data_8YP4
#
_model_server_result.job_id            u45wQX550Hu_VKJ_mb4l9g 
_model_server_result.datetime_utc      '2025-07-13 11:09:05' 
_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          8yp4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8YP4 
#
_exptl.entry_id    8YP4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              364.39 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4~{S},9~{S},10~{S},12~{E})-16-methoxy-4-methyl-9,10,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.86 
_cell.angle_gamma         90 
_cell.entry_id            8YP4 
_cell.length_a            47.364 
_cell.length_b            128.947 
_cell.length_c            65.689 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YP4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F 1 1 
B,D,E,G 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N 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
covale ? covale1 A SG CYS 175 A CYS 207 1_555 C C14 WNT . A WNT 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? 
covale ? covale2 B SG CYS 175 B CYS 207 1_555 E C14 WNT . B WNT 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
#
_chem_comp.formula           'C19 H24 O7' 
_chem_comp.formula_weight    364.39 
_chem_comp.id                WNT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4~{S},9~{S},10~{S},12~{E})-16-methoxy-4-methyl-9,10,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione 
_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
O6 C18 WNT doub 389 n n 
C18 C4 WNT sing 390 n n 
C18 O5 WNT sing 391 n n 
C4 C3 WNT doub 392 n y 
C4 C5 WNT sing 393 n y 
C3 O1 WNT sing 394 n n 
C3 C2 WNT sing 395 n y 
C2 C1 WNT doub 396 n y 
O5 C16 WNT sing 397 n n 
C16 C17 WNT sing 398 n n 
C16 C15 WNT sing 399 n n 
C15 C14 WNT sing 400 n n 
C14 C13 WNT sing 401 n n 
C13 C12 WNT sing 402 n n 
C12 O4 WNT doub 403 n n 
C12 C11 WNT sing 404 n n 
C11 O3 WNT sing 405 n n 
C11 C10 WNT sing 406 n n 
C10 O2 WNT sing 407 n n 
C10 C9 WNT sing 408 n n 
C9 C8 WNT sing 409 n n 
C8 C7 WNT doub 410 e n 
C7 C5 WNT sing 411 n n 
C5 C6 WNT doub 412 n y 
C6 C1 WNT sing 413 n y 
C1 O WNT sing 414 n n 
O C WNT sing 415 n n 
C6 H8 WNT sing 416 n n 
C9 H11 WNT sing 417 n n 
C9 H12 WNT sing 418 n n 
C10 H WNT sing 419 n n 
C11 H1 WNT sing 420 n n 
C8 H10 WNT sing 421 n n 
C2 H6 WNT sing 422 n n 
C7 H9 WNT sing 423 n n 
C16 H2 WNT sing 424 n n 
C15 H18 WNT sing 425 n n 
C15 H17 WNT sing 426 n n 
C13 H15 WNT sing 427 n n 
C13 H131 WNT sing 428 n n 
C17 H21 WNT sing 429 n n 
C17 H20 WNT sing 430 n n 
C17 H19 WNT sing 431 n n 
C H5 WNT sing 432 n n 
C H4 WNT sing 433 n n 
C H3 WNT sing 434 n n 
C14 H16 WNT sing 435 n n 
C14 H141 WNT sing 436 n n 
O1 H7 WNT sing 437 n n 
O2 H13 WNT sing 438 n n 
O3 H14 WNT sing 439 n n 
#
_atom_sites.entry_id                     8YP4 
_atom_sites.fract_transf_matrix[1][1]    0.021113 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001794 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007755 
_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]    0.015278 
_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 2 WNT A 1 401 401 WNT 2FM . 
D 3 GOL B 1 401 402 GOL GOL . 
E 2 WNT B 1 402 403 WNT 2FM . 
F 4 HOH A 1 501 155 HOH HOH . 
F 4 HOH A 2 502 137 HOH HOH . 
F 4 HOH A 3 503 28 HOH HOH . 
F 4 HOH A 4 504 35 HOH HOH . 
F 4 HOH A 5 505 33 HOH HOH . 
F 4 HOH A 6 506 103 HOH HOH . 
F 4 HOH A 7 507 132 HOH HOH . 
F 4 HOH A 8 508 39 HOH HOH . 
F 4 HOH A 9 509 11 HOH HOH . 
F 4 HOH A 10 510 3 HOH HOH . 
F 4 HOH A 11 511 1 HOH HOH . 
F 4 HOH A 12 512 152 HOH HOH . 
F 4 HOH A 13 513 107 HOH HOH . 
F 4 HOH A 14 514 52 HOH HOH . 
F 4 HOH A 15 515 90 HOH HOH . 
F 4 HOH A 16 516 27 HOH HOH . 
F 4 HOH A 17 517 122 HOH HOH . 
F 4 HOH A 18 518 63 HOH HOH . 
F 4 HOH A 19 519 80 HOH HOH . 
F 4 HOH A 20 520 102 HOH HOH . 
F 4 HOH A 21 521 51 HOH HOH . 
F 4 HOH A 22 522 82 HOH HOH . 
F 4 HOH A 23 523 150 HOH HOH . 
F 4 HOH A 24 524 76 HOH HOH . 
F 4 HOH A 25 525 141 HOH HOH . 
F 4 HOH A 26 526 83 HOH HOH . 
F 4 HOH A 27 527 88 HOH HOH . 
F 4 HOH A 28 528 97 HOH HOH . 
F 4 HOH A 29 529 189 HOH HOH . 
F 4 HOH A 30 530 30 HOH HOH . 
F 4 HOH A 31 531 34 HOH HOH . 
F 4 HOH A 32 532 143 HOH HOH . 
F 4 HOH A 33 533 81 HOH HOH . 
F 4 HOH A 34 534 144 HOH HOH . 
F 4 HOH A 35 535 136 HOH HOH . 
F 4 HOH A 36 536 140 HOH HOH . 
F 4 HOH A 37 537 86 HOH HOH . 
F 4 HOH A 38 538 79 HOH HOH . 
F 4 HOH A 39 539 36 HOH HOH . 
F 4 HOH A 40 540 133 HOH HOH . 
F 4 HOH A 41 541 55 HOH HOH . 
F 4 HOH A 42 542 22 HOH HOH . 
F 4 HOH A 43 543 138 HOH HOH . 
F 4 HOH A 44 544 139 HOH HOH . 
F 4 HOH A 45 545 87 HOH HOH . 
F 4 HOH A 46 546 37 HOH HOH . 
F 4 HOH A 47 547 26 HOH HOH . 
F 4 HOH A 48 548 31 HOH HOH . 
F 4 HOH A 49 549 142 HOH HOH . 
F 4 HOH A 50 550 160 HOH HOH . 
F 4 HOH A 51 551 41 HOH HOH . 
F 4 HOH A 52 552 38 HOH HOH . 
F 4 HOH A 53 553 21 HOH HOH . 
F 4 HOH A 54 554 4 HOH HOH . 
F 4 HOH A 55 555 145 HOH HOH . 
F 4 HOH A 56 556 74 HOH HOH . 
F 4 HOH A 57 557 194 HOH HOH . 
F 4 HOH A 58 558 156 HOH HOH . 
F 4 HOH A 59 559 158 HOH HOH . 
F 4 HOH A 60 560 148 HOH HOH . 
F 4 HOH A 61 561 108 HOH HOH . 
F 4 HOH A 62 562 25 HOH HOH . 
F 4 HOH A 63 563 159 HOH HOH . 
F 4 HOH A 64 564 135 HOH HOH . 
F 4 HOH A 65 565 100 HOH HOH . 
F 4 HOH A 66 566 42 HOH HOH . 
F 4 HOH A 67 567 96 HOH HOH . 
F 4 HOH A 68 568 53 HOH HOH . 
F 4 HOH A 69 569 98 HOH HOH . 
F 4 HOH A 70 570 164 HOH HOH . 
F 4 HOH A 71 571 106 HOH HOH . 
F 4 HOH A 72 572 191 HOH HOH . 
F 4 HOH A 73 573 128 HOH HOH . 
F 4 HOH A 74 574 153 HOH HOH . 
F 4 HOH A 75 575 54 HOH HOH . 
G 4 HOH B 1 501 188 HOH HOH . 
G 4 HOH B 2 502 125 HOH HOH . 
G 4 HOH B 3 503 14 HOH HOH . 
G 4 HOH B 4 504 61 HOH HOH . 
G 4 HOH B 5 505 169 HOH HOH . 
G 4 HOH B 6 506 50 HOH HOH . 
G 4 HOH B 7 507 12 HOH HOH . 
G 4 HOH B 8 508 45 HOH HOH . 
G 4 HOH B 9 509 72 HOH HOH . 
G 4 HOH B 10 510 180 HOH HOH . 
G 4 HOH B 11 511 10 HOH HOH . 
G 4 HOH B 12 512 49 HOH HOH . 
G 4 HOH B 13 513 172 HOH HOH . 
G 4 HOH B 14 514 6 HOH HOH . 
G 4 HOH B 15 515 43 HOH HOH . 
G 4 HOH B 16 516 19 HOH HOH . 
G 4 HOH B 17 517 119 HOH HOH . 
G 4 HOH B 18 518 151 HOH HOH . 
G 4 HOH B 19 519 64 HOH HOH . 
G 4 HOH B 20 520 171 HOH HOH . 
G 4 HOH B 21 521 67 HOH HOH . 
G 4 HOH B 22 522 2 HOH HOH . 
G 4 HOH B 23 523 15 HOH HOH . 
G 4 HOH B 24 524 177 HOH HOH . 
G 4 HOH B 25 525 70 HOH HOH . 
G 4 HOH B 26 526 120 HOH HOH . 
G 4 HOH B 27 527 187 HOH HOH . 
G 4 HOH B 28 528 84 HOH HOH . 
G 4 HOH B 29 529 124 HOH HOH . 
G 4 HOH B 30 530 71 HOH HOH . 
G 4 HOH B 31 531 118 HOH HOH . 
G 4 HOH B 32 532 17 HOH HOH . 
G 4 HOH B 33 533 178 HOH HOH . 
G 4 HOH B 34 534 184 HOH HOH . 
G 4 HOH B 35 535 182 HOH HOH . 
G 4 HOH B 36 536 176 HOH HOH . 
G 4 HOH B 37 537 66 HOH HOH . 
G 4 HOH B 38 538 16 HOH HOH . 
G 4 HOH B 39 539 18 HOH HOH . 
G 4 HOH B 40 540 93 HOH HOH . 
G 4 HOH B 41 541 9 HOH HOH . 
G 4 HOH B 42 542 121 HOH HOH . 
G 4 HOH B 43 543 154 HOH HOH . 
G 4 HOH B 44 544 126 HOH HOH . 
G 4 HOH B 45 545 65 HOH HOH . 
G 4 HOH B 46 546 78 HOH HOH . 
G 4 HOH B 47 547 161 HOH HOH . 
G 4 HOH B 48 548 62 HOH HOH . 
G 4 HOH B 49 549 167 HOH HOH . 
G 4 HOH B 50 550 190 HOH HOH . 
G 4 HOH B 51 551 123 HOH HOH . 
G 4 HOH B 52 552 60 HOH HOH . 
G 4 HOH B 53 553 179 HOH HOH . 
G 4 HOH B 54 554 181 HOH HOH . 
G 4 HOH B 55 555 192 HOH HOH . 
G 4 HOH B 56 556 193 HOH HOH . 
G 4 HOH B 57 557 149 HOH HOH . 
G 4 HOH B 58 558 91 HOH HOH . 
G 4 HOH B 59 559 89 HOH HOH . 
G 4 HOH B 60 560 130 HOH HOH . 
G 4 HOH B 61 561 92 HOH HOH . 
G 4 HOH B 62 562 46 HOH HOH . 
#
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 C3 WNT . . . C 2 -10.809 1.226 19.541 1 57.7 ? C3 WNT 401 A 1 
HETATM 2 C C5 WNT . . . C 2 -10.528 1.003 21.924 1 52.74 ? C5 WNT 401 A 1 
HETATM 3 C C6 WNT . . . C 2 -11.166 -0.232 21.844 1 46.02 ? C6 WNT 401 A 1 
HETATM 4 C C9 WNT . . . C 2 -9.317 1.092 25.683 1 80 ? C9 WNT 401 A 1 
HETATM 5 C C10 WNT . . . C 2 -7.748 1.069 25.683 1 81.46 ? C10 WNT 401 A 1 
HETATM 6 C C11 WNT . . . C 2 -7.191 2.215 26.591 1 79.98 ? C11 WNT 401 A 1 
HETATM 7 C C8 WNT . . . C 2 -9.809 0.682 24.328 1 66.99 ? C8 WNT 401 A 1 
HETATM 8 C C2 WNT . . . C 2 -11.463 -0.019 19.472 1 59.77 ? C2 WNT 401 A 1 
HETATM 9 C C7 WNT . . . C 2 -10.054 1.451 23.273 1 61.66 ? C7 WNT 401 A 1 
HETATM 10 C C16 WNT . . . C 2 -9.067 5.082 21.945 1 65.24 ? C16 WNT 401 A 1 
HETATM 11 C C15 WNT . . . C 2 -8.253 4.885 23.262 1 63.92 ? C15 WNT 401 A 1 
HETATM 12 C C13 WNT . . . C 2 -6.677 2.998 24.171 1 82.84 ? C13 WNT 401 A 1 
HETATM 13 C C12 WNT . . . C 2 -6.862 3.395 25.652 1 84.79 ? C12 WNT 401 A 1 
HETATM 14 C C18 WNT . . . C 2 -9.644 3.141 20.728 1 54.99 ? C18 WNT 401 A 1 
HETATM 15 C C17 WNT . . . C 2 -10.021 6.263 22.167 1 63.11 ? C17 WNT 401 A 1 
HETATM 16 C C WNT . . . C 2 -12.942 -2.377 19.443 1 62.09 ? C WNT 401 A 1 
HETATM 17 O O WNT . . . C 2 -12.265 -1.967 20.617 1 59.14 ? O WNT 401 A 1 
HETATM 18 C C1 WNT . . . C 2 -11.635 -0.752 20.64 1 57.42 ? C1 WNT 401 A 1 
HETATM 19 C C14 WNT . . . C 2 -6.751 4.235 23.112 1 72.52 ? C14 WNT 401 A 1 
HETATM 20 C C4 WNT . . . C 2 -10.337 1.744 20.745 1 53.18 ? C4 WNT 401 A 1 
HETATM 21 O O1 WNT . . . C 2 -10.64 1.931 18.405 1 60.92 ? O1 WNT 401 A 1 
HETATM 22 O O2 WNT . . . C 2 -7.286 -0.146 26.161 1 90.76 ? O2 WNT 401 A 1 
HETATM 23 O O3 WNT . . . C 2 -8.255 2.657 27.396 1 98.74 ? O3 WNT 401 A 1 
HETATM 24 O O4 WNT . . . C 2 -6.758 4.505 26.044 1 79.68 ? O4 WNT 401 A 1 
HETATM 25 O O5 WNT . . . C 2 -9.951 3.977 21.77 1 70.1 ? O5 WNT 401 A 1 
HETATM 26 O O6 WNT . . . C 2 -8.953 3.486 19.855 1 67.71 ? O6 WNT 401 A 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    51 
_model_server_stats.query_time_ms           1434 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           26 
#