data_5ZYA
#
_model_server_result.job_id            B9tUQYH9yfDO6TU9BkAsCw 
_model_server_result.datetime_utc      '2025-03-20 11:17:26' 
_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          5zya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1401}' 
#
_entry.id    5ZYA 
#
_exptl.entry_id    5ZYA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              718.96 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate' 
_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            5ZYA 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZYA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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    ? 
_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                             E 
_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 C SG CYS 5 D CYS 11 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc2 C SG CYS 17 D CYS 23 1_555 F ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
metalc ? metalc3 C SG CYS 24 D CYS 30 1_555 H ZN ZN . D ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc4 C SG CYS 27 D CYS 33 1_555 H ZN ZN . D ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc5 C SG CYS 40 D CYS 46 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
metalc ? metalc6 C SG CYS 52 D CYS 58 1_555 F ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc7 C SG CYS 55 D CYS 61 1_555 F ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc8 C SG CYS 66 D CYS 72 1_555 H ZN ZN . D ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? 
metalc ? metalc9 C SG CYS 69 D CYS 75 1_555 H ZN ZN . D ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc10 C SG CYS 79 D CYS 85 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc11 D O VAL 611 A VAL 610 1_555 I K K . A K 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.035 ? 
metalc ? metalc12 D OD1 ASN 613 A ASN 612 1_555 I K K . A K 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? 
metalc ? metalc13 D OE1 GLN 637 A GLN 636 1_555 I K K . A K 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.071 ? 
#
_chem_comp.formula           'C40 H66 N2 O9' 
_chem_comp.formula_weight    718.96 
_chem_comp.id                9B0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate' 
_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
O9 C26 9B0 sing 1 n n 
C28 C27 9B0 sing 2 n n 
C27 C26 9B0 sing 3 n n 
C26 C24 9B0 sing 4 n n 
C25 C24 9B0 sing 5 n n 
C24 C23 9B0 sing 6 n n 
C23 C22 9B0 sing 7 n n 
C23 O8 9B0 sing 8 n n 
C22 O8 9B0 sing 9 n n 
C22 C21 9B0 sing 10 n n 
C21 C19 9B0 sing 11 n n 
C39 C38 9B0 sing 12 n n 
C39 C40 9B0 sing 13 n n 
C38 C37 9B0 sing 14 n n 
C40 C34 9B0 sing 15 n n 
C12 C11 9B0 sing 16 n n 
O7 C19 9B0 sing 17 n n 
C19 C18 9B0 sing 18 n n 
C19 C20 9B0 sing 19 n n 
C37 C36 9B0 sing 20 n n 
C15 C14 9B0 sing 21 n n 
C17 C18 9B0 doub 22 e n 
C17 C16 9B0 sing 23 n n 
C34 C35 9B0 sing 24 n n 
C34 N2 9B0 sing 25 n n 
C14 C16 9B0 doub 26 e n 
C14 C13 9B0 sing 27 n n 
C31 N2 9B0 sing 28 n n 
C31 C30 9B0 sing 29 n n 
O6 C29 9B0 doub 30 n n 
C35 C36 9B0 sing 31 n n 
C11 C13 9B0 sing 32 n n 
C11 C10 9B0 sing 33 n n 
C29 O5 9B0 sing 34 n n 
C29 N1 9B0 sing 35 n n 
O5 C8 9B0 sing 36 n n 
C32 N2 9B0 sing 37 n n 
C32 C33 9B0 sing 38 n n 
C13 O1 9B0 sing 39 n n 
C9 C10 9B0 doub 40 e n 
C9 C8 9B0 sing 41 n n 
C30 N1 9B0 sing 42 n n 
N1 C33 9B0 sing 43 n n 
C8 C6 9B0 sing 44 n n 
O2 C1 9B0 doub 45 n n 
O1 C1 9B0 sing 46 n n 
C1 C2 9B0 sing 47 n n 
C6 O4 9B0 sing 48 n n 
C6 C7 9B0 sing 49 n n 
C6 C5 9B0 sing 50 n n 
C4 C5 9B0 sing 51 n n 
C4 C3 9B0 sing 52 n n 
O3 C3 9B0 sing 53 n n 
C3 C2 9B0 sing 54 n n 
C35 H1 9B0 sing 55 n n 
C35 H2 9B0 sing 56 n n 
C36 H3 9B0 sing 57 n n 
C36 H4 9B0 sing 58 n n 
C37 H5 9B0 sing 59 n n 
C37 H6 9B0 sing 60 n n 
C38 H7 9B0 sing 61 n n 
C38 H8 9B0 sing 62 n n 
C39 H9 9B0 sing 63 n n 
C39 H10 9B0 sing 64 n n 
C40 H11 9B0 sing 65 n n 
C40 H12 9B0 sing 66 n n 
C34 H13 9B0 sing 67 n n 
C32 H15 9B0 sing 68 n n 
C32 H16 9B0 sing 69 n n 
C33 H17 9B0 sing 70 n n 
C33 H18 9B0 sing 71 n n 
C31 H19 9B0 sing 72 n n 
C31 H20 9B0 sing 73 n n 
C30 H21 9B0 sing 74 n n 
C30 H22 9B0 sing 75 n n 
C8 H23 9B0 sing 76 n n 
C9 H24 9B0 sing 77 n n 
C10 H25 9B0 sing 78 n n 
C11 H26 9B0 sing 79 n n 
C12 H27 9B0 sing 80 n n 
C12 H28 9B0 sing 81 n n 
C12 H29 9B0 sing 82 n n 
C7 H30 9B0 sing 83 n n 
C7 H31 9B0 sing 84 n n 
C7 H32 9B0 sing 85 n n 
O4 H33 9B0 sing 86 n n 
C5 H34 9B0 sing 87 n n 
C5 H35 9B0 sing 88 n n 
C4 H36 9B0 sing 89 n n 
C4 H37 9B0 sing 90 n n 
C3 H38 9B0 sing 91 n n 
O3 H39 9B0 sing 92 n n 
C2 H40 9B0 sing 93 n n 
C2 H41 9B0 sing 94 n n 
C13 H42 9B0 sing 95 n n 
C15 H44 9B0 sing 96 n n 
C15 H45 9B0 sing 97 n n 
C15 H46 9B0 sing 98 n n 
C16 H47 9B0 sing 99 n n 
C17 H49 9B0 sing 100 n n 
C18 H51 9B0 sing 101 n n 
C20 H53 9B0 sing 102 n n 
C20 H54 9B0 sing 103 n n 
C20 H55 9B0 sing 104 n n 
O7 H56 9B0 sing 105 n n 
C21 H57 9B0 sing 106 n n 
C21 H58 9B0 sing 107 n n 
C22 H59 9B0 sing 108 n n 
C23 H60 9B0 sing 109 n n 
C24 H61 9B0 sing 110 n n 
C25 H62 9B0 sing 111 n n 
C25 H63 9B0 sing 112 n n 
C25 H64 9B0 sing 113 n n 
C26 H65 9B0 sing 114 n n 
O9 H66 9B0 sing 115 n n 
C27 H67 9B0 sing 116 n n 
C27 H68 9B0 sing 117 n n 
C28 H69 9B0 sing 118 n n 
C28 H70 9B0 sing 119 n n 
C28 H71 9B0 sing 120 n n 
#
_atom_sites.entry_id                     5ZYA 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 9B0 C 1 1401 1 9B0 H3B . 
F 6 ZN D 1 201 201 ZN ZN . 
G 6 ZN D 1 202 202 ZN ZN . 
H 6 ZN D 1 203 203 ZN ZN . 
I 7 K A 1 1301 1301 K K . 
#
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 C35 9B0 . . . E 5 105.498 127.014 132.74 1 20 ? C35 9B0 1401 C 1 
HETATM 2 C C36 9B0 . . . E 5 105.362 125.448 132.289 1 20 ? C36 9B0 1401 C 1 
HETATM 3 C C37 9B0 . . . E 5 104.659 124.834 131.074 1 20 ? C37 9B0 1401 C 1 
HETATM 4 C C38 9B0 . . . E 5 103.24 124.705 130.338 1 20 ? C38 9B0 1401 C 1 
HETATM 5 C C39 9B0 . . . E 5 103.259 126.153 130.212 1 20 ? C39 9B0 1401 C 1 
HETATM 6 C C40 9B0 . . . E 5 103.235 127.076 131.504 1 20 ? C40 9B0 1401 C 1 
HETATM 7 C C34 9B0 . . . E 5 104.063 127.339 132.911 1 20 ? C34 9B0 1401 C 1 
HETATM 8 N N2 9B0 . . . E 5 103.206 128.536 133.349 1 20 ? N2 9B0 1401 C 1 
HETATM 9 C C32 9B0 . . . E 5 103.306 129.665 132.367 1 20 ? C32 9B0 1401 C 1 
HETATM 10 C C33 9B0 . . . E 5 102.501 130.897 132.775 1 20 ? C33 9B0 1401 C 1 
HETATM 11 C C31 9B0 . . . E 5 101.716 128.277 133.41 1 20 ? C31 9B0 1401 C 1 
HETATM 12 C C30 9B0 . . . E 5 100.866 129.493 133.869 1 20 ? C30 9B0 1401 C 1 
HETATM 13 N N1 9B0 . . . E 5 101.073 130.635 132.935 1 20 ? N1 9B0 1401 C 1 
HETATM 14 C C29 9B0 . . . E 5 100.161 131.539 132.539 1 20 ? C29 9B0 1401 C 1 
HETATM 15 O O6 9B0 . . . E 5 100.571 132.525 131.943 1 20 ? O6 9B0 1401 C 1 
HETATM 16 O O5 9B0 . . . E 5 98.873 131.521 132.965 1 20 ? O5 9B0 1401 C 1 
HETATM 17 C C8 9B0 . . . E 5 98.519 132.681 133.792 1 20 ? C8 9B0 1401 C 1 
HETATM 18 C C9 9B0 . . . E 5 97.22 133.312 133.581 1 20 ? C9 9B0 1401 C 1 
HETATM 19 C C10 9B0 . . . E 5 96.874 134.257 132.579 1 20 ? C10 9B0 1401 C 1 
HETATM 20 C C11 9B0 . . . E 5 95.537 134.714 132.588 1 20 ? C11 9B0 1401 C 1 
HETATM 21 C C12 9B0 . . . E 5 95.345 134.761 131.064 1 20 ? C12 9B0 1401 C 1 
HETATM 22 C C6 9B0 . . . E 5 98.974 132.588 135.448 1 20 ? C6 9B0 1401 C 1 
HETATM 23 C C7 9B0 . . . E 5 100.469 132.553 135.752 1 20 ? C7 9B0 1401 C 1 
HETATM 24 O O4 9B0 . . . E 5 98.409 131.443 136.026 1 20 ? O4 9B0 1401 C 1 
HETATM 25 C C5 9B0 . . . E 5 98.523 133.834 136.231 1 20 ? C5 9B0 1401 C 1 
HETATM 26 C C4 9B0 . . . E 5 99.12 135.093 135.684 1 20 ? C4 9B0 1401 C 1 
HETATM 27 C C3 9B0 . . . E 5 98.767 136.389 136.354 1 20 ? C3 9B0 1401 C 1 
HETATM 28 O O3 9B0 . . . E 5 99.354 137.482 135.656 1 20 ? O3 9B0 1401 C 1 
HETATM 29 C C2 9B0 . . . E 5 97.193 136.483 136.203 1 20 ? C2 9B0 1401 C 1 
HETATM 30 C C1 9B0 . . . E 5 96.769 136.447 134.873 1 20 ? C1 9B0 1401 C 1 
HETATM 31 O O2 9B0 . . . E 5 97.426 137.034 134.009 1 20 ? O2 9B0 1401 C 1 
HETATM 32 O O1 9B0 . . . E 5 95.428 136.242 134.66 1 20 ? O1 9B0 1401 C 1 
HETATM 33 C C13 9B0 . . . E 5 95.106 136.213 133.247 1 20 ? C13 9B0 1401 C 1 
HETATM 34 C C14 9B0 . . . E 5 93.619 136.103 132.991 1 20 ? C14 9B0 1401 C 1 
HETATM 35 C C15 9B0 . . . E 5 92.705 134.951 133.457 1 20 ? C15 9B0 1401 C 1 
HETATM 36 C C16 9B0 . . . E 5 93.033 137.398 132.458 1 20 ? C16 9B0 1401 C 1 
HETATM 37 C C17 9B0 . . . E 5 91.562 137.489 132.14 1 20 ? C17 9B0 1401 C 1 
HETATM 38 C C18 9B0 . . . E 5 91.257 138.881 131.624 1 20 ? C18 9B0 1401 C 1 
HETATM 39 C C19 9B0 . . . E 5 89.831 139.219 131.238 1 20 ? C19 9B0 1401 C 1 
HETATM 40 C C20 9B0 . . . E 5 89.033 139.581 132.494 1 20 ? C20 9B0 1401 C 1 
HETATM 41 O O7 9B0 . . . E 5 89.208 138.12 130.602 1 20 ? O7 9B0 1401 C 1 
HETATM 42 C C21 9B0 . . . E 5 89.947 140.42 130.304 1 20 ? C21 9B0 1401 C 1 
HETATM 43 C C22 9B0 . . . E 5 88.589 140.869 129.789 1 20 ? C22 9B0 1401 C 1 
HETATM 44 O O8 9B0 . . . E 5 88.106 142.169 130.212 1 20 ? O8 9B0 1401 C 1 
HETATM 45 C C23 9B0 . . . E 5 88.709 142.075 128.902 1 20 ? C23 9B0 1401 C 1 
HETATM 46 C C24 9B0 . . . E 5 87.793 142.023 127.684 1 20 ? C24 9B0 1401 C 1 
HETATM 47 C C25 9B0 . . . E 5 88.241 140.842 126.813 1 20 ? C25 9B0 1401 C 1 
HETATM 48 C C26 9B0 . . . E 5 87.954 143.314 126.882 1 20 ? C26 9B0 1401 C 1 
HETATM 49 O O9 9B0 . . . E 5 89.314 143.443 126.458 1 20 ? O9 9B0 1401 C 1 
HETATM 50 C C27 9B0 . . . E 5 87.029 143.287 125.662 1 20 ? C27 9B0 1401 C 1 
HETATM 51 C C28 9B0 . . . E 5 87.189 144.582 124.865 1 20 ? C28 9B0 1401 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           51 
#