data_1YNJ
#
_model_server_result.job_id            t5o29qA351YLG45PFkQwHQ 
_model_server_result.datetime_utc      '2024-10-20 00:29:19' 
_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          1ynj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1120}' 
#
_entry.id    1YNJ 
#
_exptl.entry_id    1YNJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              807.02 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SORANGICIN A' 
_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            1YNJ 
_cell.length_a            199.19 
_cell.length_b            199.19 
_cell.length_c            289.306 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YNJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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                      5 
_struct_asym.id                             G 
_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 D SG CYS 58 D CYS 58 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc2 D SG CYS 60 D CYS 60 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc3 D SG CYS 73 D CYS 73 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc4 D SG CYS 76 D CYS 76 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? 
metalc ? metalc5 D SG CYS 1112 D CYS 1112 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc6 D SG CYS 1194 D CYS 1194 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc7 D SG CYS 1201 D CYS 1201 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
#
_chem_comp.formula           'C47 H66 O11' 
_chem_comp.formula_weight    807.02 
_chem_comp.id                SRN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SORANGICIN A' 
_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
O11 C45 SRN doub 288 n n 
C45 O10 SRN sing 289 n n 
C45 C44 SRN sing 290 n n 
O10 H10 SRN sing 291 n n 
C44 C43 SRN sing 292 n n 
C44 H441 SRN sing 293 n n 
C44 H442 SRN sing 294 n n 
C43 C42 SRN sing 295 n n 
C43 H431 SRN sing 296 n n 
C43 H432 SRN sing 297 n n 
C42 C41 SRN sing 298 n n 
C42 H421 SRN sing 299 n n 
C42 H422 SRN sing 300 n n 
C41 C39 SRN sing 301 n n 
C41 H411 SRN sing 302 n n 
C41 H412 SRN sing 303 n n 
C39 C40 SRN sing 304 n n 
C39 C38 SRN sing 305 n n 
C39 H39 SRN sing 306 n n 
C40 H401 SRN sing 307 n n 
C40 H402 SRN sing 308 n n 
C40 H403 SRN sing 309 n n 
C38 C36 SRN doub 310 e n 
C38 H38 SRN sing 311 n n 
C36 C37 SRN sing 312 n n 
C36 C32 SRN sing 313 n n 
C37 H371 SRN sing 314 n n 
C37 H372 SRN sing 315 n n 
C37 H373 SRN sing 316 n n 
C32 C33 SRN sing 317 n n 
C32 O7 SRN sing 318 n n 
C32 H32 SRN sing 319 n n 
C33 C47 SRN sing 320 n n 
C33 O1 SRN sing 321 n n 
C33 H33 SRN sing 322 n n 
C47 C46 SRN doub 323 n n 
C47 H47 SRN sing 324 n n 
C46 C31 SRN sing 325 n n 
C46 H46 SRN sing 326 n n 
O1 C1 SRN sing 327 n n 
O7 C31 SRN sing 328 n n 
C31 C30 SRN sing 329 n n 
C31 H31 SRN sing 330 n n 
C30 C29 SRN sing 331 n n 
C30 H301 SRN sing 332 n n 
C30 H302 SRN sing 333 n n 
C29 C28 SRN doub 334 e n 
C29 H29 SRN sing 335 n n 
C28 C27 SRN sing 336 n n 
C28 H28 SRN sing 337 n n 
C27 C26 SRN sing 338 n n 
C27 H271 SRN sing 339 n n 
C27 H272 SRN sing 340 n n 
C26 C25 SRN sing 341 n n 
C26 H261 SRN sing 342 n n 
C26 H262 SRN sing 343 n n 
C25 C24 SRN doub 344 e n 
C25 H25 SRN sing 345 n n 
C24 C23 SRN sing 346 n n 
C24 H24 SRN sing 347 n n 
C23 O6 SRN sing 348 n n 
C23 C22 SRN sing 349 n n 
C23 H23 SRN sing 350 n n 
O6 HO6 SRN sing 351 n n 
C22 O5 SRN sing 352 n n 
C22 C21 SRN sing 353 n n 
C22 H22 SRN sing 354 n n 
O5 HO5 SRN sing 355 n n 
C21 O9 SRN sing 356 n n 
C21 C20 SRN sing 357 n n 
C21 H21 SRN sing 358 n n 
O9 C16 SRN sing 359 n n 
C20 C19 SRN sing 360 n n 
C20 H201 SRN sing 361 n n 
C20 H202 SRN sing 362 n n 
C19 O4 SRN sing 363 n n 
C19 C17 SRN sing 364 n n 
C19 H19 SRN sing 365 n n 
O4 HO4 SRN sing 366 n n 
C17 C18 SRN sing 367 n n 
C17 C16 SRN sing 368 n n 
C17 H17 SRN sing 369 n n 
C18 H181 SRN sing 370 n n 
C18 H182 SRN sing 371 n n 
C18 H183 SRN sing 372 n n 
C16 C15 SRN sing 373 n n 
C16 H16 SRN sing 374 n n 
C15 C14 SRN sing 375 n n 
C15 H151 SRN sing 376 n n 
C15 H152 SRN sing 377 n n 
C14 C13 SRN doub 378 e n 
C14 H14 SRN sing 379 n n 
C13 C12 SRN sing 380 n n 
C13 H13 SRN sing 381 n n 
C12 O8 SRN sing 382 n n 
C12 C10 SRN sing 383 n n 
C12 H12 SRN sing 384 n n 
O8 C35 SRN sing 385 n n 
C35 C34 SRN sing 386 n n 
C35 C8 SRN sing 387 n n 
C35 H35 SRN sing 388 n n 
C34 C9 SRN sing 389 n n 
C34 H341 SRN sing 390 n n 
C34 H342 SRN sing 391 n n 
C9 C10 SRN sing 392 n n 
C9 O3 SRN sing 393 n n 
C9 H9 SRN sing 394 n n 
C10 C11 SRN sing 395 n n 
C10 H1 SRN sing 396 n n 
C11 H111 SRN sing 397 n n 
C11 H112 SRN sing 398 n n 
C11 H113 SRN sing 399 n n 
O3 C8 SRN sing 400 n n 
C8 C7 SRN sing 401 n n 
C8 H8 SRN sing 402 n n 
C7 C6 SRN doub 403 e n 
C7 H7 SRN sing 404 n n 
C6 C5 SRN sing 405 n n 
C6 H6 SRN sing 406 n n 
C5 C4 SRN doub 407 z n 
C5 H5 SRN sing 408 n n 
C4 C3 SRN sing 409 n n 
C4 H4 SRN sing 410 n n 
C3 C2 SRN doub 411 z n 
C3 H3 SRN sing 412 n n 
C2 C1 SRN sing 413 n n 
C2 H2 SRN sing 414 n n 
C1 O2 SRN doub 415 n n 
#
_atom_sites.entry_id                     1YNJ 
_atom_sites.fract_transf_matrix[1][1]    0.00502 
_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]    0.00502 
_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]    0.003457 
_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
G 5 SRN C 1 1120 1 SRN SRN . 
H 6 ZN D 1 1525 2 ZN ZN . 
I 6 ZN D 1 1526 3 ZN ZN . 
#
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 O11 SRN . . . G 5 46.871 93.79 28.643 1 57.5 ? O11 SRN 1120 C 1 
HETATM 2 C C45 SRN . . . G 5 47.654 94.561 29.285 1 57.91 ? C45 SRN 1120 C 1 
HETATM 3 O O10 SRN . . . G 5 47.581 94.731 30.524 1 59.06 ? O10 SRN 1120 C 1 
HETATM 4 C C44 SRN . . . G 5 48.753 95.354 28.593 1 55.97 ? C44 SRN 1120 C 1 
HETATM 5 C C43 SRN . . . G 5 49.432 94.544 27.488 1 53.3 ? C43 SRN 1120 C 1 
HETATM 6 C C42 SRN . . . G 5 49.219 95.175 26.114 1 49.69 ? C42 SRN 1120 C 1 
HETATM 7 C C41 SRN . . . G 5 49.47 94.148 25.011 1 48.74 ? C41 SRN 1120 C 1 
HETATM 8 C C39 SRN . . . G 5 50.909 94.099 24.467 1 47.28 ? C39 SRN 1120 C 1 
HETATM 9 C C40 SRN . . . G 5 51.117 92.896 23.555 1 46.95 ? C40 SRN 1120 C 1 
HETATM 10 C C38 SRN . . . G 5 51.177 95.384 23.727 1 45.89 ? C38 SRN 1120 C 1 
HETATM 11 C C36 SRN . . . G 5 51.926 96.304 24.33 1 45.61 ? C36 SRN 1120 C 1 
HETATM 12 C C37 SRN . . . G 5 52.469 96.053 25.711 1 46.39 ? C37 SRN 1120 C 1 
HETATM 13 C C32 SRN . . . G 5 52.178 97.628 23.682 1 45.36 ? C32 SRN 1120 C 1 
HETATM 14 C C33 SRN . . . G 5 53.599 98.024 23.233 1 46.92 ? C33 SRN 1120 C 1 
HETATM 15 C C47 SRN . . . G 5 53.609 99.062 22.145 1 44.88 ? C47 SRN 1120 C 1 
HETATM 16 C C46 SRN . . . G 5 52.51 99.445 21.508 1 42.45 ? C46 SRN 1120 C 1 
HETATM 17 O O1 SRN . . . G 5 54.162 96.894 22.539 1 52.44 ? O1 SRN 1120 C 1 
HETATM 18 O O7 SRN . . . G 5 51.036 98.011 22.918 1 42.49 ? O7 SRN 1120 C 1 
HETATM 19 C C31 SRN . . . G 5 51.122 98.955 21.86 1 41.22 ? C31 SRN 1120 C 1 
HETATM 20 C C30 SRN . . . G 5 50.219 100.107 22.25 1 38.25 ? C30 SRN 1120 C 1 
HETATM 21 C C29 SRN . . . G 5 48.792 99.629 22.425 1 35.4 ? C29 SRN 1120 C 1 
HETATM 22 C C28 SRN . . . G 5 48.359 99.113 23.573 1 33.44 ? C28 SRN 1120 C 1 
HETATM 23 C C27 SRN . . . G 5 46.917 98.689 23.642 1 33.54 ? C27 SRN 1120 C 1 
HETATM 24 C C26 SRN . . . G 5 46.787 97.354 24.36 1 35.16 ? C26 SRN 1120 C 1 
HETATM 25 C C25 SRN . . . G 5 45.453 96.743 24.005 1 35.7 ? C25 SRN 1120 C 1 
HETATM 26 C C24 SRN . . . G 5 44.723 96.216 24.978 1 37.15 ? C24 SRN 1120 C 1 
HETATM 27 C C23 SRN . . . G 5 43.378 95.608 24.659 1 38.3 ? C23 SRN 1120 C 1 
HETATM 28 O O6 SRN . . . G 5 42.343 96.52 25.032 1 40.1 ? O6 SRN 1120 C 1 
HETATM 29 C C22 SRN . . . G 5 43.21 94.274 25.379 1 37.66 ? C22 SRN 1120 C 1 
HETATM 30 O O5 SRN . . . G 5 42.803 94.493 26.721 1 39.18 ? O5 SRN 1120 C 1 
HETATM 31 C C21 SRN . . . G 5 44.505 93.488 25.344 1 37.6 ? C21 SRN 1120 C 1 
HETATM 32 O O9 SRN . . . G 5 44.748 93.188 23.977 1 37.87 ? O9 SRN 1120 C 1 
HETATM 33 C C20 SRN . . . G 5 44.398 92.177 26.117 1 38.32 ? C20 SRN 1120 C 1 
HETATM 34 C C19 SRN . . . G 5 45.625 91.308 25.831 1 38.41 ? C19 SRN 1120 C 1 
HETATM 35 O O4 SRN . . . G 5 46.799 91.999 26.25 1 40.27 ? O4 SRN 1120 C 1 
HETATM 36 C C17 SRN . . . G 5 45.764 91.057 24.348 1 37.4 ? C17 SRN 1120 C 1 
HETATM 37 C C18 SRN . . . G 5 44.567 90.274 23.816 1 36.73 ? C18 SRN 1120 C 1 
HETATM 38 C C16 SRN . . . G 5 45.925 92.426 23.711 1 38.16 ? C16 SRN 1120 C 1 
HETATM 39 C C15 SRN . . . G 5 46.073 92.334 22.204 1 40.97 ? C15 SRN 1120 C 1 
HETATM 40 C C14 SRN . . . G 5 47.494 92.093 21.747 1 43.02 ? C14 SRN 1120 C 1 
HETATM 41 C C13 SRN . . . G 5 47.689 91.147 20.833 1 44.9 ? C13 SRN 1120 C 1 
HETATM 42 C C12 SRN . . . G 5 49.083 90.896 20.335 1 47.51 ? C12 SRN 1120 C 1 
HETATM 43 O O8 SRN . . . G 5 49.027 91.034 18.897 1 49.1 ? O8 SRN 1120 C 1 
HETATM 44 C C35 SRN . . . G 5 50.104 90.481 18.108 1 48.58 ? C35 SRN 1120 C 1 
HETATM 45 C C34 SRN . . . G 5 50.145 89.005 18.439 1 48.72 ? C34 SRN 1120 C 1 
HETATM 46 C C9 SRN . . . G 5 50.776 89.111 19.819 1 48.88 ? C9 SRN 1120 C 1 
HETATM 47 C C10 SRN . . . G 5 49.649 89.527 20.773 1 49.12 ? C10 SRN 1120 C 1 
HETATM 48 C C11 SRN . . . G 5 50.136 89.487 22.228 1 50.52 ? C11 SRN 1120 C 1 
HETATM 49 O O3 SRN . . . G 5 51.776 90.152 19.719 1 48.29 ? O3 SRN 1120 C 1 
HETATM 50 C C8 SRN . . . G 5 51.502 90.944 18.548 1 48.05 ? C8 SRN 1120 C 1 
HETATM 51 C C7 SRN . . . G 5 51.615 92.439 18.794 1 46.43 ? C7 SRN 1120 C 1 
HETATM 52 C C6 SRN . . . G 5 52.345 92.876 19.804 1 47.25 ? C6 SRN 1120 C 1 
HETATM 53 C C5 SRN . . . G 5 52.469 94.186 20.038 1 49.94 ? C5 SRN 1120 C 1 
HETATM 54 C C4 SRN . . . G 5 53.185 94.707 21.061 1 51.38 ? C4 SRN 1120 C 1 
HETATM 55 C C3 SRN . . . G 5 53.866 93.973 21.963 1 52.23 ? C3 SRN 1120 C 1 
HETATM 56 C C2 SRN . . . G 5 54.575 94.461 22.994 1 53.44 ? C2 SRN 1120 C 1 
HETATM 57 C C1 SRN . . . G 5 54.76 95.778 23.312 1 54.76 ? C1 SRN 1120 C 1 
HETATM 58 O O2 SRN . . . G 5 55.457 96.055 24.292 1 56.87 ? O2 SRN 1120 C 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           58 
#