data_1YNN
#
_model_server_result.job_id            aP1Zz4XKL0OwbxnyodzTXg 
_model_server_result.datetime_utc      '2024-10-11 02:20:58' 
_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          1ynn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1120}' 
#
_entry.id    1YNN 
#
_exptl.entry_id    1YNN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              822.94 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RIFAMPICIN 
_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            1YNN 
_cell.length_a            200.76 
_cell.length_b            200.76 
_cell.length_c            292.938 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YNN 
_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 N ALA 59 D ALA 59 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
metalc ? metalc2 D O CYS 76 D CYS 76 1_555 H ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? 
metalc ? metalc3 D SG CYS 1112 D CYS 1112 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc4 D SG CYS 1194 D CYS 1194 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc5 D SG CYS 1201 D CYS 1201 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? 
metalc ? metalc6 D SG CYS 1204 D CYS 1204 1_555 I ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
#
_chem_comp.formula           'C43 H58 N4 O12' 
_chem_comp.formula_weight    822.94 
_chem_comp.id                RFP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RIFAMPICIN 
_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
C1 C2 RFP doub 275 n y 
C1 C9 RFP sing 276 n y 
C1 O1 RFP sing 277 n n 
C2 C3 RFP sing 278 n y 
C2 N1 RFP sing 279 n n 
C3 C4 RFP doub 280 n y 
C3 C43 RFP sing 281 n n 
C4 C10 RFP sing 282 n y 
C4 O12 RFP sing 283 n n 
C5 C6 RFP doub 284 n y 
C5 C10 RFP sing 285 n y 
C5 C11 RFP sing 286 n n 
C6 C7 RFP sing 287 n y 
C6 O3 RFP sing 288 n n 
C7 C8 RFP doub 289 n y 
C7 C14 RFP sing 290 n n 
C8 C9 RFP sing 291 n y 
C8 O2 RFP sing 292 n n 
C9 C10 RFP doub 293 n y 
C11 C12 RFP sing 294 n n 
C11 O4 RFP doub 295 n n 
C12 C13 RFP sing 296 n n 
C12 O3 RFP sing 297 n n 
C12 O5 RFP sing 298 n n 
C13 H131 RFP sing 299 n n 
C13 H132 RFP sing 300 n n 
C13 H133 RFP sing 301 n n 
C14 H141 RFP sing 302 n n 
C14 H142 RFP sing 303 n n 
C14 H143 RFP sing 304 n n 
C15 C16 RFP sing 305 n n 
C15 N1 RFP sing 306 n n 
C15 O11 RFP doub 307 n n 
C16 C17 RFP doub 308 z n 
C16 C30 RFP sing 309 n n 
C17 C18 RFP sing 310 n n 
C17 H17C RFP sing 311 n n 
C18 C19 RFP doub 312 e n 
C18 H18C RFP sing 313 n n 
C19 C20 RFP sing 314 n n 
C19 H19C RFP sing 315 n n 
C20 C21 RFP sing 316 n n 
C20 C31 RFP sing 317 n n 
C20 H20C RFP sing 318 n n 
C21 C22 RFP sing 319 n n 
C21 O10 RFP sing 320 n n 
C21 H211 RFP sing 321 n n 
C22 C23 RFP sing 322 n n 
C22 C32 RFP sing 323 n n 
C22 H22C RFP sing 324 n n 
C23 C24 RFP sing 325 n n 
C23 O9 RFP sing 326 n n 
C23 H23C RFP sing 327 n n 
C24 C25 RFP sing 328 n n 
C24 C33 RFP sing 329 n n 
C24 H24C RFP sing 330 n n 
C25 C26 RFP sing 331 n n 
C25 O7 RFP sing 332 n n 
C25 H25C RFP sing 333 n n 
C26 C27 RFP sing 334 n n 
C26 C34 RFP sing 335 n n 
C26 H26C RFP sing 336 n n 
C27 C28 RFP sing 337 n n 
C27 O6 RFP sing 338 n n 
C27 H27C RFP sing 339 n n 
C28 C29 RFP doub 340 e n 
C28 H28C RFP sing 341 n n 
C29 O5 RFP sing 342 n n 
C29 H29C RFP sing 343 n n 
C30 H301 RFP sing 344 n n 
C30 H302 RFP sing 345 n n 
C30 H303 RFP sing 346 n n 
C31 H311 RFP sing 347 n n 
C31 H312 RFP sing 348 n n 
C31 H313 RFP sing 349 n n 
C32 H321 RFP sing 350 n n 
C32 H322 RFP sing 351 n n 
C32 H323 RFP sing 352 n n 
C33 H331 RFP sing 353 n n 
C33 H332 RFP sing 354 n n 
C33 H333 RFP sing 355 n n 
C34 H341 RFP sing 356 n n 
C34 H342 RFP sing 357 n n 
C34 H343 RFP sing 358 n n 
C35 C36 RFP sing 359 n n 
C35 O7 RFP sing 360 n n 
C35 O8 RFP doub 361 n n 
C36 H361 RFP sing 362 n n 
C36 H362 RFP sing 363 n n 
C36 H363 RFP sing 364 n n 
C37 O6 RFP sing 365 n n 
C37 H371 RFP sing 366 n n 
C37 H372 RFP sing 367 n n 
C37 H373 RFP sing 368 n n 
C38 N4 RFP sing 369 n n 
C38 H381 RFP sing 370 n n 
C38 H382 RFP sing 371 n n 
C38 H383 RFP sing 372 n n 
C39 C40 RFP sing 373 n n 
C39 N4 RFP sing 374 n n 
C39 H391 RFP sing 375 n n 
C39 H392 RFP sing 376 n n 
C40 N3 RFP sing 377 n n 
C40 H401 RFP sing 378 n n 
C40 H402 RFP sing 379 n n 
C41 C42 RFP sing 380 n n 
C41 N3 RFP sing 381 n n 
C41 H411 RFP sing 382 n n 
C41 H412 RFP sing 383 n n 
C42 N4 RFP sing 384 n n 
C42 H421 RFP sing 385 n n 
C42 H422 RFP sing 386 n n 
C43 N2 RFP doub 387 e n 
C43 HC43 RFP sing 388 n n 
N1 HN1 RFP sing 389 n n 
N2 N3 RFP sing 390 n n 
O1 HO1 RFP sing 391 n n 
O2 HO2 RFP sing 392 n n 
O9 HO9 RFP sing 393 n n 
O10 H10O RFP sing 394 n n 
O12 H12O RFP sing 395 n n 
#
_atom_sites.entry_id                     1YNN 
_atom_sites.fract_transf_matrix[1][1]    0.004981 
_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]    0.004981 
_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]    0.003414 
_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 RFP C 1 1120 1 RFP RIF . 
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 C C1 RFP . . . G 5 48.816 98.133 25.352 1 47.62 ? C1 RFP 1120 C 1 
HETATM 2 C C2 RFP . . . G 5 48.799 97.116 26.312 1 47.21 ? C2 RFP 1120 C 1 
HETATM 3 C C3 RFP . . . G 5 49.946 96.367 26.588 1 48.29 ? C3 RFP 1120 C 1 
HETATM 4 C C4 RFP . . . G 5 51.121 96.631 25.94 1 48.02 ? C4 RFP 1120 C 1 
HETATM 5 C C5 RFP . . . G 5 52.455 97.961 24.269 1 46.99 ? C5 RFP 1120 C 1 
HETATM 6 C C6 RFP . . . G 5 52.539 98.952 23.324 1 46.61 ? C6 RFP 1120 C 1 
HETATM 7 C C7 RFP . . . G 5 51.466 99.743 22.964 1 45.86 ? C7 RFP 1120 C 1 
HETATM 8 C C8 RFP . . . G 5 50.144 99.521 23.622 1 45.95 ? C8 RFP 1120 C 1 
HETATM 9 C C9 RFP . . . G 5 49.997 98.443 24.667 1 47.23 ? C9 RFP 1120 C 1 
HETATM 10 C C10 RFP . . . G 5 51.203 97.634 24.992 1 47.57 ? C10 RFP 1120 C 1 
HETATM 11 C C11 RFP . . . G 5 53.797 97.335 24.361 1 47.16 ? C11 RFP 1120 C 1 
HETATM 12 C C12 RFP . . . G 5 54.625 97.939 23.272 1 47.77 ? C12 RFP 1120 C 1 
HETATM 13 C C13 RFP . . . G 5 55.943 98.509 23.781 1 47.69 ? C13 RFP 1120 C 1 
HETATM 14 C C14 RFP . . . G 5 51.657 100.807 21.919 1 45.22 ? C14 RFP 1120 C 1 
HETATM 15 C C15 RFP . . . G 5 46.815 97.527 27.731 1 45.52 ? C15 RFP 1120 C 1 
HETATM 16 C C16 RFP . . . G 5 45.367 97.494 27.461 1 45.02 ? C16 RFP 1120 C 1 
HETATM 17 C C17 RFP . . . G 5 44.71 96.554 26.754 1 45.05 ? C17 RFP 1120 C 1 
HETATM 18 C C18 RFP . . . G 5 45.264 95.382 26.078 1 45.49 ? C18 RFP 1120 C 1 
HETATM 19 C C19 RFP . . . G 5 44.414 94.504 25.528 1 45.8 ? C19 RFP 1120 C 1 
HETATM 20 C C20 RFP . . . G 5 44.843 93.254 24.783 1 46.24 ? C20 RFP 1120 C 1 
HETATM 21 C C21 RFP . . . G 5 45.892 93.597 23.718 1 47.16 ? C21 RFP 1120 C 1 
HETATM 22 C C22 RFP . . . G 5 46.157 92.499 22.671 1 47.62 ? C22 RFP 1120 C 1 
HETATM 23 C C23 RFP . . . G 5 47.326 92.861 21.749 1 47.46 ? C23 RFP 1120 C 1 
HETATM 24 C C24 RFP . . . G 5 48.663 92.987 22.476 1 46.97 ? C24 RFP 1120 C 1 
HETATM 25 C C25 RFP . . . G 5 49.797 93.382 21.533 1 46.72 ? C25 RFP 1120 C 1 
HETATM 26 C C26 RFP . . . G 5 50.783 94.396 22.098 1 47.61 ? C26 RFP 1120 C 1 
HETATM 27 C C27 RFP . . . G 5 51.93 94.649 21.1 1 48.39 ? C27 RFP 1120 C 1 
HETATM 28 C C28 RFP . . . G 5 52.83 95.84 21.41 1 48.16 ? C28 RFP 1120 C 1 
HETATM 29 C C29 RFP . . . G 5 54.004 95.727 22.033 1 48.12 ? C29 RFP 1120 C 1 
HETATM 30 C C30 RFP . . . G 5 44.508 98.577 28.031 1 44.95 ? C30 RFP 1120 C 1 
HETATM 31 C C31 RFP . . . G 5 45.357 92.216 25.774 1 46.69 ? C31 RFP 1120 C 1 
HETATM 32 C C32 RFP . . . G 5 44.938 92.132 21.821 1 48.24 ? C32 RFP 1120 C 1 
HETATM 33 C C33 RFP . . . G 5 48.964 91.655 23.15 1 48.39 ? C33 RFP 1120 C 1 
HETATM 34 C C34 RFP . . . G 5 50.031 95.658 22.485 1 48.31 ? C34 RFP 1120 C 1 
HETATM 35 C C35 RFP . . . G 5 50.364 91.767 19.866 1 47.43 ? C35 RFP 1120 C 1 
HETATM 36 C C36 RFP . . . G 5 51.569 91.602 18.987 1 48.19 ? C36 RFP 1120 C 1 
HETATM 37 C C37 RFP . . . G 5 52.324 94.915 18.757 1 49.52 ? C37 RFP 1120 C 1 
HETATM 38 C C38 RFP . . . G 5 47.659 90.455 31.264 1 63.5 ? C38 RFP 1120 C 1 
HETATM 39 C C39 RFP . . . G 5 47.878 92.922 31.009 1 60.76 ? C39 RFP 1120 C 1 
HETATM 40 C C40 RFP . . . G 5 48.174 94.1 30.089 1 58.71 ? C40 RFP 1120 C 1 
HETATM 41 C C41 RFP . . . G 5 48.536 92.424 28.096 1 59.7 ? C41 RFP 1120 C 1 
HETATM 42 C C42 RFP . . . G 5 48.239 91.246 29.015 1 61.63 ? C42 RFP 1120 C 1 
HETATM 43 C C43 RFP . . . G 5 50.037 95.239 27.594 1 50.91 ? C43 RFP 1120 C 1 
HETATM 44 N N1 RFP . . . G 5 47.604 96.786 26.963 1 46.37 ? N1 RFP 1120 C 1 
HETATM 45 N N2 RFP . . . G 5 48.725 94.733 27.885 1 55.1 ? N2 RFP 1120 C 1 
HETATM 46 N N3 RFP . . . G 5 48.489 93.744 28.713 1 57.77 ? N3 RFP 1120 C 1 
HETATM 47 N N4 RFP . . . G 5 47.936 91.594 30.398 1 62.12 ? N4 RFP 1120 C 1 
HETATM 48 O O1 RFP . . . G 5 47.694 98.807 25.107 1 48.85 ? O1 RFP 1120 C 1 
HETATM 49 O O2 RFP . . . G 5 49.19 100.244 23.28 1 45.02 ? O2 RFP 1120 C 1 
HETATM 50 O O3 RFP . . . G 5 53.806 99.03 22.805 1 47.21 ? O3 RFP 1120 C 1 
HETATM 51 O O4 RFP . . . G 5 54.176 96.46 25.116 1 46.89 ? O4 RFP 1120 C 1 
HETATM 52 O O5 RFP . . . G 5 54.833 96.917 22.274 1 48.92 ? O5 RFP 1120 C 1 
HETATM 53 O O6 RFP . . . G 5 51.353 94.822 19.8 1 48.74 ? O6 RFP 1120 C 1 
HETATM 54 O O7 RFP . . . G 5 50.554 92.225 21.226 1 46.8 ? O7 RFP 1120 C 1 
HETATM 55 O O8 RFP . . . G 5 49.231 91.518 19.49 1 47.5 ? O8 RFP 1120 C 1 
HETATM 56 O O9 RFP . . . G 5 47.01 94.055 21.054 1 47.81 ? O9 RFP 1120 C 1 
HETATM 57 O O10 RFP . . . G 5 45.547 94.815 23.064 1 48.05 ? O10 RFP 1120 C 1 
HETATM 58 O O11 RFP . . . G 5 47.248 98.181 28.662 1 44.96 ? O11 RFP 1120 C 1 
HETATM 59 O O12 RFP . . . G 5 52.164 95.886 26.264 1 48.56 ? O12 RFP 1120 C 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           59 
#