.3 11.03 ? C1 VZP 201 A 1 HETATM 14 C C2 VZP . . . B 2 13.151 -9.068 1.124 0.3 11.22 ? C2 VZP 201 A 1 HETATM 15 C C VZP . . . B 2 13.849 -10.808 -0.541 0.3 11.27 ? C VZP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 15 #