data_6RVK # _model_server_result.job_id LAQIUJFtgyNA0VlnhlHYUg _model_server_result.datetime_utc '2024-11-21 22:43:12' _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 6rvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6RVK # _exptl.entry_id 6RVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 299.11 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(phenylmethyl)urea _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 104.23 _cell.angle_gamma 90 _cell.entry_id 6RVK _cell.length_a 42.35 _cell.length_b 41.36 _cell.length_c 72.17 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RVK _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 _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 3 _struct_asym.id C _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 metalc ? metalc1 A NE2 HIS 96 A HIS 94 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc2 A NE2 HIS 98 A HIS 96 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc3 A ND1 HIS 121 A HIS 119 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc4 B ZN ZN . A ZN 301 1_555 C O2 R29 . A R29 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? # _chem_comp.formula 'C15 H16 B N2 O4 -1' _chem_comp.formula_weight 299.11 _chem_comp.id R29 _chem_comp.mon_nstd_flag . _chem_comp.name 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(phenylmethyl)urea _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 C9 C10 R29 sing 277 n n C9 N2 R29 sing 278 n n C11 C10 R29 doub 279 n y C11 C12 R29 sing 280 n y C10 C15 R29 sing 281 n y C12 C13 R29 doub 282 n y N2 C8 R29 sing 283 n n O4 C8 R29 doub 284 n n C8 N1 R29 sing 285 n n C15 C14 R29 doub 286 n y N1 C3 R29 sing 287 n n C13 C14 R29 sing 288 n y C4 C3 R29 doub 289 n y C4 C5 R29 sing 290 n y C3 C2 R29 sing 291 n y C5 C6 R29 doub 292 n y C2 C1 R29 doub 293 n y C6 C1 R29 sing 294 n y C6 C7 R29 sing 295 n n C1 B1 R29 sing 296 n n O2 B1 R29 sing 297 n n O1 C7 R29 sing 298 n n O1 B1 R29 sing 299 n n B1 O3 R29 sing 300 n n C2 H1 R29 sing 301 n n C4 H2 R29 sing 302 n n C5 H3 R29 sing 303 n n C7 H4 R29 sing 304 n n C7 H5 R29 sing 305 n n C9 H6 R29 sing 306 n n C9 H7 R29 sing 307 n n C11 H8 R29 sing 308 n n C12 H9 R29 sing 309 n n C13 H10 R29 sing 310 n n C14 H11 R29 sing 311 n n C15 H12 R29 sing 312 n n O3 H13 R29 sing 313 n n N1 H14 R29 sing 314 n n N2 H15 R29 sing 315 n n O2 H16 R29 sing 316 n n # _atom_sites.entry_id 6RVK _atom_sites.fract_transf_matrix[1][1] 0.023613 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005988 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024178 _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] 0.014295 _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 ZN A 1 301 262 ZN ZN . C 3 R29 A 1 302 263 R29 R29 . D 4 HOH A 1 401 354 HOH HOH . D 4 HOH A 2 402 451 HOH HOH . D 4 HOH A 3 403 480 HOH HOH . D 4 HOH A 4 404 438 HOH HOH . D 4 HOH A 5 405 469 HOH HOH . D 4 HOH A 6 406 404 HOH HOH . D 4 HOH A 7 407 374 HOH HOH . D 4 HOH A 8 408 393 HOH HOH . D 4 HOH A 9 409 428 HOH HOH . D 4 HOH A 10 410 307 HOH HOH . D 4 HOH A 11 411 403 HOH HOH . D 4 HOH A 12 412 392 HOH HOH . D 4 HOH A 13 413 380 HOH HOH . D 4 HOH A 14 414 344 HOH HOH . D 4 HOH A 15 415 368 HOH HOH . D 4 HOH A 16 416 377 HOH HOH . D 4 HOH A 17 417 337 HOH HOH . D 4 HOH A 18 418 302 HOH HOH . D 4 HOH A 19 419 348 HOH HOH . D 4 HOH A 20 420 417 HOH HOH . D 4 HOH A 21 421 379 HOH HOH . D 4 HOH A 22 422 396 HOH HOH . D 4 HOH A 23 423 450 HOH HOH . D 4 HOH A 24 424 455 HOH HOH . D 4 HOH A 25 425 476 HOH HOH . D 4 HOH A 26 426 401 HOH HOH . D 4 HOH A 27 427 320 HOH HOH . D 4 HOH A 28 428 486 HOH HOH . D 4 HOH A 29 429 355 HOH HOH . D 4 HOH A 30 430 318 HOH HOH . D 4 HOH A 31 431 331 HOH HOH . D 4 HOH A 32 432 365 HOH HOH . D 4 HOH A 33 433 411 HOH HOH . D 4 HOH A 34 434 443 HOH HOH . D 4 HOH A 35 435 394 HOH HOH . D 4 HOH A 36 436 441 HOH HOH . D 4 HOH A 37 437 381 HOH HOH . D 4 HOH A 38 438 347 HOH HOH . D 4 HOH A 39 439 434 HOH HOH . D 4 HOH A 40 440 322 HOH HOH . D 4 HOH A 41 441 485 HOH HOH . D 4 HOH A 42 442 350 HOH HOH . D 4 HOH A 43 443 359 HOH HOH . D 4 HOH A 44 444 334 HOH HOH . D 4 HOH A 45 445 431 HOH HOH . D 4 HOH A 46 446 346 HOH HOH . D 4 HOH A 47 447 364 HOH HOH . D 4 HOH A 48 448 360 HOH HOH . D 4 HOH A 49 449 304 HOH HOH . D 4 HOH A 50 450 329 HOH HOH . D 4 HOH A 51 451 316 HOH HOH . D 4 HOH A 52 452 366 HOH HOH . D 4 HOH A 53 453 467 HOH HOH . D 4 HOH A 54 454 363 HOH HOH . D 4 HOH A 55 455 422 HOH HOH . D 4 HOH A 56 456 312 HOH HOH . D 4 HOH A 57 457 432 HOH HOH . D 4 HOH A 58 458 420 HOH HOH . D 4 HOH A 59 459 367 HOH HOH . D 4 HOH A 60 460 343 HOH HOH . D 4 HOH A 61 461 315 HOH HOH . D 4 HOH A 62 462 319 HOH HOH . D 4 HOH A 63 463 325 HOH HOH . D 4 HOH A 64 464 488 HOH HOH . D 4 HOH A 65 465 328 HOH HOH . D 4 HOH A 66 466 330 HOH HOH . D 4 HOH A 67 467 341 HOH HOH . D 4 HOH A 68 468 493 HOH HOH . D 4 HOH A 69 469 435 HOH HOH . D 4 HOH A 70 470 305 HOH HOH . D 4 HOH A 71 471 332 HOH HOH . D 4 HOH A 72 472 324 HOH HOH . D 4 HOH A 73 473 378 HOH HOH . D 4 HOH A 74 474 496 HOH HOH . D 4 HOH A 75 475 301 HOH HOH . D 4 HOH A 76 476 361 HOH HOH . D 4 HOH A 77 477 308 HOH HOH . D 4 HOH A 78 478 313 HOH HOH . D 4 HOH A 79 479 376 HOH HOH . D 4 HOH A 80 480 436 HOH HOH . D 4 HOH A 81 481 497 HOH HOH . D 4 HOH A 82 482 353 HOH HOH . D 4 HOH A 83 483 336 HOH HOH . D 4 HOH A 84 484 340 HOH HOH . D 4 HOH A 85 485 433 HOH HOH . D 4 HOH A 86 486 502 HOH HOH . D 4 HOH A 87 487 444 HOH HOH . D 4 HOH A 88 488 311 HOH HOH . D 4 HOH A 89 489 342 HOH HOH . D 4 HOH A 90 490 373 HOH HOH . D 4 HOH A 91 491 369 HOH HOH . D 4 HOH A 92 492 306 HOH HOH . D 4 HOH A 93 493 448 HOH HOH . D 4 HOH A 94 494 385 HOH HOH . D 4 HOH A 95 495 335 HOH HOH . D 4 HOH A 96 496 303 HOH HOH . D 4 HOH A 97 497 414 HOH HOH . D 4 HOH A 98 498 440 HOH HOH . D 4 HOH A 99 499 317 HOH HOH . D 4 HOH A 100 500 413 HOH HOH . D 4 HOH A 101 501 400 HOH HOH . D 4 HOH A 102 502 384 HOH HOH . D 4 HOH A 103 503 309 HOH HOH . D 4 HOH A 104 504 423 HOH HOH . D 4 HOH A 105 505 398 HOH HOH . D 4 HOH A 106 506 415 HOH HOH . D 4 HOH A 107 507 468 HOH HOH . D 4 HOH A 108 508 395 HOH HOH . D 4 HOH A 109 509 473 HOH HOH . D 4 HOH A 110 510 416 HOH HOH . D 4 HOH A 111 511 427 HOH HOH . D 4 HOH A 112 512 459 HOH HOH . D 4 HOH A 113 513 323 HOH HOH . D 4 HOH A 114 514 439 HOH HOH . D 4 HOH A 115 515 352 HOH HOH . D 4 HOH A 116 516 326 HOH HOH . D 4 HOH A 117 517 375 HOH HOH . D 4 HOH A 118 518 465 HOH HOH . D 4 HOH A 119 519 382 HOH HOH . D 4 HOH A 120 520 356 HOH HOH . D 4 HOH A 121 521 500 HOH HOH . D 4 HOH A 122 522 410 HOH HOH . D 4 HOH A 123 523 487 HOH HOH . D 4 HOH A 124 524 338 HOH HOH . D 4 HOH A 125 525 339 HOH HOH . D 4 HOH A 126 526 407 HOH HOH . D 4 HOH A 127 527 491 HOH HOH . D 4 HOH A 128 528 390 HOH HOH . D 4 HOH A 129 529 357 HOH HOH . D 4 HOH A 130 530 504 HOH HOH . D 4 HOH A 131 531 479 HOH HOH . D 4 HOH A 132 532 333 HOH HOH . D 4 HOH A 133 533 492 HOH HOH . D 4 HOH A 134 534 489 HOH HOH . D 4 HOH A 135 535 460 HOH HOH . D 4 HOH A 136 536 310 HOH HOH . D 4 HOH A 137 537 370 HOH HOH . D 4 HOH A 138 538 314 HOH HOH . D 4 HOH A 139 539 358 HOH HOH . D 4 HOH A 140 540 345 HOH HOH . D 4 HOH A 141 541 406 HOH HOH . D 4 HOH A 142 542 490 HOH HOH . D 4 HOH A 143 543 507 HOH HOH . D 4 HOH A 144 544 371 HOH HOH . D 4 HOH A 145 545 442 HOH HOH . D 4 HOH A 146 546 321 HOH HOH . D 4 HOH A 147 547 372 HOH HOH . D 4 HOH A 148 548 452 HOH HOH . D 4 HOH A 149 549 362 HOH HOH . D 4 HOH A 150 550 463 HOH HOH . D 4 HOH A 151 551 327 HOH HOH . D 4 HOH A 152 552 424 HOH HOH . D 4 HOH A 153 553 383 HOH HOH . D 4 HOH A 154 554 501 HOH HOH . D 4 HOH A 155 555 447 HOH HOH . D 4 HOH A 156 556 412 HOH HOH . D 4 HOH A 157 557 351 HOH HOH . D 4 HOH A 158 558 471 HOH HOH . D 4 HOH A 159 559 474 HOH HOH . D 4 HOH A 160 560 349 HOH HOH . D 4 HOH A 161 561 405 HOH HOH . D 4 HOH A 162 562 430 HOH HOH . D 4 HOH A 163 563 387 HOH HOH . D 4 HOH A 164 564 409 HOH HOH . D 4 HOH A 165 565 484 HOH HOH . D 4 HOH A 166 566 461 HOH HOH . D 4 HOH A 167 567 421 HOH HOH . D 4 HOH A 168 568 466 HOH HOH . D 4 HOH A 169 569 402 HOH HOH . D 4 HOH A 170 570 418 HOH HOH . D 4 HOH A 171 571 464 HOH HOH . D 4 HOH A 172 572 437 HOH HOH . D 4 HOH A 173 573 454 HOH HOH . D 4 HOH A 174 574 472 HOH HOH . D 4 HOH A 175 575 453 HOH HOH . D 4 HOH A 176 576 483 HOH HOH . D 4 HOH A 177 577 498 HOH HOH . D 4 HOH A 178 578 386 HOH HOH . D 4 HOH A 179 579 425 HOH HOH . D 4 HOH A 180 580 475 HOH HOH . D 4 HOH A 181 581 389 HOH HOH . D 4 HOH A 182 582 458 HOH HOH . D 4 HOH A 183 583 457 HOH HOH . D 4 HOH A 184 584 462 HOH HOH . D 4 HOH A 185 585 397 HOH HOH . D 4 HOH A 186 586 445 HOH HOH . D 4 HOH A 187 587 446 HOH HOH . D 4 HOH A 188 588 470 HOH HOH . D 4 HOH A 189 589 495 HOH HOH . D 4 HOH A 190 590 426 HOH HOH . D 4 HOH A 191 591 429 HOH HOH . D 4 HOH A 192 592 408 HOH HOH . D 4 HOH A 193 593 449 HOH HOH . D 4 HOH A 194 594 477 HOH HOH . D 4 HOH A 195 595 456 HOH HOH . D 4 HOH A 196 596 505 HOH HOH . D 4 HOH A 197 597 478 HOH HOH . D 4 HOH A 198 598 399 HOH HOH . D 4 HOH A 199 599 482 HOH HOH . D 4 HOH A 200 600 388 HOH HOH . D 4 HOH A 201 601 419 HOH HOH . D 4 HOH A 202 602 506 HOH HOH . D 4 HOH A 203 603 391 HOH HOH . D 4 HOH A 204 604 494 HOH HOH . D 4 HOH A 205 605 499 HOH HOH . D 4 HOH A 206 606 481 HOH HOH . D 4 HOH A 207 607 503 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 R29 . . . C 3 -5.075 2.294 15.967 1 20.06 ? C1 R29 302 A 1 HETATM 2 C C2 R29 . . . C 3 -3.891 2.82 15.396 1 21.92 ? C2 R29 302 A 1 HETATM 3 C C3 R29 . . . C 3 -3.853 4.114 14.832 1 23.04 ? C3 R29 302 A 1 HETATM 4 C C4 R29 . . . C 3 -5.006 4.897 14.829 1 19.59 ? C4 R29 302 A 1 HETATM 5 C C5 R29 . . . C 3 -6.169 4.411 15.385 1 18.08 ? C5 R29 302 A 1 HETATM 6 C C6 R29 . . . C 3 -6.197 3.139 15.948 1 17.92 ? C6 R29 302 A 1 HETATM 7 C C7 R29 . . . C 3 -7.33 2.44 16.607 1 18.94 ? C7 R29 302 A 1 HETATM 8 C C8 R29 . . . C 3 -2.563 5.852 13.563 1 32.19 ? C8 R29 302 A 1 HETATM 9 C C9 R29 . . . C 3 -1.007 7.33 12.359 1 36.37 ? C9 R29 302 A 1 HETATM 10 C C10 R29 . . . C 3 -1.144 8.672 13.044 1 37.07 ? C10 R29 302 A 1 HETATM 11 C C11 R29 . . . C 3 -1.908 9.682 12.468 1 37.18 ? C11 R29 302 A 1 HETATM 12 C C12 R29 . . . C 3 -2.029 10.924 13.078 1 37.35 ? C12 R29 302 A 1 HETATM 13 C C13 R29 . . . C 3 -1.386 11.173 14.276 1 37.11 ? C13 R29 302 A 1 HETATM 14 C C14 R29 . . . C 3 -0.623 10.18 14.862 1 36.53 ? C14 R29 302 A 1 HETATM 15 C C15 R29 . . . C 3 -0.502 8.939 14.25 1 37.34 ? C15 R29 302 A 1 HETATM 16 O O1 R29 . . . C 3 -6.964 1.081 16.493 1 14.16 ? O1 R29 302 A 1 HETATM 17 O O3 R29 . . . C 3 -5.294 0.785 18.14 1 12.72 ? O3 R29 302 A 1 HETATM 18 O O4 R29 . . . C 3 -3.521 6.555 13.243 1 34.22 ? O4 R29 302 A 1 HETATM 19 N N1 R29 . . . C 3 -2.672 4.672 14.272 1 28.5 ? N1 R29 302 A 1 HETATM 20 N N2 R29 . . . C 3 -1.304 6.165 13.187 1 34.19 ? N2 R29 302 A 1 HETATM 21 B B1 R29 . . . C 3 -5.514 0.883 16.69 1 16.78 ? B1 R29 302 A 1 HETATM 22 O O2 R29 . . . C 3 -5.149 -0.406 16.065 1 10.75 ? O2 R29 302 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #