data_9GYA
#
_model_server_result.job_id            qvkg39PULRXNn5ASjrfkfA 
_model_server_result.datetime_utc      '2024-12-16 02:43:54' 
_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          9gya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    9GYA 
#
_exptl.entry_id    9GYA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              412.68 
_entity.id                          4 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-dimethylsilylpent-4-yn-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-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          90 
_cell.angle_gamma         120 
_cell.entry_id            9GYA 
_cell.length_a            65.92 
_cell.length_b            65.92 
_cell.length_c            263.57 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9GYA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -32.96 57.088395 -43.928333 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C26 H40 O2 Si' 
_chem_comp.formula_weight    412.68 
_chem_comp.id                A1IQQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-dimethylsilylpent-4-yn-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-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
C29 SI27 A1IQQ sing 1 n n 
SI27 C28 A1IQQ sing 2 n n 
SI27 C26 A1IQQ sing 3 n n 
C26 C25 A1IQQ trip 4 n n 
C25 C24 A1IQQ sing 5 n n 
C21 C5 A1IQQ sing 6 n n 
C18 C17 A1IQQ doub 7 n n 
C1 C6 A1IQQ sing 8 n n 
C1 C2 A1IQQ sing 9 n n 
C24 C22 A1IQQ sing 10 n n 
C6 C5 A1IQQ sing 11 n n 
C22 C23 A1IQQ sing 12 n n 
C22 C9 A1IQQ sing 13 n n 
C17 C12 A1IQQ sing 14 n n 
C17 C16 A1IQQ sing 15 n n 
C13 C12 A1IQQ sing 16 n n 
C13 C14 A1IQQ sing 17 n n 
C15 C16 A1IQQ sing 18 n n 
C15 C14 A1IQQ sing 19 n n 
C5 C9 A1IQQ sing 20 n n 
C5 C4 A1IQQ sing 21 n n 
O19 C16 A1IQQ sing 22 n n 
C12 C11 A1IQQ doub 23 z n 
C2 C3 A1IQQ sing 24 n n 
C14 O20 A1IQQ sing 25 n n 
C9 C8 A1IQQ sing 26 n n 
C11 C10 A1IQQ sing 27 n n 
C3 C10 A1IQQ doub 28 e n 
C3 C4 A1IQQ sing 29 n n 
C4 C7 A1IQQ sing 30 n n 
C8 C7 A1IQQ sing 31 n n 
C7 H1 A1IQQ sing 32 n n 
C7 H2 A1IQQ sing 33 n n 
C8 H3 A1IQQ sing 34 n n 
C8 H4 A1IQQ sing 35 n n 
C9 H5 A1IQQ sing 36 n n 
C1 H6 A1IQQ sing 37 n n 
C1 H7 A1IQQ sing 38 n n 
C6 H8 A1IQQ sing 39 n n 
C6 H9 A1IQQ sing 40 n n 
C4 H10 A1IQQ sing 41 n n 
C2 H11 A1IQQ sing 42 n n 
C2 H12 A1IQQ sing 43 n n 
C10 H13 A1IQQ sing 44 n n 
C11 H14 A1IQQ sing 45 n n 
C13 H15 A1IQQ sing 46 n n 
C13 H16 A1IQQ sing 47 n n 
C14 H17 A1IQQ sing 48 n n 
C15 H18 A1IQQ sing 49 n n 
C15 H19 A1IQQ sing 50 n n 
C16 H20 A1IQQ sing 51 n n 
C18 H21 A1IQQ sing 52 n n 
C18 H22 A1IQQ sing 53 n n 
C21 H23 A1IQQ sing 54 n n 
C21 H24 A1IQQ sing 55 n n 
C21 H25 A1IQQ sing 56 n n 
C22 H26 A1IQQ sing 57 n n 
C23 H27 A1IQQ sing 58 n n 
C23 H28 A1IQQ sing 59 n n 
C23 H29 A1IQQ sing 60 n n 
C24 H30 A1IQQ sing 61 n n 
C24 H31 A1IQQ sing 62 n n 
O19 H32 A1IQQ sing 63 n n 
O20 H33 A1IQQ sing 64 n n 
C28 H34 A1IQQ sing 65 n n 
C28 H35 A1IQQ sing 66 n n 
C28 H36 A1IQQ sing 67 n n 
C29 H37 A1IQQ sing 68 n n 
C29 H38 A1IQQ sing 69 n n 
C29 H39 A1IQQ sing 70 n n 
SI27 H40 A1IQQ sing 71 n n 
#
_atom_sites.entry_id                     9GYA 
_atom_sites.fract_transf_matrix[1][1]    0.01517 
_atom_sites.fract_transf_matrix[1][2]    0.008758 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017517 
_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]    0.003794 
_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 ACT A 1 501 502 ACT ACT . 
D 4 A1IQQ A 1 502 1 A1IQQ XXX . 
E 5 HOH A 1 601 136 HOH HOH . 
E 5 HOH A 2 602 122 HOH HOH . 
E 5 HOH A 3 603 170 HOH HOH . 
E 5 HOH A 4 604 152 HOH HOH . 
E 5 HOH A 5 605 165 HOH HOH . 
E 5 HOH A 6 606 153 HOH HOH . 
E 5 HOH A 7 607 168 HOH HOH . 
E 5 HOH A 8 608 120 HOH HOH . 
E 5 HOH A 9 609 12 HOH HOH . 
E 5 HOH A 10 610 145 HOH HOH . 
E 5 HOH A 11 611 130 HOH HOH . 
E 5 HOH A 12 612 42 HOH HOH . 
E 5 HOH A 13 613 16 HOH HOH . 
E 5 HOH A 14 614 110 HOH HOH . 
E 5 HOH A 15 615 92 HOH HOH . 
E 5 HOH A 16 616 96 HOH HOH . 
E 5 HOH A 17 617 7 HOH HOH . 
E 5 HOH A 18 618 103 HOH HOH . 
E 5 HOH A 19 619 140 HOH HOH . 
E 5 HOH A 20 620 113 HOH HOH . 
E 5 HOH A 21 621 151 HOH HOH . 
E 5 HOH A 22 622 123 HOH HOH . 
E 5 HOH A 23 623 66 HOH HOH . 
E 5 HOH A 24 624 102 HOH HOH . 
E 5 HOH A 25 625 14 HOH HOH . 
E 5 HOH A 26 626 107 HOH HOH . 
E 5 HOH A 27 627 157 HOH HOH . 
E 5 HOH A 28 628 1 HOH HOH . 
E 5 HOH A 29 629 39 HOH HOH . 
E 5 HOH A 30 630 116 HOH HOH . 
E 5 HOH A 31 631 37 HOH HOH . 
E 5 HOH A 32 632 71 HOH HOH . 
E 5 HOH A 33 633 24 HOH HOH . 
E 5 HOH A 34 634 155 HOH HOH . 
E 5 HOH A 35 635 18 HOH HOH . 
E 5 HOH A 36 636 15 HOH HOH . 
E 5 HOH A 37 637 11 HOH HOH . 
E 5 HOH A 38 638 45 HOH HOH . 
E 5 HOH A 39 639 9 HOH HOH . 
E 5 HOH A 40 640 6 HOH HOH . 
E 5 HOH A 41 641 161 HOH HOH . 
E 5 HOH A 42 642 25 HOH HOH . 
E 5 HOH A 43 643 99 HOH HOH . 
E 5 HOH A 44 644 13 HOH HOH . 
E 5 HOH A 45 645 58 HOH HOH . 
E 5 HOH A 46 646 169 HOH HOH . 
E 5 HOH A 47 647 19 HOH HOH . 
E 5 HOH A 48 648 53 HOH HOH . 
E 5 HOH A 49 649 156 HOH HOH . 
E 5 HOH A 50 650 28 HOH HOH . 
E 5 HOH A 51 651 79 HOH HOH . 
E 5 HOH A 52 652 117 HOH HOH . 
E 5 HOH A 53 653 40 HOH HOH . 
E 5 HOH A 54 654 26 HOH HOH . 
E 5 HOH A 55 655 119 HOH HOH . 
E 5 HOH A 56 656 67 HOH HOH . 
E 5 HOH A 57 657 49 HOH HOH . 
E 5 HOH A 58 658 3 HOH HOH . 
E 5 HOH A 59 659 100 HOH HOH . 
E 5 HOH A 60 660 17 HOH HOH . 
E 5 HOH A 61 661 70 HOH HOH . 
E 5 HOH A 62 662 20 HOH HOH . 
E 5 HOH A 63 663 86 HOH HOH . 
E 5 HOH A 64 664 124 HOH HOH . 
E 5 HOH A 65 665 5 HOH HOH . 
E 5 HOH A 66 666 2 HOH HOH . 
E 5 HOH A 67 667 150 HOH HOH . 
E 5 HOH A 68 668 27 HOH HOH . 
E 5 HOH A 69 669 111 HOH HOH . 
E 5 HOH A 70 670 35 HOH HOH . 
E 5 HOH A 71 671 10 HOH HOH . 
E 5 HOH A 72 672 8 HOH HOH . 
E 5 HOH A 73 673 54 HOH HOH . 
E 5 HOH A 74 674 158 HOH HOH . 
E 5 HOH A 75 675 133 HOH HOH . 
E 5 HOH A 76 676 104 HOH HOH . 
E 5 HOH A 77 677 41 HOH HOH . 
E 5 HOH A 78 678 52 HOH HOH . 
E 5 HOH A 79 679 4 HOH HOH . 
E 5 HOH A 80 680 34 HOH HOH . 
E 5 HOH A 81 681 30 HOH HOH . 
E 5 HOH A 82 682 166 HOH HOH . 
E 5 HOH A 83 683 98 HOH HOH . 
E 5 HOH A 84 684 94 HOH HOH . 
E 5 HOH A 85 685 50 HOH HOH . 
E 5 HOH A 86 686 31 HOH HOH . 
E 5 HOH A 87 687 32 HOH HOH . 
E 5 HOH A 88 688 38 HOH HOH . 
E 5 HOH A 89 689 135 HOH HOH . 
E 5 HOH A 90 690 33 HOH HOH . 
E 5 HOH A 91 691 89 HOH HOH . 
E 5 HOH A 92 692 36 HOH HOH . 
E 5 HOH A 93 693 22 HOH HOH . 
E 5 HOH A 94 694 115 HOH HOH . 
E 5 HOH A 95 695 118 HOH HOH . 
E 5 HOH A 96 696 87 HOH HOH . 
E 5 HOH A 97 697 84 HOH HOH . 
E 5 HOH A 98 698 97 HOH HOH . 
E 5 HOH A 99 699 83 HOH HOH . 
E 5 HOH A 100 700 134 HOH HOH . 
E 5 HOH A 101 701 76 HOH HOH . 
E 5 HOH A 102 702 77 HOH HOH . 
E 5 HOH A 103 703 47 HOH HOH . 
E 5 HOH A 104 704 90 HOH HOH . 
E 5 HOH A 105 705 146 HOH HOH . 
E 5 HOH A 106 706 75 HOH HOH . 
E 5 HOH A 107 707 164 HOH HOH . 
E 5 HOH A 108 708 80 HOH HOH . 
E 5 HOH A 109 709 126 HOH HOH . 
E 5 HOH A 110 710 65 HOH HOH . 
E 5 HOH A 111 711 44 HOH HOH . 
E 5 HOH A 112 712 129 HOH HOH . 
E 5 HOH A 113 713 73 HOH HOH . 
E 5 HOH A 114 714 51 HOH HOH . 
E 5 HOH A 115 715 78 HOH HOH . 
E 5 HOH A 116 716 114 HOH HOH . 
E 5 HOH A 117 717 105 HOH HOH . 
E 5 HOH A 118 718 60 HOH HOH . 
E 5 HOH A 119 719 74 HOH HOH . 
E 5 HOH A 120 720 21 HOH HOH . 
E 5 HOH A 121 721 56 HOH HOH . 
E 5 HOH A 122 722 88 HOH HOH . 
E 5 HOH A 123 723 55 HOH HOH . 
E 5 HOH A 124 724 64 HOH HOH . 
E 5 HOH A 125 725 63 HOH HOH . 
E 5 HOH A 126 726 82 HOH HOH . 
E 5 HOH A 127 727 81 HOH HOH . 
E 5 HOH A 128 728 46 HOH HOH . 
E 5 HOH A 129 729 162 HOH HOH . 
E 5 HOH A 130 730 127 HOH HOH . 
E 5 HOH A 131 731 160 HOH HOH . 
E 5 HOH A 132 732 48 HOH HOH . 
E 5 HOH A 133 733 59 HOH HOH . 
E 5 HOH A 134 734 85 HOH HOH . 
E 5 HOH A 135 735 159 HOH HOH . 
E 5 HOH A 136 736 141 HOH HOH . 
E 5 HOH A 137 737 154 HOH HOH . 
E 5 HOH A 138 738 61 HOH HOH . 
E 5 HOH A 139 739 142 HOH HOH . 
E 5 HOH A 140 740 93 HOH HOH . 
E 5 HOH A 141 741 101 HOH HOH . 
E 5 HOH A 142 742 106 HOH HOH . 
E 5 HOH A 143 743 57 HOH HOH . 
E 5 HOH A 144 744 163 HOH HOH . 
E 5 HOH A 145 745 108 HOH HOH . 
E 5 HOH A 146 746 109 HOH HOH . 
E 5 HOH A 147 747 125 HOH HOH . 
E 5 HOH A 148 748 143 HOH HOH . 
E 5 HOH A 149 749 128 HOH HOH . 
F 5 HOH B 1 701 62 HOH HOH . 
F 5 HOH B 2 702 43 HOH HOH . 
F 5 HOH B 3 703 29 HOH HOH . 
F 5 HOH B 4 704 149 HOH HOH . 
F 5 HOH B 5 705 148 HOH HOH . 
F 5 HOH B 6 706 147 HOH HOH . 
F 5 HOH B 7 707 131 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 C7 A1IQQ . . . D 4 -29.647 18.382 -3.733 1 42.54 ? C7 A1IQQ 502 A 1 
HETATM 2 C C8 A1IQQ . . . D 4 -28.15 18.202 -4.11 1 43.06 ? C8 A1IQQ 502 A 1 
HETATM 3 C C9 A1IQQ . . . D 4 -28.108 17.006 -5.091 1 43.44 ? C9 A1IQQ 502 A 1 
HETATM 4 C C1 A1IQQ . . . D 4 -31.504 15.645 -6.604 1 42.7 ? C1 A1IQQ 502 A 1 
HETATM 5 C C5 A1IQQ . . . D 4 -29.519 16.981 -5.722 1 40.85 ? C5 A1IQQ 502 A 1 
HETATM 6 C C6 A1IQQ . . . D 4 -30.004 15.647 -6.31 1 37.58 ? C6 A1IQQ 502 A 1 
HETATM 7 C C4 A1IQQ . . . D 4 -30.37 17.223 -4.449 1 39.52 ? C4 A1IQQ 502 A 1 
HETATM 8 C C3 A1IQQ . . . D 4 -31.845 17.294 -4.77 1 39.82 ? C3 A1IQQ 502 A 1 
HETATM 9 C C2 A1IQQ . . . D 4 -32.326 15.994 -5.352 1 47.05 ? C2 A1IQQ 502 A 1 
HETATM 10 C C10 A1IQQ . . . D 4 -32.57 18.416 -4.665 1 37.74 ? C10 A1IQQ 502 A 1 
HETATM 11 C C11 A1IQQ . . . D 4 -33.931 18.579 -5.059 1 34.34 ? C11 A1IQQ 502 A 1 
HETATM 12 C C12 A1IQQ . . . D 4 -34.519 19.698 -5.544 1 35.89 ? C12 A1IQQ 502 A 1 
HETATM 13 C C13 A1IQQ . . . D 4 -35.995 19.746 -5.865 1 38.46 ? C13 A1IQQ 502 A 1 
HETATM 14 C C14 A1IQQ . . . D 4 -36.69 20.985 -5.324 1 44.49 ? C14 A1IQQ 502 A 1 
HETATM 15 C C15 A1IQQ . . . D 4 -35.941 22.227 -5.771 1 39.23 ? C15 A1IQQ 502 A 1 
HETATM 16 C C16 A1IQQ . . . D 4 -34.486 22.156 -5.327 1 34.24 ? C16 A1IQQ 502 A 1 
HETATM 17 C C17 A1IQQ . . . D 4 -33.819 20.923 -5.887 1 42.95 ? C17 A1IQQ 502 A 1 
HETATM 18 C C18 A1IQQ . . . D 4 -32.765 21.007 -6.684 1 45.01 ? C18 A1IQQ 502 A 1 
HETATM 19 C C21 A1IQQ . . . D 4 -29.763 18.126 -6.722 1 37.56 ? C21 A1IQQ 502 A 1 
HETATM 20 C C22 A1IQQ . . . D 4 -26.857 17.004 -5.997 1 45.57 ? C22 A1IQQ 502 A 1 
HETATM 21 C C23 A1IQQ . . . D 4 -25.64 16.377 -5.326 1 43.46 ? C23 A1IQQ 502 A 1 
HETATM 22 C C24 A1IQQ . . . D 4 -26.493 18.398 -6.555 1 49.45 ? C24 A1IQQ 502 A 1 
HETATM 23 C C25 A1IQQ . . . D 4 -25.838 18.337 -7.868 1 52.77 ? C25 A1IQQ 502 A 1 
HETATM 24 C C26 A1IQQ . . . D 4 -25.242 18.221 -8.903 1 52.37 ? C26 A1IQQ 502 A 1 
HETATM 25 O O19 A1IQQ . . . D 4 -33.812 23.351 -5.687 1 40.96 ? O19 A1IQQ 502 A 1 
HETATM 26 O O20 A1IQQ . . . D 4 -36.759 20.931 -3.878 1 45.66 ? O20 A1IQQ 502 A 1 
HETATM 27 C C28 A1IQQ . . . D 4 -22.681 17.782 -10.234 0.36 40.7 ? C28 A1IQQ 502 A 1 
HETATM 28 C C29 A1IQQ . . . D 4 -25.317 16.769 -11.389 0.36 47.85 ? C29 A1IQQ 502 A 1 
HETATM 29 SI SI27 A1IQQ . . . D 4 -24.479 18.173 -10.509 0.36 47.65 ? SI27 A1IQQ 502 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           29 
#