data_5DGJ # _model_server_result.job_id yYq10vCP2XGFRRRS8Cl9Fw _model_server_result.datetime_utc '2024-11-22 07:45:03' _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 5dgj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5DGJ # _exptl.entry_id 5DGJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 592.727 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate' _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 109.36 _cell.angle_gamma 90 _cell.entry_id 5DGJ _cell.length_a 65.169 _cell.length_b 41.176 _cell.length_c 61.679 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 _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 covale ? covale1 A SG CYS 146 A CYS 139 1_555 B C24 V64 . A V64 201 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale2 A SG CYS 146 A CYS 139 1_555 B C24 V64 . A V64 201 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.795 ? # _chem_comp.formula 'C29 H48 N6 O7' _chem_comp.formula_weight 592.727 _chem_comp.id V64 _chem_comp.mon_nstd_flag . _chem_comp.name 'tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate' _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 O25 C24 V64 sing 358 n n C24 C14 V64 sing 359 n n C14 C15 V64 sing 360 n n C14 N13 V64 sing 361 n n C15 C16 V64 sing 362 n n C5 N18 V64 sing 363 n n O23 C17 V64 doub 364 n n N18 C17 V64 sing 365 n n C17 C16 V64 sing 366 n n N13 C12 V64 sing 367 n n O26 C12 V64 doub 368 n n C12 C04 V64 sing 369 n n C05 C04 V64 sing 370 n n C05 C06 V64 sing 371 n n C04 N03 V64 sing 372 n n C11 C06 V64 sing 373 n n C11 C10 V64 sing 374 n n C06 C07 V64 sing 375 n n O01 C02 V64 doub 376 n n N03 C02 V64 sing 377 n n C10 C09 V64 sing 378 n n C02 C27 V64 sing 379 n n C07 C08 V64 sing 380 n n C09 C08 V64 sing 381 n n C28 C27 V64 sing 382 n n C28 C29 V64 sing 383 n n C27 N35 V64 sing 384 n n N35 C36 V64 sing 385 n n C36 O37 V64 sing 386 n n C36 O42 V64 doub 387 n n O37 C38 V64 sing 388 n n C38 C41 V64 sing 389 n n C38 C40 V64 sing 390 n n C38 C39 V64 sing 391 n n N03 H1 V64 sing 392 n n C04 H2 V64 sing 393 n n C05 H3 V64 sing 394 n n C05 H4 V64 sing 395 n n C06 H5 V64 sing 396 n n C07 H6 V64 sing 397 n n C07 H7 V64 sing 398 n n C08 H8 V64 sing 399 n n C08 H9 V64 sing 400 n n C09 H10 V64 sing 401 n n C09 H11 V64 sing 402 n n C10 H12 V64 sing 403 n n C10 H13 V64 sing 404 n n C11 H14 V64 sing 405 n n C11 H15 V64 sing 406 n n N13 H16 V64 sing 407 n n C14 H17 V64 sing 408 n n C15 H18 V64 sing 409 n n C15 H19 V64 sing 410 n n C16 H20 V64 sing 411 n n C16 H21 V64 sing 412 n n N18 H22 V64 sing 413 n n C5 H23 V64 sing 414 n n C5 H24 V64 sing 415 n n C24 H26 V64 sing 416 n n C24 H27 V64 sing 417 n n O25 H28 V64 sing 418 n n C27 H29 V64 sing 419 n n C28 H30 V64 sing 420 n n C28 H31 V64 sing 421 n n C29 H32 V64 sing 422 n n C29 H33 V64 sing 423 n n N35 H35 V64 sing 424 n n C39 H36 V64 sing 425 n n C39 H37 V64 sing 426 n n C39 H38 V64 sing 427 n n C40 H39 V64 sing 428 n n C40 H40 V64 sing 429 n n C40 H41 V64 sing 430 n n C41 H42 V64 sing 431 n n C41 H43 V64 sing 432 n n C41 H44 V64 sing 433 n n C29 C6 V64 sing 434 n n C6 N1 V64 doub 435 n y N1 N2 V64 sing 436 n y N2 C4 V64 doub 437 n y C4 O1 V64 sing 438 n y O1 C6 V64 sing 439 n y C4 C1 V64 sing 440 n n C1 C2 V64 sing 441 n n C2 C3 V64 sing 442 n n C3 C5 V64 sing 443 n n C1 H34 V64 sing 444 n n C1 H45 V64 sing 445 n n C2 H46 V64 sing 446 n n C2 H47 V64 sing 447 n n C3 H48 V64 sing 448 n n C3 H49 V64 sing 449 n n # _atom_sites.entry_id 5DGJ _atom_sites.fract_transf_matrix[1][1] 0.015345 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00539 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024286 _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] 0.017184 _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 V64 A 1 201 1 V64 V64 . C 3 HOH A 1 301 100 HOH HOH . C 3 HOH A 2 302 41 HOH HOH . C 3 HOH A 3 303 80 HOH HOH . C 3 HOH A 4 304 43 HOH HOH . C 3 HOH A 5 305 86 HOH HOH . C 3 HOH A 6 306 110 HOH HOH . C 3 HOH A 7 307 45 HOH HOH . C 3 HOH A 8 308 71 HOH HOH . C 3 HOH A 9 309 16 HOH HOH . C 3 HOH A 10 310 23 HOH HOH . C 3 HOH A 11 311 105 HOH HOH . C 3 HOH A 12 312 97 HOH HOH . C 3 HOH A 13 313 84 HOH HOH . C 3 HOH A 14 314 30 HOH HOH . C 3 HOH A 15 315 28 HOH HOH . C 3 HOH A 16 316 31 HOH HOH . C 3 HOH A 17 317 132 HOH HOH . C 3 HOH A 18 318 25 HOH HOH . C 3 HOH A 19 319 104 HOH HOH . C 3 HOH A 20 320 68 HOH HOH . C 3 HOH A 21 321 98 HOH HOH . C 3 HOH A 22 322 6 HOH HOH . C 3 HOH A 23 323 53 HOH HOH . C 3 HOH A 24 324 1 HOH HOH . C 3 HOH A 25 325 11 HOH HOH . C 3 HOH A 26 326 15 HOH HOH . C 3 HOH A 27 327 47 HOH HOH . C 3 HOH A 28 328 66 HOH HOH . C 3 HOH A 29 329 109 HOH HOH . C 3 HOH A 30 330 83 HOH HOH . C 3 HOH A 31 331 9 HOH HOH . C 3 HOH A 32 332 79 HOH HOH . C 3 HOH A 33 333 57 HOH HOH . C 3 HOH A 34 334 18 HOH HOH . C 3 HOH A 35 335 38 HOH HOH . C 3 HOH A 36 336 101 HOH HOH . C 3 HOH A 37 337 20 HOH HOH . C 3 HOH A 38 338 33 HOH HOH . C 3 HOH A 39 339 36 HOH HOH . C 3 HOH A 40 340 117 HOH HOH . C 3 HOH A 41 341 90 HOH HOH . C 3 HOH A 42 342 35 HOH HOH . C 3 HOH A 43 343 115 HOH HOH . C 3 HOH A 44 344 26 HOH HOH . C 3 HOH A 45 345 27 HOH HOH . C 3 HOH A 46 346 91 HOH HOH . C 3 HOH A 47 347 21 HOH HOH . C 3 HOH A 48 348 62 HOH HOH . C 3 HOH A 49 349 118 HOH HOH . C 3 HOH A 50 350 5 HOH HOH . C 3 HOH A 51 351 42 HOH HOH . C 3 HOH A 52 352 54 HOH HOH . C 3 HOH A 53 353 29 HOH HOH . C 3 HOH A 54 354 14 HOH HOH . C 3 HOH A 55 355 24 HOH HOH . C 3 HOH A 56 356 4 HOH HOH . C 3 HOH A 57 357 50 HOH HOH . C 3 HOH A 58 358 78 HOH HOH . C 3 HOH A 59 359 103 HOH HOH . C 3 HOH A 60 360 61 HOH HOH . C 3 HOH A 61 361 108 HOH HOH . C 3 HOH A 62 362 85 HOH HOH . C 3 HOH A 63 363 69 HOH HOH . C 3 HOH A 64 364 70 HOH HOH . C 3 HOH A 65 365 40 HOH HOH . C 3 HOH A 66 366 32 HOH HOH . C 3 HOH A 67 367 7 HOH HOH . C 3 HOH A 68 368 2 HOH HOH . C 3 HOH A 69 369 102 HOH HOH . C 3 HOH A 70 370 67 HOH HOH . C 3 HOH A 71 371 119 HOH HOH . C 3 HOH A 72 372 87 HOH HOH . C 3 HOH A 73 373 77 HOH HOH . C 3 HOH A 74 374 51 HOH HOH . C 3 HOH A 75 375 72 HOH HOH . C 3 HOH A 76 376 126 HOH HOH . C 3 HOH A 77 377 22 HOH HOH . C 3 HOH A 78 378 65 HOH HOH . C 3 HOH A 79 379 8 HOH HOH . C 3 HOH A 80 380 44 HOH HOH . C 3 HOH A 81 381 112 HOH HOH . C 3 HOH A 82 382 12 HOH HOH . C 3 HOH A 83 383 56 HOH HOH . C 3 HOH A 84 384 39 HOH HOH . C 3 HOH A 85 385 48 HOH HOH . C 3 HOH A 86 386 49 HOH HOH . C 3 HOH A 87 387 17 HOH HOH . C 3 HOH A 88 388 73 HOH HOH . C 3 HOH A 89 389 10 HOH HOH . C 3 HOH A 90 390 59 HOH HOH . C 3 HOH A 91 391 82 HOH HOH . C 3 HOH A 92 392 13 HOH HOH . C 3 HOH A 93 393 19 HOH HOH . C 3 HOH A 94 394 52 HOH HOH . C 3 HOH A 95 395 58 HOH HOH . C 3 HOH A 96 396 124 HOH HOH . C 3 HOH A 97 397 88 HOH HOH . C 3 HOH A 98 398 113 HOH HOH . C 3 HOH A 99 399 127 HOH HOH . C 3 HOH A 100 400 94 HOH HOH . C 3 HOH A 101 401 55 HOH HOH . C 3 HOH A 102 402 46 HOH HOH . C 3 HOH A 103 403 123 HOH HOH . C 3 HOH A 104 404 3 HOH HOH . C 3 HOH A 105 405 99 HOH HOH . C 3 HOH A 106 406 34 HOH HOH . C 3 HOH A 107 407 64 HOH HOH . C 3 HOH A 108 408 37 HOH HOH . C 3 HOH A 109 409 130 HOH HOH . C 3 HOH A 110 410 120 HOH HOH . C 3 HOH A 111 411 75 HOH HOH . C 3 HOH A 112 412 81 HOH HOH . C 3 HOH A 113 413 121 HOH HOH . C 3 HOH A 114 414 74 HOH HOH . C 3 HOH A 115 415 128 HOH HOH . C 3 HOH A 116 416 129 HOH HOH . C 3 HOH A 117 417 93 HOH HOH . C 3 HOH A 118 418 107 HOH HOH . C 3 HOH A 119 419 114 HOH HOH . C 3 HOH A 120 420 111 HOH HOH . C 3 HOH A 121 421 76 HOH HOH . C 3 HOH A 122 422 131 HOH HOH . C 3 HOH A 123 423 122 HOH HOH . C 3 HOH A 124 424 63 HOH HOH . C 3 HOH A 125 425 60 HOH HOH . C 3 HOH A 126 426 96 HOH HOH . C 3 HOH A 127 427 92 HOH HOH . C 3 HOH A 128 428 89 HOH HOH . C 3 HOH A 129 429 106 HOH HOH . C 3 HOH A 130 430 116 HOH HOH . C 3 HOH A 131 431 125 HOH HOH . C 3 HOH A 132 432 95 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 O O42 V64 . . . B 2 17.277 -57.245 140.498 1 27.59 ? O42 V64 201 A 1 HETATM 2 C C36 V64 . . . B 2 16.59 -56.516 139.854 1 26.35 ? C36 V64 201 A 1 HETATM 3 O O37 V64 . . . B 2 16.264 -55.199 140.254 1 27.52 ? O37 V64 201 A 1 HETATM 4 C C38 V64 . . . B 2 16.627 -54.76 141.561 1 28.54 ? C38 V64 201 A 1 HETATM 5 C C39 V64 . . . B 2 15.91 -55.6 142.646 1 28.84 ? C39 V64 201 A 1 HETATM 6 C C40 V64 . . . B 2 18.166 -54.841 141.729 1 28.51 ? C40 V64 201 A 1 HETATM 7 C C41 V64 . . . B 2 16.2 -53.274 141.673 1 29.1 ? C41 V64 201 A 1 HETATM 8 O O01 V64 . . . B 2 17.532 -56.341 136.406 1 17.47 ? O01 V64 201 A 1 HETATM 9 C C02 V64 . . . B 2 17.63 -57.447 136.843 1 18.74 ? C02 V64 201 A 1 HETATM 10 N N18 V64 . . . B 2 14.284 -54.129 132.917 1 23.93 ? N18 V64 201 A 1 HETATM 11 C C27 V64 . . . B 2 16.638 -58.023 137.833 1 22.09 ? C27 V64 201 A 1 HETATM 12 C C28 V64 . . . B 2 15.563 -58.779 137.048 1 23.86 ? C28 V64 201 A 1 HETATM 13 C C29 V64 . . . B 2 14.724 -59.682 137.984 1 25.03 ? C29 V64 201 A 1 HETATM 14 N N35 V64 . . . B 2 16.018 -56.956 138.575 1 24.15 ? N35 V64 201 A 1 HETATM 15 C C5 V64 . . . B 2 13.281 -53.07 132.748 1 25.03 ? C5 V64 201 A 1 HETATM 16 N N13 V64 . . . B 2 19.439 -56.252 133.551 1 14.32 ? N13 V64 201 A 1 HETATM 17 C C14 V64 . . . B 2 18.9 -55.782 132.285 1 14.11 ? C14 V64 201 A 1 HETATM 18 C C15 V64 . . . B 2 18.031 -54.544 132.541 1 15.17 ? C15 V64 201 A 1 HETATM 19 C C16 V64 . . . B 2 16.677 -54.94 133.144 1 17.95 ? C16 V64 201 A 1 HETATM 20 C C17 V64 . . . B 2 15.691 -53.778 132.957 1 20.94 ? C17 V64 201 A 1 HETATM 21 O O23 V64 . . . B 2 16.05 -52.643 132.84 1 20.55 ? O23 V64 201 A 1 HETATM 22 C C24 V64 . . . B 2 20.058 -55.475 131.348 1 13.55 ? C24 V64 201 A 1 HETATM 23 O O25 V64 . . . B 2 20.686 -56.588 130.979 1 15.52 ? O25 V64 201 A 1 HETATM 24 N N03 V64 . . . B 2 18.725 -58.331 136.441 1 17.52 ? N03 V64 201 A 1 HETATM 25 C C04 V64 . . . B 2 19.674 -57.811 135.491 1 16.58 ? C04 V64 201 A 1 HETATM 26 C C12 V64 . . . B 2 18.944 -57.453 134.197 1 15.48 ? C12 V64 201 A 1 HETATM 27 O O26 V64 . . . B 2 18.056 -58.103 133.719 1 16.45 ? O26 V64 201 A 1 HETATM 28 C C05 V64 . . . B 2 20.742 -58.851 135.114 1 17.32 ? C05 V64 201 A 1 HETATM 29 C C06 V64 . . . B 2 21.748 -59.192 136.264 1 18.8 ? C06 V64 201 A 1 HETATM 30 C C07 V64 . . . B 2 22.48 -57.916 136.711 1 19.64 ? C07 V64 201 A 1 HETATM 31 C C08 V64 . . . B 2 23.633 -58.233 137.665 1 20.98 ? C08 V64 201 A 1 HETATM 32 C C09 V64 . . . B 2 24.633 -59.2 137.027 1 21.46 ? C09 V64 201 A 1 HETATM 33 C C10 V64 . . . B 2 23.96 -60.508 136.584 1 21.31 ? C10 V64 201 A 1 HETATM 34 C C11 V64 . . . B 2 22.701 -60.279 135.724 1 20.29 ? C11 V64 201 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #