data_5SYG
#
_model_server_result.job_id            0PABjBSM5IwdrZd_bGgwqg 
_model_server_result.datetime_utc      '2025-07-07 23:15:56' 
_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          5syg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    5SYG 
#
_exptl.entry_id    5SYG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              497.623 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 130-meric 130 'representative helical assembly' 1 
? pentameric 5 'helical asymmetric unit' 2 
? pentameric 5 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 (1-26) 
A,B,C,D,E,F 2 14 
A,B,C,D,E,F 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 -56.4 
3 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 24.6 
4 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 -47 
5 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 34 
6 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 -37.6 
7 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 43.4 
8 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 -28.2 
9 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 52.8 
10 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 -18.8 
11 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 62.2 
12 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 -9.4 
13 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 71.6 
14 'helical symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 81 
15 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 9.4 
16 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 90.4 
17 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 18.8 
18 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 99.8 
19 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 28.2 
20 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 109.2 
21 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 37.6 
22 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 118.6 
23 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 47 
24 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 128 
25 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 56.4 
26 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 137.4 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_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 A OE1 GLU 71 A GLU 71 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 C O1B GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
#
_chem_comp.formula           'C29 H39 N O6' 
_chem_comp.formula_weight    497.623 
_chem_comp.id                ZPN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(-)-ZAMPANOLIDE (Bound form)' 
#
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
O7 C7 ZPN doub 469 n n 
C21 C5 ZPN sing 470 n n 
C7 C6 ZPN sing 471 n n 
C7 C8 ZPN sing 472 n n 
C6 C5 ZPN sing 473 n n 
C5 C4 ZPN doub 474 z n 
C8 C9 ZPN sing 475 n n 
C4 C3 ZPN sing 476 n n 
C9 C10 ZPN sing 477 n n 
C10 C11 ZPN sing 478 n n 
C3 C2 ZPN doub 479 e n 
C2 C1 ZPN sing 480 n n 
C11 C12 ZPN sing 481 n n 
C11 O11 ZPN sing 482 n n 
C12 C13 ZPN sing 483 n n 
O11 C15 ZPN sing 484 n n 
O1 C1 ZPN doub 485 n n 
C1 O19 ZPN sing 486 n n 
C13 C22 ZPN doub 487 n n 
C13 C14 ZPN sing 488 n n 
O19 C19 ZPN sing 489 n n 
C15 C14 ZPN sing 490 n n 
C15 C16 ZPN sing 491 n n 
C16 C17 ZPN doub 492 e n 
C17 C23 ZPN sing 493 n n 
C17 C18 ZPN sing 494 n n 
C19 C18 ZPN sing 495 n n 
C19 C20 ZPN sing 496 n n 
O20 C20 ZPN sing 497 n n 
C20 N20 ZPN sing 498 n n 
N20 C1' ZPN sing 499 n n 
C2' C1' ZPN sing 500 n n 
C2' C3' ZPN doub 501 z n 
C1' O1' ZPN doub 502 n n 
C3' C4' ZPN sing 503 n n 
C4' C5' ZPN doub 504 e n 
C5' C6' ZPN sing 505 n n 
C2 H21 ZPN sing 506 n n 
C3 H31 ZPN sing 507 n n 
C4 H41 ZPN sing 508 n n 
C21 H211 ZPN sing 509 n n 
C21 H212 ZPN sing 510 n n 
C21 H213 ZPN sing 511 n n 
C6 H62 ZPN sing 512 n n 
C6 H61 ZPN sing 513 n n 
C8 H81 ZPN sing 514 n n 
C8 H82 ZPN sing 515 n n 
C9 H91 ZPN sing 516 n n 
C9 H92 ZPN sing 517 n n 
C10 H102 ZPN sing 518 n n 
C10 H162 ZPN sing 519 n n 
C11 H141 ZPN sing 520 n n 
C12 H151 ZPN sing 521 n n 
C12 H142 ZPN sing 522 n n 
C22 H223 ZPN sing 523 n n 
C22 H222 ZPN sing 524 n n 
C14 H121 ZPN sing 525 n n 
C14 H122 ZPN sing 526 n n 
C15 H111 ZPN sing 527 n n 
C16 H101 ZPN sing 528 n n 
C23 H231 ZPN sing 529 n n 
C23 H232 ZPN sing 530 n n 
C23 H233 ZPN sing 531 n n 
C18 H181 ZPN sing 532 n n 
C18 H182 ZPN sing 533 n n 
C19 H191 ZPN sing 534 n n 
C20 H201 ZPN sing 535 n n 
O20 H202 ZPN sing 536 n n 
N20 H203 ZPN sing 537 n n 
C2' "H2'1" ZPN sing 538 n n 
C3' "H3'1" ZPN sing 539 n n 
C4' "H4'1" ZPN sing 540 n n 
C5' H6 ZPN sing 541 n n 
C6' H7 ZPN sing 542 n n 
C6' H8 ZPN sing 543 n n 
C6' H9 ZPN sing 544 n n 
#
_atom_sites.entry_id                     5SYG 
_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
C 3 GTP A 1 501 1 GTP GTP . 
D 4 MG A 1 502 2 MG MG . 
E 5 GDP B 1 501 1 GDP GDP . 
F 6 ZPN B 1 502 1 ZPN ZPN . 
#
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 ZPN . . . F 6 333.881 435.447 323.741 1 39.26 ? C1 ZPN 502 B 1 
HETATM 2 O O1 ZPN . . . F 6 333.699 436.098 322.71 1 36.79 ? O1 ZPN 502 B 1 
HETATM 3 C C2 ZPN . . . F 6 333.635 434.021 323.875 1 39.81 ? C2 ZPN 502 B 1 
HETATM 4 C C3 ZPN . . . F 6 332.93 433.316 322.973 1 37.94 ? C3 ZPN 502 B 1 
HETATM 5 C C4 ZPN . . . F 6 332.607 431.93 323.266 1 46.14 ? C4 ZPN 502 B 1 
HETATM 6 C C5 ZPN . . . F 6 331.836 431.198 322.457 1 59.67 ? C5 ZPN 502 B 1 
HETATM 7 C C21 ZPN . . . F 6 331.315 429.86 322.903 1 67.58 ? C21 ZPN 502 B 1 
HETATM 8 C C6 ZPN . . . F 6 331.175 431.83 321.268 1 39.01 ? C6 ZPN 502 B 1 
HETATM 9 C C7 ZPN . . . F 6 329.732 432.036 321.614 1 57.12 ? C7 ZPN 502 B 1 
HETATM 10 O O7 ZPN . . . F 6 328.86 431.486 320.951 1 64.39 ? O7 ZPN 502 B 1 
HETATM 11 C C8 ZPN . . . F 6 329.469 432.433 323.037 1 61.59 ? C8 ZPN 502 B 1 
HETATM 12 C C9 ZPN . . . F 6 328.634 433.716 323.08 1 58.22 ? C9 ZPN 502 B 1 
HETATM 13 C C10 ZPN . . . F 6 328.329 434.056 324.55 1 39.73 ? C10 ZPN 502 B 1 
HETATM 14 C C11 ZPN . . . F 6 328.608 435.485 325.033 1 38.44 ? C11 ZPN 502 B 1 
HETATM 15 C C12 ZPN . . . F 6 327.757 435.676 326.293 1 34.69 ? C12 ZPN 502 B 1 
HETATM 16 C C13 ZPN . . . F 6 328.14 436.956 326.99 1 36.05 ? C13 ZPN 502 B 1 
HETATM 17 C C22 ZPN . . . F 6 327.227 437.864 327.324 1 37.61 ? C22 ZPN 502 B 1 
HETATM 18 C C14 ZPN . . . F 6 329.612 437.188 327.163 1 31.98 ? C14 ZPN 502 B 1 
HETATM 19 C C15 ZPN . . . F 6 330.306 436.953 325.81 1 37.03 ? C15 ZPN 502 B 1 
HETATM 20 O O11 ZPN . . . F 6 329.988 435.633 325.355 1 33.23 ? O11 ZPN 502 B 1 
HETATM 21 C C16 ZPN . . . F 6 331.799 437.08 325.979 1 29.6 ? C16 ZPN 502 B 1 
HETATM 22 C C17 ZPN . . . F 6 332.583 437.855 325.215 1 32.79 ? C17 ZPN 502 B 1 
HETATM 23 C C23 ZPN . . . F 6 332.069 438.84 324.204 1 32.43 ? C23 ZPN 502 B 1 
HETATM 24 C C18 ZPN . . . F 6 333.987 438.142 325.613 1 35.89 ? C18 ZPN 502 B 1 
HETATM 25 C C19 ZPN . . . F 6 335.008 437.249 324.875 1 36.4 ? C19 ZPN 502 B 1 
HETATM 26 O O19 ZPN . . . F 6 334.771 435.859 324.636 1 37.77 ? O19 ZPN 502 B 1 
HETATM 27 C C20 ZPN . . . F 6 336.468 437.663 324.998 1 32.52 ? C20 ZPN 502 B 1 
HETATM 28 O O20 ZPN . . . F 6 337.271 437.23 323.91 1 35.26 ? O20 ZPN 502 B 1 
HETATM 29 N N20 ZPN . . . F 6 336.865 436.996 326.243 1 32.04 ? N20 ZPN 502 B 1 
HETATM 30 C C1' ZPN . . . F 6 337.859 437.487 327.014 1 30.87 ? C1' ZPN 502 B 1 
HETATM 31 O O1' ZPN . . . F 6 338.456 438.507 326.626 1 30.95 ? O1' ZPN 502 B 1 
HETATM 32 C C2' ZPN . . . F 6 338.138 436.694 328.214 1 32.31 ? C2' ZPN 502 B 1 
HETATM 33 C C3' ZPN . . . F 6 339.207 436.903 329.023 1 34.54 ? C3' ZPN 502 B 1 
HETATM 34 C C4' ZPN . . . F 6 340.062 438.082 328.963 1 35.56 ? C4' ZPN 502 B 1 
HETATM 35 C C5' ZPN . . . F 6 341.122 438.182 329.782 1 36.08 ? C5' ZPN 502 B 1 
HETATM 36 C C6' ZPN . . . F 6 342.091 439.33 329.753 1 40.57 ? C6' ZPN 502 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           36 
#