data_3VT4
#
_model_server_result.job_id            SUFYKfkijU9ATNp8blrr1A 
_model_server_result.datetime_utc      '2024-12-11 23:22:30' 
_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          3vt4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3VT4 
#
_exptl.entry_id    3VT4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              476.712 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-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          95.92 
_cell.angle_gamma         90 
_cell.entry_id            3VT4 
_cell.length_a            153.725 
_cell.length_b            41.865 
_cell.length_c            42.217 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VT4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
PISA dimeric 2 software_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,B,C,D,E 1 1 
A,C,D 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 
#
_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           'C28 H44 O4 S' 
_chem_comp.formula_weight    476.712 
_chem_comp.id                5YI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-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
O04 C31 5YI sing 1 n n 
C31 C30 5YI sing 2 n n 
C30 C02 5YI doub 3 z n 
O01 C01 5YI sing 4 n n 
C02 C01 5YI sing 5 n n 
C02 C03 5YI sing 6 n n 
C01 C10 5YI sing 7 n n 
C03 O02 5YI sing 8 n n 
C03 C04 5YI sing 9 n n 
C10 C05 5YI sing 10 n n 
C04 C05 5YI sing 11 n n 
C05 C06 5YI doub 12 z n 
C06 C07 5YI sing 13 n n 
C07 C08 5YI doub 14 e n 
C08 C14 5YI sing 15 n n 
C08 C09 5YI sing 16 n n 
C15 C14 5YI sing 17 n n 
C15 C16 5YI sing 18 n n 
C28 C26 5YI sing 19 n n 
C14 C13 5YI sing 20 n n 
C18 C13 5YI sing 21 n n 
C09 C11 5YI sing 22 n n 
C16 C17 5YI doub 23 n n 
C26 C24 5YI sing 24 n n 
C13 C17 5YI sing 25 n n 
C13 C12 5YI sing 26 n n 
C11 C12 5YI sing 27 n n 
C17 C20 5YI sing 28 n n 
C23 C24 5YI sing 29 n n 
C23 S22 5YI sing 30 n n 
C24 O03 5YI sing 31 n n 
C24 C27 5YI sing 32 n n 
C29 C27 5YI sing 33 n n 
C20 S22 5YI sing 34 n n 
C20 C21 5YI sing 35 n n 
C12 H1 5YI sing 36 n n 
C12 H2 5YI sing 37 n n 
C14 H3 5YI sing 38 n n 
C15 H4 5YI sing 39 n n 
C15 H5 5YI sing 40 n n 
C16 H6 5YI sing 41 n n 
C21 H8 5YI sing 42 n n 
C21 H9 5YI sing 43 n n 
C21 H10 5YI sing 44 n n 
C23 H11 5YI sing 45 n n 
C23 H12 5YI sing 46 n n 
C29 H13 5YI sing 47 n n 
C29 H14 5YI sing 48 n n 
C29 H15 5YI sing 49 n n 
C27 H16 5YI sing 50 n n 
C27 H17 5YI sing 51 n n 
C26 H18 5YI sing 52 n n 
C26 H19 5YI sing 53 n n 
C28 H20 5YI sing 54 n n 
C28 H21 5YI sing 55 n n 
C28 H22 5YI sing 56 n n 
O03 H23 5YI sing 57 n n 
C20 H24 5YI sing 58 n n 
C18 H26 5YI sing 59 n n 
C18 H27 5YI sing 60 n n 
C18 H28 5YI sing 61 n n 
C11 H29 5YI sing 62 n n 
C11 H30 5YI sing 63 n n 
C09 H31 5YI sing 64 n n 
C09 H32 5YI sing 65 n n 
C07 H33 5YI sing 66 n n 
C06 H34 5YI sing 67 n n 
C10 H35 5YI sing 68 n n 
C10 H36 5YI sing 69 n n 
C01 H37 5YI sing 70 n n 
O01 H38 5YI sing 71 n n 
C04 H39 5YI sing 72 n n 
C04 H40 5YI sing 73 n n 
C03 H41 5YI sing 74 n n 
O02 H42 5YI sing 75 n n 
C30 H43 5YI sing 76 n n 
C31 H44 5YI sing 77 n n 
C31 H45 5YI sing 78 n n 
O04 H46 5YI sing 79 n n 
#
_atom_sites.entry_id                     3VT4 
_atom_sites.fract_transf_matrix[1][1]    0.006505 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000675 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023886 
_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]    0.023814 
_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 5YI A 1 500 500 5YI YI5 . 
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 9 HOH HOH . 
D 4 HOH A 10 610 10 HOH HOH . 
D 4 HOH A 11 611 11 HOH HOH . 
D 4 HOH A 12 612 12 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 . 
D 4 HOH A 21 621 22 HOH HOH . 
D 4 HOH A 22 622 23 HOH HOH . 
D 4 HOH A 23 623 24 HOH HOH . 
D 4 HOH A 24 624 26 HOH HOH . 
D 4 HOH A 25 625 27 HOH HOH . 
D 4 HOH A 26 626 28 HOH HOH . 
D 4 HOH A 27 627 29 HOH HOH . 
D 4 HOH A 28 628 30 HOH HOH . 
D 4 HOH A 29 629 31 HOH HOH . 
D 4 HOH A 30 630 32 HOH HOH . 
D 4 HOH A 31 631 33 HOH HOH . 
D 4 HOH A 32 632 34 HOH HOH . 
D 4 HOH A 33 633 35 HOH HOH . 
D 4 HOH A 34 634 36 HOH HOH . 
D 4 HOH A 35 635 37 HOH HOH . 
D 4 HOH A 36 636 38 HOH HOH . 
D 4 HOH A 37 637 39 HOH HOH . 
D 4 HOH A 38 638 40 HOH HOH . 
D 4 HOH A 39 639 41 HOH HOH . 
D 4 HOH A 40 640 42 HOH HOH . 
D 4 HOH A 41 641 43 HOH HOH . 
D 4 HOH A 42 642 44 HOH HOH . 
D 4 HOH A 43 643 45 HOH HOH . 
D 4 HOH A 44 644 46 HOH HOH . 
D 4 HOH A 45 645 47 HOH HOH . 
D 4 HOH A 46 646 48 HOH HOH . 
D 4 HOH A 47 647 49 HOH HOH . 
D 4 HOH A 48 648 50 HOH HOH . 
D 4 HOH A 49 649 51 HOH HOH . 
D 4 HOH A 50 650 52 HOH HOH . 
D 4 HOH A 51 651 53 HOH HOH . 
D 4 HOH A 52 652 54 HOH HOH . 
D 4 HOH A 53 653 55 HOH HOH . 
D 4 HOH A 54 654 56 HOH HOH . 
D 4 HOH A 55 655 57 HOH HOH . 
D 4 HOH A 56 656 58 HOH HOH . 
D 4 HOH A 57 657 59 HOH HOH . 
D 4 HOH A 58 658 60 HOH HOH . 
D 4 HOH A 59 659 61 HOH HOH . 
D 4 HOH A 60 660 62 HOH HOH . 
D 4 HOH A 61 661 63 HOH HOH . 
D 4 HOH A 62 662 64 HOH HOH . 
D 4 HOH A 63 663 66 HOH HOH . 
D 4 HOH A 64 664 67 HOH HOH . 
D 4 HOH A 65 665 68 HOH HOH . 
D 4 HOH A 66 666 69 HOH HOH . 
D 4 HOH A 67 667 70 HOH HOH . 
D 4 HOH A 68 668 72 HOH HOH . 
D 4 HOH A 69 669 73 HOH HOH . 
D 4 HOH A 70 670 74 HOH HOH . 
D 4 HOH A 71 671 75 HOH HOH . 
D 4 HOH A 72 672 76 HOH HOH . 
D 4 HOH A 73 673 77 HOH HOH . 
D 4 HOH A 74 674 78 HOH HOH . 
D 4 HOH A 75 675 79 HOH HOH . 
D 4 HOH A 76 676 80 HOH HOH . 
D 4 HOH A 77 677 81 HOH HOH . 
D 4 HOH A 78 678 82 HOH HOH . 
D 4 HOH A 79 679 83 HOH HOH . 
D 4 HOH A 80 680 84 HOH HOH . 
D 4 HOH A 81 681 85 HOH HOH . 
D 4 HOH A 82 682 86 HOH HOH . 
D 4 HOH A 83 683 87 HOH HOH . 
D 4 HOH A 84 684 88 HOH HOH . 
D 4 HOH A 85 685 89 HOH HOH . 
D 4 HOH A 86 686 90 HOH HOH . 
D 4 HOH A 87 687 91 HOH HOH . 
D 4 HOH A 88 688 92 HOH HOH . 
D 4 HOH A 89 689 93 HOH HOH . 
D 4 HOH A 90 690 94 HOH HOH . 
D 4 HOH A 91 691 95 HOH HOH . 
D 4 HOH A 92 692 96 HOH HOH . 
D 4 HOH A 93 693 97 HOH HOH . 
D 4 HOH A 94 694 99 HOH HOH . 
D 4 HOH A 95 695 100 HOH HOH . 
D 4 HOH A 96 696 101 HOH HOH . 
D 4 HOH A 97 697 102 HOH HOH . 
D 4 HOH A 98 698 103 HOH HOH . 
D 4 HOH A 99 699 104 HOH HOH . 
D 4 HOH A 100 700 105 HOH HOH . 
D 4 HOH A 101 701 106 HOH HOH . 
D 4 HOH A 102 702 107 HOH HOH . 
D 4 HOH A 103 703 108 HOH HOH . 
E 4 HOH C 1 701 13 HOH HOH . 
E 4 HOH C 2 702 25 HOH HOH . 
E 4 HOH C 3 703 65 HOH HOH . 
E 4 HOH C 4 704 71 HOH HOH . 
E 4 HOH C 5 705 98 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 C12 5YI . . . C 3 13.443 10.056 27.34 1 32.01 ? C12 5YI 500 A 1 
HETATM 2 C C13 5YI . . . C 3 13.322 8.909 26.272 1 25.38 ? C13 5YI 500 A 1 
HETATM 3 C C14 5YI . . . C 3 14.608 8.96 25.391 1 27.14 ? C14 5YI 500 A 1 
HETATM 4 C C15 5YI . . . C 3 14.534 7.642 24.611 1 26.78 ? C15 5YI 500 A 1 
HETATM 5 C C16 5YI . . . C 3 14.195 6.736 25.826 1 26.35 ? C16 5YI 500 A 1 
HETATM 6 C C21 5YI . . . C 3 13.501 5.505 28.404 1 28.42 ? C21 5YI 500 A 1 
HETATM 7 C C23 5YI . . . C 3 10.544 5.942 27.021 1 31.84 ? C23 5YI 500 A 1 
HETATM 8 C C24 5YI . . . C 3 9.636 4.764 27.462 1 39.71 ? C24 5YI 500 A 1 
HETATM 9 C C29 5YI . . . C 3 7.709 6.606 27.936 1 44.84 ? C29 5YI 500 A 1 
HETATM 10 C C27 5YI . . . C 3 8.477 5.315 28.348 1 33.16 ? C27 5YI 500 A 1 
HETATM 11 C C26 5YI . . . C 3 9.175 3.992 26.167 1 30.7 ? C26 5YI 500 A 1 
HETATM 12 C C28 5YI . . . C 3 7.966 4.471 25.346 1 44.64 ? C28 5YI 500 A 1 
HETATM 13 O O03 5YI . . . C 3 10.421 3.862 28.253 1 38.28 ? O03 5YI 500 A 1 
HETATM 14 S S22 5YI . . . C 3 11.168 7.044 28.356 1 31.15 ? S22 5YI 500 A 1 
HETATM 15 C C20 5YI . . . C 3 13.006 6.941 28.177 1 29.74 ? C20 5YI 500 A 1 
HETATM 16 C C17 5YI . . . C 3 13.514 7.457 26.771 1 26.19 ? C17 5YI 500 A 1 
HETATM 17 C C18 5YI . . . C 3 11.908 8.979 25.561 1 28.92 ? C18 5YI 500 A 1 
HETATM 18 C C11 5YI . . . C 3 13.571 11.478 26.692 1 26.75 ? C11 5YI 500 A 1 
HETATM 19 C C09 5YI . . . C 3 14.649 11.541 25.581 1 32.22 ? C09 5YI 500 A 1 
HETATM 20 C C08 5YI . . . C 3 14.577 10.332 24.601 1 29.86 ? C08 5YI 500 A 1 
HETATM 21 C C07 5YI . . . C 3 14.478 10.463 23.204 1 28.21 ? C07 5YI 500 A 1 
HETATM 22 C C06 5YI . . . C 3 14.427 11.718 22.522 1 31.73 ? C06 5YI 500 A 1 
HETATM 23 C C05 5YI . . . C 3 14.205 11.907 21.151 1 28.87 ? C05 5YI 500 A 1 
HETATM 24 C C10 5YI . . . C 3 13.977 10.738 20.149 1 21.81 ? C10 5YI 500 A 1 
HETATM 25 C C01 5YI . . . C 3 14.651 10.951 18.757 1 25.72 ? C01 5YI 500 A 1 
HETATM 26 O O01 5YI . . . C 3 14.101 10.006 17.819 1 26.73 ? O01 5YI 500 A 1 
HETATM 27 C C04 5YI . . . C 3 14.181 13.379 20.638 1 27.92 ? C04 5YI 500 A 1 
HETATM 28 C C03 5YI . . . C 3 14.882 13.558 19.273 1 24.04 ? C03 5YI 500 A 1 
HETATM 29 O O02 5YI . . . C 3 16.276 13.481 19.476 1 22.89 ? O02 5YI 500 A 1 
HETATM 30 C C02 5YI . . . C 3 14.447 12.43 18.288 1 26.4 ? C02 5YI 500 A 1 
HETATM 31 C C30 5YI . . . C 3 13.891 12.733 17.034 1 33.17 ? C30 5YI 500 A 1 
HETATM 32 C C31 5YI . . . C 3 13.643 14.003 16.468 1 33.63 ? C31 5YI 500 A 1 
HETATM 33 O O04 5YI . . . C 3 12.876 13.889 15.266 1 32.99 ? O04 5YI 500 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#