data_5XPN # _model_server_result.job_id 2-T8Bm_ysYCQumajZBbjbw _model_server_result.datetime_utc '2024-11-19 04:33:20' _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 5xpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5XPN # _exptl.entry_id 5XPN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.705 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-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 95.32 _cell.angle_gamma 90 _cell.entry_id 5XPN _cell.length_a 153.74 _cell.length_b 43.16 _cell.length_c 42.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XPN _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,F _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 'C32 H46 O4' _chem_comp.formula_weight 494.705 _chem_comp.id 8BO _chem_comp.mon_nstd_flag . _chem_comp.name (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3' # 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 C7 C1 8BO doub 1 n n O8 C6 8BO sing 2 n n C1 C6 8BO sing 3 n n C1 C2 8BO sing 4 n n C6 C5 8BO sing 5 n n C2 O9 8BO sing 6 n n C2 C3 8BO sing 7 n n C5 C4 8BO sing 8 n n C3 C4 8BO sing 9 n n C4 C10 8BO doub 10 n n C10 C11 8BO sing 11 n n C11 C12 8BO doub 12 e n C12 C17 8BO sing 13 n n C12 C13 8BO sing 14 n n C18 C17 8BO sing 15 n n C18 C19 8BO sing 16 n n C29 O28 8BO sing 17 n n C23 C16 8BO sing 18 n n C17 C16 8BO sing 19 n n C13 C14 8BO sing 20 n n C19 C20 8BO sing 21 n n C16 C20 8BO sing 22 n n C16 C15 8BO sing 23 n n O28 C27 8BO sing 24 n n C14 C15 8BO sing 25 n n C20 C21 8BO sing 26 n n C24 C21 8BO sing 27 n n C24 C25 8BO sing 28 n n C27 C26 8BO sing 29 n n C27 C30 8BO sing 30 n n C26 C25 8BO sing 31 n n C21 C22 8BO sing 32 n n C30 C31 8BO doub 33 n y C30 C35 8BO sing 34 n y C31 C32 8BO sing 35 n y C35 C34 8BO doub 36 n y C32 C33 8BO doub 37 n y C34 C33 8BO sing 38 n y C33 O36 8BO sing 39 n n O36 H1 8BO sing 40 n n C32 H2 8BO sing 41 n n C31 H3 8BO sing 42 n n C34 H4 8BO sing 43 n n C35 H5 8BO sing 44 n n C27 H6 8BO sing 45 n n C29 H7 8BO sing 46 n n C29 H8 8BO sing 47 n n C29 H9 8BO sing 48 n n C26 H10 8BO sing 49 n n C26 H11 8BO sing 50 n n C25 H12 8BO sing 51 n n C25 H13 8BO sing 52 n n C24 H14 8BO sing 53 n n C24 H15 8BO sing 54 n n C21 H16 8BO sing 55 n n C22 H17 8BO sing 56 n n C22 H18 8BO sing 57 n n C22 H19 8BO sing 58 n n C20 H20 8BO sing 59 n n C23 H21 8BO sing 60 n n C23 H22 8BO sing 61 n n C23 H23 8BO sing 62 n n C15 H24 8BO sing 63 n n C15 H25 8BO sing 64 n n C14 H26 8BO sing 65 n n C14 H27 8BO sing 66 n n C13 H28 8BO sing 67 n n C13 H29 8BO sing 68 n n C19 H30 8BO sing 69 n n C19 H31 8BO sing 70 n n C18 H32 8BO sing 71 n n C18 H33 8BO sing 72 n n C17 H34 8BO sing 73 n n C11 H35 8BO sing 74 n n C10 H36 8BO sing 75 n n C3 H37 8BO sing 76 n n C3 H38 8BO sing 77 n n C2 H39 8BO sing 78 n n O9 H40 8BO sing 79 n n C5 H41 8BO sing 80 n n C5 H42 8BO sing 81 n n C6 H43 8BO sing 82 n n O8 H44 8BO sing 83 n n C7 H45 8BO sing 84 n n C7 H46 8BO sing 85 n n # _atom_sites.entry_id 5XPN _atom_sites.fract_transf_matrix[1][1] 0.006504 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000606 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02317 _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] 0.023895 _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 8BO A 1 501 501 8BO 8BO . D 4 9RO A 1 502 502 9RO 8BO . E 5 HOH A 1 601 601 HOH HOH . E 5 HOH A 2 602 602 HOH HOH . E 5 HOH A 3 603 603 HOH HOH . E 5 HOH A 4 604 604 HOH HOH . E 5 HOH A 5 605 605 HOH HOH . E 5 HOH A 6 606 606 HOH HOH . E 5 HOH A 7 607 607 HOH HOH . E 5 HOH A 8 608 608 HOH HOH . E 5 HOH A 9 609 609 HOH HOH . E 5 HOH A 10 610 610 HOH HOH . E 5 HOH A 11 611 611 HOH HOH . E 5 HOH A 12 612 612 HOH HOH . E 5 HOH A 13 613 613 HOH HOH . E 5 HOH A 14 614 614 HOH HOH . E 5 HOH A 15 615 615 HOH HOH . E 5 HOH A 16 616 616 HOH HOH . E 5 HOH A 17 617 617 HOH HOH . E 5 HOH A 18 618 618 HOH HOH . E 5 HOH A 19 619 619 HOH HOH . E 5 HOH A 20 620 620 HOH HOH . E 5 HOH A 21 621 621 HOH HOH . E 5 HOH A 22 622 622 HOH HOH . E 5 HOH A 23 623 623 HOH HOH . E 5 HOH A 24 624 624 HOH HOH . E 5 HOH A 25 625 625 HOH HOH . E 5 HOH A 26 626 626 HOH HOH . E 5 HOH A 27 627 627 HOH HOH . E 5 HOH A 28 628 628 HOH HOH . E 5 HOH A 29 629 629 HOH HOH . E 5 HOH A 30 630 630 HOH HOH . E 5 HOH A 31 631 631 HOH HOH . E 5 HOH A 32 632 632 HOH HOH . E 5 HOH A 33 633 633 HOH HOH . E 5 HOH A 34 634 634 HOH HOH . E 5 HOH A 35 635 635 HOH HOH . E 5 HOH A 36 636 636 HOH HOH . E 5 HOH A 37 637 637 HOH HOH . E 5 HOH A 38 638 638 HOH HOH . E 5 HOH A 39 639 639 HOH HOH . E 5 HOH A 40 640 640 HOH HOH . E 5 HOH A 41 641 641 HOH HOH . E 5 HOH A 42 642 642 HOH HOH . E 5 HOH A 43 643 643 HOH HOH . E 5 HOH A 44 644 644 HOH HOH . E 5 HOH A 45 645 645 HOH HOH . E 5 HOH A 46 646 646 HOH HOH . E 5 HOH A 47 647 647 HOH HOH . E 5 HOH A 48 648 648 HOH HOH . E 5 HOH A 49 649 649 HOH HOH . E 5 HOH A 50 650 650 HOH HOH . E 5 HOH A 51 651 651 HOH HOH . E 5 HOH A 52 652 652 HOH HOH . E 5 HOH A 53 653 653 HOH HOH . E 5 HOH A 54 654 654 HOH HOH . E 5 HOH A 55 655 655 HOH HOH . E 5 HOH A 56 656 656 HOH HOH . E 5 HOH A 57 657 657 HOH HOH . E 5 HOH A 58 658 658 HOH HOH . E 5 HOH A 59 659 659 HOH HOH . E 5 HOH A 60 660 660 HOH HOH . E 5 HOH A 61 661 661 HOH HOH . E 5 HOH A 62 662 662 HOH HOH . E 5 HOH A 63 663 663 HOH HOH . E 5 HOH A 64 664 664 HOH HOH . E 5 HOH A 65 665 665 HOH HOH . E 5 HOH A 66 666 666 HOH HOH . E 5 HOH A 67 667 667 HOH HOH . E 5 HOH A 68 668 668 HOH HOH . E 5 HOH A 69 669 669 HOH HOH . E 5 HOH A 70 670 670 HOH HOH . E 5 HOH A 71 671 671 HOH HOH . E 5 HOH A 72 672 672 HOH HOH . E 5 HOH A 73 673 673 HOH HOH . E 5 HOH A 74 674 674 HOH HOH . E 5 HOH A 75 675 675 HOH HOH . E 5 HOH A 76 676 676 HOH HOH . E 5 HOH A 77 677 677 HOH HOH . E 5 HOH A 78 678 678 HOH HOH . E 5 HOH A 79 679 679 HOH HOH . E 5 HOH A 80 680 680 HOH HOH . E 5 HOH A 81 681 681 HOH HOH . E 5 HOH A 82 682 682 HOH HOH . E 5 HOH A 83 683 683 HOH HOH . E 5 HOH A 84 684 684 HOH HOH . E 5 HOH A 85 685 685 HOH HOH . E 5 HOH A 86 686 686 HOH HOH . E 5 HOH A 87 687 687 HOH HOH . E 5 HOH A 88 688 688 HOH HOH . E 5 HOH A 89 689 689 HOH HOH . E 5 HOH A 90 690 690 HOH HOH . E 5 HOH A 91 691 691 HOH HOH . E 5 HOH A 92 692 692 HOH HOH . E 5 HOH A 93 693 693 HOH HOH . E 5 HOH A 94 694 694 HOH HOH . E 5 HOH A 95 695 695 HOH HOH . E 5 HOH A 96 696 696 HOH HOH . E 5 HOH A 97 697 697 HOH HOH . E 5 HOH A 98 698 698 HOH HOH . E 5 HOH A 99 699 699 HOH HOH . E 5 HOH A 100 700 700 HOH HOH . E 5 HOH A 101 701 701 HOH HOH . E 5 HOH A 102 702 702 HOH HOH . E 5 HOH A 103 703 703 HOH HOH . E 5 HOH A 104 704 704 HOH HOH . E 5 HOH A 105 705 705 HOH HOH . E 5 HOH A 106 706 706 HOH HOH . E 5 HOH A 107 707 707 HOH HOH . E 5 HOH A 108 708 708 HOH HOH . E 5 HOH A 109 709 709 HOH HOH . E 5 HOH A 110 710 710 HOH HOH . E 5 HOH A 111 711 711 HOH HOH . E 5 HOH A 112 712 712 HOH HOH . E 5 HOH A 113 713 713 HOH HOH . E 5 HOH A 114 714 714 HOH HOH . E 5 HOH A 115 715 715 HOH HOH . E 5 HOH A 116 716 716 HOH HOH . E 5 HOH A 117 717 717 HOH HOH . E 5 HOH A 118 718 718 HOH HOH . E 5 HOH A 119 719 719 HOH HOH . E 5 HOH A 120 720 720 HOH HOH . E 5 HOH A 121 721 721 HOH HOH . E 5 HOH A 122 722 722 HOH HOH . E 5 HOH A 123 723 723 HOH HOH . E 5 HOH A 124 724 724 HOH HOH . E 5 HOH A 125 725 725 HOH HOH . E 5 HOH A 126 726 726 HOH HOH . E 5 HOH A 127 727 727 HOH HOH . E 5 HOH A 128 728 728 HOH HOH . E 5 HOH A 129 729 729 HOH HOH . E 5 HOH A 130 730 730 HOH HOH . E 5 HOH A 131 731 731 HOH HOH . E 5 HOH A 132 732 732 HOH HOH . E 5 HOH A 133 733 733 HOH HOH . E 5 HOH A 134 734 734 HOH HOH . E 5 HOH A 135 735 735 HOH HOH . E 5 HOH A 136 736 736 HOH HOH . E 5 HOH A 137 737 737 HOH HOH . E 5 HOH A 138 738 738 HOH HOH . E 5 HOH A 139 739 739 HOH HOH . E 5 HOH A 140 740 740 HOH HOH . E 5 HOH A 141 741 741 HOH HOH . E 5 HOH A 142 742 742 HOH HOH . E 5 HOH A 143 743 743 HOH HOH . E 5 HOH A 144 744 744 HOH HOH . E 5 HOH A 145 745 745 HOH HOH . E 5 HOH A 146 746 746 HOH HOH . E 5 HOH A 147 747 747 HOH HOH . E 5 HOH A 148 748 748 HOH HOH . E 5 HOH A 149 749 749 HOH HOH . E 5 HOH A 150 750 750 HOH HOH . E 5 HOH A 151 751 751 HOH HOH . E 5 HOH A 152 752 752 HOH HOH . E 5 HOH A 153 753 753 HOH HOH . F 5 HOH C 1 701 701 HOH HOH . F 5 HOH C 2 702 702 HOH HOH . F 5 HOH C 3 703 703 HOH HOH . F 5 HOH C 4 704 704 HOH HOH . F 5 HOH C 5 705 705 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 O O36 8BO . A . C 3 8.164 -2.16 32.047 0.5 58.35 ? O36 8BO 501 A 1 HETATM 2 C C33 8BO . A . C 3 8.394 -1.608 30.814 0.5 51.43 ? C33 8BO 501 A 1 HETATM 3 C C32 8BO . A . C 3 9.058 -2.319 29.805 0.5 48.59 ? C32 8BO 501 A 1 HETATM 4 C C31 8BO . A . C 3 9.262 -1.722 28.559 0.5 44.34 ? C31 8BO 501 A 1 HETATM 5 C C34 8BO . A . C 3 7.943 -0.315 30.558 0.5 49.87 ? C34 8BO 501 A 1 HETATM 6 C C35 8BO . A . C 3 8.145 0.281 29.318 0.5 44.31 ? C35 8BO 501 A 1 HETATM 7 C C30 8BO . A . C 3 8.814 -0.423 28.323 0.5 43.13 ? C30 8BO 501 A 1 HETATM 8 C C27 8BO . A . C 3 9.013 0.245 27.018 0.5 40.36 ? C27 8BO 501 A 1 HETATM 9 O O28 8BO . A . C 3 7.767 0.154 26.343 0.5 42.87 ? O28 8BO 501 A 1 HETATM 10 C C29 8BO . A . C 3 7.823 -0.735 25.23 0.5 43.57 ? C29 8BO 501 A 1 HETATM 11 C C26 8BO . A . C 3 9.347 1.733 27.194 0.5 37.23 ? C26 8BO 501 A 1 HETATM 12 C C25 8BO . A . C 3 10.67 2.023 27.905 0.5 34.32 ? C25 8BO 501 A 1 HETATM 13 C C24 8BO . A . C 3 11.911 1.928 27.007 0.5 33.69 ? C24 8BO 501 A 1 HETATM 14 C C21 8BO . A . C 3 13.113 2.495 27.774 0.5 32.9 ? C21 8BO 501 A 1 HETATM 15 C C22 8BO . A . C 3 13.796 1.467 28.663 0.5 35.23 ? C22 8BO 501 A 1 HETATM 16 C C20 8BO . A . C 3 14.216 3.189 26.965 0.5 31.9 ? C20 8BO 501 A 1 HETATM 17 C C16 8BO . A . C 3 13.81 4.511 26.328 0.5 30.5 ? C16 8BO 501 A 1 HETATM 18 C C23 8BO . A . C 3 12.721 4.326 25.266 0.5 28.31 ? C23 8BO 501 A 1 HETATM 19 C C15 8BO . A . C 3 13.416 5.661 27.26 0.5 29.85 ? C15 8BO 501 A 1 HETATM 20 C C14 8BO . A . C 3 13.465 7.012 26.518 0.5 28.8 ? C14 8BO 501 A 1 HETATM 21 C C13 8BO . A . C 3 14.81 7.261 25.812 0.5 29.03 ? C13 8BO 501 A 1 HETATM 22 C C19 8BO . A . C 3 14.928 2.427 25.837 0.5 31.51 ? C19 8BO 501 A 1 HETATM 23 C C18 8BO . A . C 3 15.689 3.529 25.09 0.5 31.08 ? C18 8BO 501 A 1 HETATM 24 C C17 8BO . A . C 3 15.168 4.816 25.731 0.5 29.39 ? C17 8BO 501 A 1 HETATM 25 C C12 8BO . A . C 3 15.04 6.062 24.914 0.5 27.97 ? C12 8BO 501 A 1 HETATM 26 C C11 8BO . A . C 3 15.103 6.076 23.563 0.5 27.12 ? C11 8BO 501 A 1 HETATM 27 C C10 8BO . A . C 3 14.929 7.297 22.778 0.5 25.96 ? C10 8BO 501 A 1 HETATM 28 C C4 8BO . A . C 3 14.761 7.351 21.434 0.5 25.71 ? C4 8BO 501 A 1 HETATM 29 C C3 8BO . A . C 3 14.531 8.723 20.827 0.5 24.89 ? C3 8BO 501 A 1 HETATM 30 C C2 8BO . A . C 3 15.161 8.853 19.438 0.5 25.4 ? C2 8BO 501 A 1 HETATM 31 O O9 8BO . A . C 3 16.599 8.839 19.48 0.5 24.65 ? O9 8BO 501 A 1 HETATM 32 C C5 8BO . A . C 3 14.74 6.114 20.563 0.5 24.36 ? C5 8BO 501 A 1 HETATM 33 C C6 8BO . A . C 3 15.105 6.334 19.089 0.5 24.06 ? C6 8BO 501 A 1 HETATM 34 O O8 8BO . A . C 3 14.464 5.319 18.322 0.5 23.73 ? O8 8BO 501 A 1 HETATM 35 C C1 8BO . A . C 3 14.7 7.692 18.595 0.5 24.42 ? C1 8BO 501 A 1 HETATM 36 C C7 8BO . A . C 3 13.986 7.856 17.491 0.5 21.95 ? C7 8BO 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #