data_7RYO
#
_model_server_result.job_id            1wOmCfGb91KEJIAoUIK_jg 
_model_server_result.datetime_utc      '2024-11-17 07:33:42' 
_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          7ryo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":403}' 
#
_entry.id    7RYO 
#
_exptl.entry_id    7RYO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              838.127 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            dideoxymycobactin-838 
_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          113.348 
_cell.angle_gamma         90 
_cell.entry_id            7RYO 
_cell.length_a            234.881 
_cell.length_b            42.239 
_cell.length_c            124.656 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7RYO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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                      6 
_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
disulf ? disulf1 A SG CYS 104 A CYS 102 1_555 A SG CYS 168 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 A SG CYS 208 A CYS 206 1_555 A SG CYS 263 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 B SG CYS 28 B CYS 26 1_555 B SG CYS 83 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 C SG CYS 25 C CYS 25 1_555 C SG CYS 97 C CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 C SG CYS 149 C CYS 149 1_555 C SG CYS 214 C CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 C SG CYS 175 C CYS 175 1_555 D SG CYS 163 D CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 D SG CYS 24 D CYS 24 1_555 D SG CYS 92 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 D SG CYS 138 D CYS 138 1_555 D SG CYS 188 D CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C47 H75 N5 O8' 
_chem_comp.formula_weight    838.127 
_chem_comp.id                WGR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              dideoxymycobactin-838 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(2R)-4-oxo-4-{[(3S)-2-oxoazepan-3-yl]amino}butan-2-yl N~2~-[(4S)-2-(2-hydroxyphenyl)-4-methyl-4,5-dihydro-1,3-oxazole-4-carbonyl]-N~6~-[(2Z)-icos-2-enoyl]-L-lysinate' 
#
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
C8 C7 WGR sing 387 n n 
C8 C9 WGR sing 388 n n 
C10 C9 WGR sing 389 n n 
C10 C11 WGR sing 390 n n 
C7 C6 WGR sing 391 n n 
C11 C12 WGR sing 392 n n 
C6 C5 WGR sing 393 n n 
C12 C13 WGR sing 394 n n 
C5 C4 WGR sing 395 n n 
C13 C14 WGR sing 396 n n 
C4 C3 WGR sing 397 n n 
C14 C15 WGR sing 398 n n 
C3 C2 WGR sing 399 n n 
C15 C16 WGR sing 400 n n 
C2 C1 WGR sing 401 n n 
C16 C17 WGR sing 402 n n 
O6 C40 WGR doub 403 n n 
C1 C WGR sing 404 n n 
C40 C39 WGR sing 405 n n 
C40 N3 WGR sing 406 n n 
C39 C37 WGR sing 407 n n 
O C19 WGR doub 408 n n 
C38 C37 WGR sing 409 n n 
C17 C18 WGR doub 410 z n 
N3 C41 WGR sing 411 n n 
C37 O5 WGR sing 412 n n 
C19 C18 WGR sing 413 n n 
C19 N WGR sing 414 n n 
O7 C46 WGR doub 415 n n 
C41 C46 WGR sing 416 n n 
C41 C42 WGR sing 417 n n 
C46 N4 WGR sing 418 n n 
N4 C45 WGR sing 419 n n 
N C20 WGR sing 420 n n 
O5 C36 WGR sing 421 n n 
C45 C44 WGR sing 422 n n 
C20 C21 WGR sing 423 n n 
C42 C43 WGR sing 424 n n 
C21 C22 WGR sing 425 n n 
O4 C36 WGR doub 426 n n 
C36 C24 WGR sing 427 n n 
C43 C44 WGR sing 428 n n 
C22 C23 WGR sing 429 n n 
C24 C23 WGR sing 430 n n 
C24 N1 WGR sing 431 n n 
O1 C25 WGR doub 432 n n 
N1 C25 WGR sing 433 n n 
C25 C26 WGR sing 434 n n 
C27 C26 WGR sing 435 n n 
O3 C35 WGR sing 436 n n 
C26 N2 WGR sing 437 n n 
C26 C28 WGR sing 438 n n 
N2 C29 WGR doub 439 n n 
C35 C34 WGR doub 440 n y 
C35 C30 WGR sing 441 n y 
C29 C30 WGR sing 442 n n 
C29 O2 WGR sing 443 n n 
C28 O2 WGR sing 444 n n 
C34 C33 WGR sing 445 n y 
C30 C31 WGR doub 446 n y 
C33 C32 WGR doub 447 n y 
C31 C32 WGR sing 448 n y 
N H1 WGR sing 449 n n 
C H2 WGR sing 450 n n 
C H3 WGR sing 451 n n 
C H4 WGR sing 452 n n 
C1 H5 WGR sing 453 n n 
C1 H6 WGR sing 454 n n 
C10 H7 WGR sing 455 n n 
C10 H8 WGR sing 456 n n 
C11 H9 WGR sing 457 n n 
C11 H10 WGR sing 458 n n 
C12 H11 WGR sing 459 n n 
C12 H12 WGR sing 460 n n 
C13 H13 WGR sing 461 n n 
C13 H14 WGR sing 462 n n 
C14 H15 WGR sing 463 n n 
C14 H16 WGR sing 464 n n 
C15 H17 WGR sing 465 n n 
C15 H18 WGR sing 466 n n 
C16 H19 WGR sing 467 n n 
C16 H20 WGR sing 468 n n 
C17 H21 WGR sing 469 n n 
C18 H22 WGR sing 470 n n 
C2 H23 WGR sing 471 n n 
C2 H24 WGR sing 472 n n 
C20 H25 WGR sing 473 n n 
C20 H26 WGR sing 474 n n 
C21 H27 WGR sing 475 n n 
C21 H28 WGR sing 476 n n 
C22 H29 WGR sing 477 n n 
C22 H30 WGR sing 478 n n 
C23 H31 WGR sing 479 n n 
C23 H32 WGR sing 480 n n 
C24 H33 WGR sing 481 n n 
C27 H34 WGR sing 482 n n 
C27 H35 WGR sing 483 n n 
C27 H36 WGR sing 484 n n 
C28 H37 WGR sing 485 n n 
C28 H38 WGR sing 486 n n 
C3 H39 WGR sing 487 n n 
C3 H40 WGR sing 488 n n 
C31 H41 WGR sing 489 n n 
C32 H42 WGR sing 490 n n 
C33 H43 WGR sing 491 n n 
C34 H44 WGR sing 492 n n 
C37 H45 WGR sing 493 n n 
C38 H46 WGR sing 494 n n 
C38 H47 WGR sing 495 n n 
C38 H48 WGR sing 496 n n 
C39 H49 WGR sing 497 n n 
C39 H50 WGR sing 498 n n 
C4 H51 WGR sing 499 n n 
C4 H52 WGR sing 500 n n 
C41 H53 WGR sing 501 n n 
C42 H54 WGR sing 502 n n 
C42 H55 WGR sing 503 n n 
C43 H56 WGR sing 504 n n 
C43 H57 WGR sing 505 n n 
C44 H58 WGR sing 506 n n 
C44 H59 WGR sing 507 n n 
C45 H60 WGR sing 508 n n 
C45 H61 WGR sing 509 n n 
C5 H62 WGR sing 510 n n 
C5 H63 WGR sing 511 n n 
C6 H64 WGR sing 512 n n 
C6 H65 WGR sing 513 n n 
C7 H66 WGR sing 514 n n 
C7 H67 WGR sing 515 n n 
C8 H68 WGR sing 516 n n 
C8 H69 WGR sing 517 n n 
C9 H70 WGR sing 518 n n 
C9 H71 WGR sing 519 n n 
N1 H72 WGR sing 520 n n 
N3 H73 WGR sing 521 n n 
N4 H74 WGR sing 522 n n 
O3 H75 WGR sing 523 n n 
#
_atom_sites.entry_id                     7RYO 
_atom_sites.fract_transf_matrix[1][1]    0.004257 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001838 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023675 
_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]    0.008738 
_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
E 5 EDO A 1 401 401 EDO EDO . 
F 5 EDO A 1 402 501 EDO EDO . 
G 6 WGR A 1 403 601 WGR WGR . 
H 7 SO4 D 1 301 1 SO4 SO4 . 
#
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 N WGR . . . G 6 15.101 10.107 -3.757 1 76.32 ? N WGR 403 A 1 
HETATM 2 C C WGR . . . G 6 17.86 18.638 -4.936 1 54.37 ? C WGR 403 A 1 
HETATM 3 O O WGR . . . G 6 15.846 9.028 -5.594 1 60.05 ? O WGR 403 A 1 
HETATM 4 C C1 WGR . . . G 6 16.778 18.17 -5.874 1 50.26 ? C1 WGR 403 A 1 
HETATM 5 C C10 WGR . . . G 6 18.748 13.338 -13.239 1 72.62 ? C10 WGR 403 A 1 
HETATM 6 C C11 WGR . . . G 6 19.463 12.385 -12.301 1 61.01 ? C11 WGR 403 A 1 
HETATM 7 C C12 WGR . . . G 6 18.628 11.978 -11.097 1 54.34 ? C12 WGR 403 A 1 
HETATM 8 C C13 WGR . . . G 6 19.189 10.783 -10.35 1 57.26 ? C13 WGR 403 A 1 
HETATM 9 C C14 WGR . . . G 6 18.353 10.337 -9.162 1 30.76 ? C14 WGR 403 A 1 
HETATM 10 C C15 WGR . . . G 6 19.016 10.596 -7.821 1 44.5 ? C15 WGR 403 A 1 
HETATM 11 C C16 WGR . . . G 6 18.394 9.82 -6.666 1 40.2 ? C16 WGR 403 A 1 
HETATM 12 C C17 WGR . . . G 6 18.254 10.667 -5.44 1 53.07 ? C17 WGR 403 A 1 
HETATM 13 C C18 WGR . . . G 6 17.231 10.716 -4.598 1 70.5 ? C18 WGR 403 A 1 
HETATM 14 C C19 WGR . . . G 6 16.006 9.894 -4.719 1 74.32 ? C19 WGR 403 A 1 
HETATM 15 C C2 WGR . . . G 6 16.781 18.902 -7.204 1 44.21 ? C2 WGR 403 A 1 
HETATM 16 C C20 WGR . . . G 6 14.203 9.061 -3.295 1 67.32 ? C20 WGR 403 A 1 
HETATM 17 C C21 WGR . . . G 6 14.978 7.85 -2.822 1 53.18 ? C21 WGR 403 A 1 
HETATM 18 C C22 WGR . . . G 6 15.031 7.678 -1.315 1 55.43 ? C22 WGR 403 A 1 
HETATM 19 C C23 WGR . . . G 6 15.355 6.252 -0.885 1 62.93 ? C23 WGR 403 A 1 
HETATM 20 C C24 WGR . . . G 6 14.254 5.263 -1.272 1 52.59 ? C24 WGR 403 A 1 
HETATM 21 C C25 WGR . . . G 6 12.862 3.711 -0.031 1 69.35 ? C25 WGR 403 A 1 
HETATM 22 C C26 WGR . . . G 6 12.754 2.627 1.055 1 66.38 ? C26 WGR 403 A 1 
HETATM 23 C C27 WGR . . . G 6 11.635 1.66 0.677 1 75.02 ? C27 WGR 403 A 1 
HETATM 24 C C28 WGR . . . G 6 12.559 3.198 2.467 1 71.71 ? C28 WGR 403 A 1 
HETATM 25 C C29 WGR . . . G 6 14.372 1.892 2.366 1 83.01 ? C29 WGR 403 A 1 
HETATM 26 C C3 WGR . . . G 6 17.679 18.28 -8.262 1 33.96 ? C3 WGR 403 A 1 
HETATM 27 C C30 WGR . . . G 6 15.574 1.267 2.923 1 68.81 ? C30 WGR 403 A 1 
HETATM 28 C C31 WGR . . . G 6 15.858 1.383 4.284 1 64.6 ? C31 WGR 403 A 1 
HETATM 29 C C32 WGR . . . G 6 17.098 1.015 4.778 1 75.95 ? C32 WGR 403 A 1 
HETATM 30 C C33 WGR . . . G 6 18.069 0.528 3.93 1 78.86 ? C33 WGR 403 A 1 
HETATM 31 C C34 WGR . . . G 6 17.815 0.406 2.576 1 69.96 ? C34 WGR 403 A 1 
HETATM 32 C C35 WGR . . . G 6 16.576 0.774 2.061 1 61.14 ? C35 WGR 403 A 1 
HETATM 33 C C36 WGR . . . G 6 14.547 4.622 -2.62 1 55.63 ? C36 WGR 403 A 1 
HETATM 34 C C37 WGR . . . G 6 13.906 4.652 -4.945 1 62.2 ? C37 WGR 403 A 1 
HETATM 35 C C38 WGR . . . G 6 15.134 5.315 -5.517 1 50.98 ? C38 WGR 403 A 1 
HETATM 36 C C39 WGR . . . G 6 12.64 5.056 -5.674 1 71.97 ? C39 WGR 403 A 1 
HETATM 37 C C4 WGR . . . G 6 16.961 17.996 -9.574 1 45.02 ? C4 WGR 403 A 1 
HETATM 38 C C40 WGR . . . G 6 11.632 3.932 -5.772 1 85.61 ? C40 WGR 403 A 1 
HETATM 39 C C41 WGR . . . G 6 9.765 3.059 -4.469 1 92.62 ? C41 WGR 403 A 1 
HETATM 40 C C42 WGR . . . G 6 10.314 2.887 -3.048 1 79.75 ? C42 WGR 403 A 1 
HETATM 41 C C43 WGR . . . G 6 9.981 1.536 -2.425 1 77.6 ? C43 WGR 403 A 1 
HETATM 42 C C44 WGR . . . G 6 8.504 1.246 -2.247 1 78.26 ? C44 WGR 403 A 1 
HETATM 43 C C45 WGR . . . G 6 7.732 1.144 -3.546 1 87.04 ? C45 WGR 403 A 1 
HETATM 44 C C46 WGR . . . G 6 8.29 3.423 -4.404 1 102.9 ? C46 WGR 403 A 1 
HETATM 45 C C5 WGR . . . G 6 17.706 18.491 -10.804 1 51.98 ? C5 WGR 403 A 1 
HETATM 46 C C6 WGR . . . G 6 18.212 17.385 -11.714 1 43.66 ? C6 WGR 403 A 1 
HETATM 47 C C7 WGR . . . G 6 17.169 16.848 -12.68 1 44.94 ? C7 WGR 403 A 1 
HETATM 48 C C8 WGR . . . G 6 17.632 15.62 -13.439 1 58.16 ? C8 WGR 403 A 1 
HETATM 49 C C9 WGR . . . G 6 18.107 14.509 -12.522 1 67.63 ? C9 WGR 403 A 1 
HETATM 50 N N1 WGR . . . G 6 14.063 4.256 -0.241 1 54.68 ? N1 WGR 403 A 1 
HETATM 51 N N2 WGR . . . G 6 14.021 1.883 1.147 1 80.46 ? N2 WGR 403 A 1 
HETATM 52 N N3 WGR . . . G 6 10.468 4.134 -5.148 1 88.97 ? N3 WGR 403 A 1 
HETATM 53 N N4 WGR . . . G 6 7.431 2.43 -4.165 1 108.31 ? N4 WGR 403 A 1 
HETATM 54 O O1 WGR . . . G 6 11.861 4.048 -0.646 1 70.42 ? O1 WGR 403 A 1 
HETATM 55 O O2 WGR . . . G 6 13.572 2.528 3.26 1 76.42 ? O2 WGR 403 A 1 
HETATM 56 O O3 WGR . . . G 6 16.381 0.647 0.723 1 56.17 ? O3 WGR 403 A 1 
HETATM 57 O O4 WGR . . . G 6 15.397 3.798 -2.817 1 77.16 ? O4 WGR 403 A 1 
HETATM 58 O O5 WGR . . . G 6 13.735 5.124 -3.567 1 61.94 ? O5 WGR 403 A 1 
HETATM 59 O O6 WGR . . . G 6 11.878 2.905 -6.399 1 79.02 ? O6 WGR 403 A 1 
HETATM 60 O O7 WGR . . . G 6 7.919 4.582 -4.567 1 100.84 ? O7 WGR 403 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           60 
#