data_3VTD
#
_model_server_result.job_id            L0tDxXUhVa9RyCuf86T3JQ 
_model_server_result.datetime_utc      '2024-12-21 17:48:10' 
_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          3vtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3VTD 
#
_exptl.entry_id    3VTD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              532.796 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol 
_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          95.73 
_cell.angle_gamma         90 
_cell.entry_id            3VTD 
_cell.length_a            153.178 
_cell.length_b            43.897 
_cell.length_c            42.526 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C36 H52 O3' 
_chem_comp.formula_weight    532.796 
_chem_comp.id                TKD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol 
_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
C28 C02 TKD doub 306 n n 
O01 C01 TKD sing 307 n n 
C02 C01 TKD sing 308 n n 
C02 C03 TKD sing 309 n n 
C01 C10 TKD sing 310 n n 
C03 O02 TKD sing 311 n n 
C03 C04 TKD sing 312 n n 
C10 C05 TKD sing 313 n n 
C04 C05 TKD sing 314 n n 
C05 C06 TKD doub 315 n n 
C06 C07 TKD sing 316 n n 
C07 C08 TKD doub 317 e n 
C08 C14 TKD sing 318 n n 
C08 C09 TKD sing 319 n n 
C15 C14 TKD sing 320 n n 
C15 C16 TKD sing 321 n n 
C18 C13 TKD sing 322 n n 
C14 C13 TKD sing 323 n n 
C16 C17 TKD sing 324 n n 
C09 C11 TKD sing 325 n n 
C38 C35 TKD sing 326 n n 
C38 C33 TKD sing 327 n n 
C13 C17 TKD sing 328 n n 
C13 C12 TKD sing 329 n n 
C37 C35 TKD sing 330 n n 
C37 C29 TKD sing 331 n n 
C35 C36 TKD sing 332 n n 
C11 C12 TKD sing 333 n n 
C17 C20 TKD sing 334 n n 
C26 C29 TKD sing 335 n n 
C26 C25 TKD sing 336 n n 
C34 C33 TKD sing 337 n n 
C34 C29 TKD sing 338 n n 
C33 C32 TKD sing 339 n n 
C29 C30 TKD sing 340 n n 
C20 C22 TKD sing 341 n n 
C20 C21 TKD sing 342 n n 
C22 C23 TKD sing 343 n n 
C36 C31 TKD sing 344 n n 
C23 C24 TKD trip 345 n n 
C24 C25 TKD sing 346 n n 
C25 O03 TKD sing 347 n n 
C32 C31 TKD sing 348 n n 
C30 C31 TKD sing 349 n n 
C30 H1 TKD sing 350 n n 
C30 H2 TKD sing 351 n n 
C31 H3 TKD sing 352 n n 
C32 H4 TKD sing 353 n n 
C32 H5 TKD sing 354 n n 
C33 H6 TKD sing 355 n n 
C34 H7 TKD sing 356 n n 
C34 H8 TKD sing 357 n n 
C37 H9 TKD sing 358 n n 
C37 H10 TKD sing 359 n n 
C36 H11 TKD sing 360 n n 
C36 H12 TKD sing 361 n n 
C38 H13 TKD sing 362 n n 
C38 H14 TKD sing 363 n n 
C35 H15 TKD sing 364 n n 
C26 H16 TKD sing 365 n n 
C26 H17 TKD sing 366 n n 
C25 H18 TKD sing 367 n n 
C22 H19 TKD sing 368 n n 
C22 H20 TKD sing 369 n n 
C20 H21 TKD sing 370 n n 
C17 H22 TKD sing 371 n n 
C21 H23 TKD sing 372 n n 
C21 H24 TKD sing 373 n n 
C21 H25 TKD sing 374 n n 
O03 H26 TKD sing 375 n n 
C14 H27 TKD sing 376 n n 
C15 H28 TKD sing 377 n n 
C15 H29 TKD sing 378 n n 
C16 H30 TKD sing 379 n n 
C16 H31 TKD sing 380 n n 
C12 H32 TKD sing 381 n n 
C12 H33 TKD sing 382 n n 
C11 H34 TKD sing 383 n n 
C11 H35 TKD sing 384 n n 
C09 H36 TKD sing 385 n n 
C09 H37 TKD sing 386 n n 
C18 H38 TKD sing 387 n n 
C18 H39 TKD sing 388 n n 
C18 H40 TKD sing 389 n n 
C07 H41 TKD sing 390 n n 
C06 H42 TKD sing 391 n n 
C04 H43 TKD sing 392 n n 
C04 H44 TKD sing 393 n n 
C03 H45 TKD sing 394 n n 
C01 H46 TKD sing 395 n n 
C10 H47 TKD sing 396 n n 
C10 H48 TKD sing 397 n n 
C28 H49 TKD sing 398 n n 
C28 H50 TKD sing 399 n n 
O01 H51 TKD sing 400 n n 
O02 H52 TKD sing 401 n n 
#
_atom_sites.entry_id                     3VTD 
_atom_sites.fract_transf_matrix[1][1]    0.006528 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000655 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022781 
_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]    0.023633 
_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 TKD A 1 500 500 TKD TKD . 
D 4 HOH A 1 601 1 HOH HOH . 
D 4 HOH A 2 602 2 HOH HOH . 
D 4 HOH A 3 603 3 HOH HOH . 
D 4 HOH A 4 604 4 HOH HOH . 
D 4 HOH A 5 605 5 HOH HOH . 
D 4 HOH A 6 606 6 HOH HOH . 
D 4 HOH A 7 607 7 HOH HOH . 
D 4 HOH A 8 608 8 HOH HOH . 
D 4 HOH A 9 609 10 HOH HOH . 
D 4 HOH A 10 610 11 HOH HOH . 
D 4 HOH A 11 611 12 HOH HOH . 
D 4 HOH A 12 612 13 HOH HOH . 
D 4 HOH A 13 613 14 HOH HOH . 
D 4 HOH A 14 614 15 HOH HOH . 
D 4 HOH A 15 615 16 HOH HOH . 
D 4 HOH A 16 616 17 HOH HOH . 
D 4 HOH A 17 617 18 HOH HOH . 
D 4 HOH A 18 618 19 HOH HOH . 
D 4 HOH A 19 619 20 HOH HOH . 
D 4 HOH A 20 620 21 HOH HOH . 
E 4 HOH B 1 701 9 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 C29 TKD . . . C 3 9.35 -2.845 27.992 1 36.7 ? C29 TKD 500 A 1 
HETATM 2 C C30 TKD . . . C 3 8.731 -2.941 29.438 1 35.52 ? C30 TKD 500 A 1 
HETATM 3 C C31 TKD . . . C 3 7.544 -1.926 29.584 1 38.07 ? C31 TKD 500 A 1 
HETATM 4 C C32 TKD . . . C 3 8.079 -0.463 29.364 1 37.93 ? C32 TKD 500 A 1 
HETATM 5 C C33 TKD . . . C 3 8.691 -0.338 27.935 1 37.19 ? C33 TKD 500 A 1 
HETATM 6 C C34 TKD . . . C 3 9.861 -1.367 27.783 1 37.49 ? C34 TKD 500 A 1 
HETATM 7 C C37 TKD . . . C 3 8.218 -3.122 26.926 1 37.09 ? C37 TKD 500 A 1 
HETATM 8 C C36 TKD . . . C 3 6.438 -2.259 28.517 1 36.62 ? C36 TKD 500 A 1 
HETATM 9 C C38 TKD . . . C 3 7.591 -0.645 26.871 1 37.37 ? C38 TKD 500 A 1 
HETATM 10 C C35 TKD . . . C 3 7.04 -2.104 27.082 1 37.62 ? C35 TKD 500 A 1 
HETATM 11 C C26 TKD . . . C 3 10.479 -3.91 27.714 1 37.63 ? C26 TKD 500 A 1 
HETATM 12 C C25 TKD . . . C 3 11.646 -4.185 28.729 1 38.76 ? C25 TKD 500 A 1 
HETATM 13 C C24 TKD . . . C 3 12.578 -3.086 28.657 1 38.84 ? C24 TKD 500 A 1 
HETATM 14 C C23 TKD . . . C 3 13.301 -2.164 28.593 1 39.81 ? C23 TKD 500 A 1 
HETATM 15 C C22 TKD . . . C 3 14.156 -0.999 28.513 1 40.34 ? C22 TKD 500 A 1 
HETATM 16 C C20 TKD . . . C 3 13.414 0.307 28.128 1 39.15 ? C20 TKD 500 A 1 
HETATM 17 C C17 TKD . . . C 3 14.372 1.41 27.519 1 39.2 ? C17 TKD 500 A 1 
HETATM 18 C C21 TKD . . . C 3 12.702 0.754 29.423 1 38.81 ? C21 TKD 500 A 1 
HETATM 19 O O03 TKD . . . C 3 11.214 -4.29 30.083 1 37.69 ? O03 TKD 500 A 1 
HETATM 20 C C13 TKD . . . C 3 13.774 2.706 26.881 1 38.28 ? C13 TKD 500 A 1 
HETATM 21 C C14 TKD . . . C 3 15.085 3.268 26.218 1 37.68 ? C14 TKD 500 A 1 
HETATM 22 C C15 TKD . . . C 3 15.671 2.059 25.484 1 34.46 ? C15 TKD 500 A 1 
HETATM 23 C C16 TKD . . . C 3 15.317 0.88 26.39 1 37.97 ? C16 TKD 500 A 1 
HETATM 24 C C12 TKD . . . C 3 13.293 3.779 27.914 1 37 ? C12 TKD 500 A 1 
HETATM 25 C C11 TKD . . . C 3 13.059 5.176 27.279 1 37.84 ? C11 TKD 500 A 1 
HETATM 26 C C09 TKD . . . C 3 14.241 5.642 26.395 1 38.95 ? C09 TKD 500 A 1 
HETATM 27 C C08 TKD . . . C 3 14.719 4.549 25.431 1 39.9 ? C08 TKD 500 A 1 
HETATM 28 C C18 TKD . . . C 3 12.624 2.36 25.836 1 37.97 ? C18 TKD 500 A 1 
HETATM 29 C C07 TKD . . . C 3 14.854 4.64 24.1 1 39.7 ? C07 TKD 500 A 1 
HETATM 30 C C06 TKD . . . C 3 14.586 5.789 23.247 1 41.71 ? C06 TKD 500 A 1 
HETATM 31 C C05 TKD . . . C 3 14.365 5.734 21.919 1 42.21 ? C05 TKD 500 A 1 
HETATM 32 C C04 TKD . . . C 3 14.149 7.031 21.151 1 41.1 ? C04 TKD 500 A 1 
HETATM 33 C C03 TKD . . . C 3 14.791 7.036 19.737 1 41.82 ? C03 TKD 500 A 1 
HETATM 34 C C02 TKD . . . C 3 14.392 5.789 18.962 1 42.06 ? C02 TKD 500 A 1 
HETATM 35 C C01 TKD . . . C 3 14.901 4.531 19.631 1 41.97 ? C01 TKD 500 A 1 
HETATM 36 C C10 TKD . . . C 3 14.346 4.444 21.071 1 42.09 ? C10 TKD 500 A 1 
HETATM 37 C C28 TKD . . . C 3 13.631 5.765 17.847 1 43.28 ? C28 TKD 500 A 1 
HETATM 38 O O01 TKD . . . C 3 14.495 3.399 18.88 1 42.46 ? O01 TKD 500 A 1 
HETATM 39 O O02 TKD . . . C 3 16.211 7.035 19.866 1 40.22 ? O02 TKD 500 A 1 
#
_model_server_stats.io_time_ms              64 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#