data_5GT4 # _model_server_result.job_id KE0IFMn1toIr2-vJJE2Bfw _model_server_result.datetime_utc '2025-07-31 04:11:50' _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 5gt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5GT4 # _exptl.entry_id 5GT4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 499.725 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile _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 90 _cell.entry_id 5GT4 _cell.length_a 44.663 _cell.length_b 51.842 _cell.length_c 131.475 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C31 H49 N O4' _chem_comp.formula_weight 499.725 _chem_comp.id 2KB _chem_comp.mon_nstd_flag . _chem_comp.name 4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile _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 C1 C4 2KB sing 1 n n C1 C2 2KB sing 2 n n N35 C34 2KB trip 3 n n C4 C5 2KB sing 4 n n C2 C3 2KB sing 5 n n C28 C26 2KB sing 6 n n C13 C14 2KB sing 7 n n C13 C12 2KB sing 8 n n C34 C33 2KB sing 9 n n C31 O19 2KB sing 10 n n C31 C32 2KB sing 11 n n C11 C12 2KB doub 12 z n C11 C10 2KB sing 13 n n O19 C15 2KB sing 14 n n C20 C5 2KB sing 15 n n C14 O30 2KB sing 16 n n C14 C15 2KB sing 17 n n C5 C6 2KB sing 18 n n C5 C9 2KB sing 19 n n C12 C17 2KB sing 20 n n C3 C10 2KB doub 21 e n C3 C6 2KB sing 22 n n C33 C32 2KB sing 23 n n C26 O36 2KB sing 24 n n C26 C25 2KB sing 25 n n C26 C27 2KB sing 26 n n C24 C25 2KB sing 27 n n C24 C23 2KB sing 28 n n C21 C9 2KB sing 29 n n C21 C23 2KB sing 30 n n C21 C22 2KB sing 31 n n C6 C7 2KB sing 32 n n C15 C16 2KB sing 33 n n C9 C8 2KB sing 34 n n C17 C29 2KB doub 35 n n C17 C16 2KB sing 36 n n C16 O18 2KB sing 37 n n C7 C8 2KB sing 38 n n C4 H1 2KB sing 39 n n C4 H2 2KB sing 40 n n C6 H3 2KB sing 41 n n C7 H4 2KB sing 42 n n C7 H5 2KB sing 43 n n C8 H6 2KB sing 44 n n C8 H7 2KB sing 45 n n C10 H8 2KB sing 46 n n C13 H9 2KB sing 47 n n C13 H10 2KB sing 48 n n C15 H11 2KB sing 49 n n C20 H12 2KB sing 50 n n C20 H13 2KB sing 51 n n C20 H14 2KB sing 52 n n C21 H15 2KB sing 53 n n C22 H16 2KB sing 54 n n C22 H17 2KB sing 55 n n C22 H18 2KB sing 56 n n C24 H19 2KB sing 57 n n C24 H20 2KB sing 58 n n C28 H21 2KB sing 59 n n C28 H22 2KB sing 60 n n C28 H23 2KB sing 61 n n C33 H24 2KB sing 62 n n C33 H25 2KB sing 63 n n C32 H26 2KB sing 64 n n C32 H27 2KB sing 65 n n C31 H28 2KB sing 66 n n C31 H29 2KB sing 67 n n C14 H30 2KB sing 68 n n O30 H31 2KB sing 69 n n C16 H32 2KB sing 70 n n O18 H33 2KB sing 71 n n C29 H34 2KB sing 72 n n C29 H35 2KB sing 73 n n C11 H36 2KB sing 74 n n C2 H37 2KB sing 75 n n C2 H38 2KB sing 76 n n C9 H39 2KB sing 77 n n C1 H40 2KB sing 78 n n C1 H41 2KB sing 79 n n C23 H42 2KB sing 80 n n C23 H43 2KB sing 81 n n C25 H44 2KB sing 82 n n C25 H45 2KB sing 83 n n O36 H46 2KB sing 84 n n C27 H47 2KB sing 85 n n C27 H48 2KB sing 86 n n C27 H49 2KB sing 87 n n # _atom_sites.entry_id 5GT4 _atom_sites.fract_transf_matrix[1][1] 0.02239 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019289 _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] 0.007606 _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 B 2 2KB A 1 501 1 2KB LIG . C 3 HOH A 1 601 63 HOH HOH . C 3 HOH A 2 602 65 HOH HOH . C 3 HOH A 3 603 67 HOH HOH . C 3 HOH A 4 604 30 HOH HOH . C 3 HOH A 5 605 66 HOH HOH . C 3 HOH A 6 606 57 HOH HOH . C 3 HOH A 7 607 32 HOH HOH . C 3 HOH A 8 608 70 HOH HOH . C 3 HOH A 9 609 10 HOH HOH . C 3 HOH A 10 610 44 HOH HOH . C 3 HOH A 11 611 54 HOH HOH . C 3 HOH A 12 612 52 HOH HOH . C 3 HOH A 13 613 33 HOH HOH . C 3 HOH A 14 614 22 HOH HOH . C 3 HOH A 15 615 6 HOH HOH . C 3 HOH A 16 616 8 HOH HOH . C 3 HOH A 17 617 39 HOH HOH . C 3 HOH A 18 618 2 HOH HOH . C 3 HOH A 19 619 29 HOH HOH . C 3 HOH A 20 620 14 HOH HOH . C 3 HOH A 21 621 28 HOH HOH . C 3 HOH A 22 622 36 HOH HOH . C 3 HOH A 23 623 24 HOH HOH . C 3 HOH A 24 624 60 HOH HOH . C 3 HOH A 25 625 35 HOH HOH . C 3 HOH A 26 626 12 HOH HOH . C 3 HOH A 27 627 19 HOH HOH . C 3 HOH A 28 628 37 HOH HOH . C 3 HOH A 29 629 17 HOH HOH . C 3 HOH A 30 630 45 HOH HOH . C 3 HOH A 31 631 47 HOH HOH . C 3 HOH A 32 632 15 HOH HOH . C 3 HOH A 33 633 41 HOH HOH . C 3 HOH A 34 634 23 HOH HOH . C 3 HOH A 35 635 48 HOH HOH . C 3 HOH A 36 636 58 HOH HOH . C 3 HOH A 37 637 7 HOH HOH . C 3 HOH A 38 638 40 HOH HOH . C 3 HOH A 39 639 11 HOH HOH . C 3 HOH A 40 640 9 HOH HOH . C 3 HOH A 41 641 56 HOH HOH . C 3 HOH A 42 642 51 HOH HOH . C 3 HOH A 43 643 18 HOH HOH . C 3 HOH A 44 644 26 HOH HOH . C 3 HOH A 45 645 53 HOH HOH . C 3 HOH A 46 646 49 HOH HOH . C 3 HOH A 47 647 3 HOH HOH . C 3 HOH A 48 648 16 HOH HOH . C 3 HOH A 49 649 43 HOH HOH . C 3 HOH A 50 650 13 HOH HOH . C 3 HOH A 51 651 20 HOH HOH . C 3 HOH A 52 652 50 HOH HOH . C 3 HOH A 53 653 62 HOH HOH . C 3 HOH A 54 654 46 HOH HOH . C 3 HOH A 55 655 21 HOH HOH . C 3 HOH A 56 656 1 HOH HOH . C 3 HOH A 57 657 27 HOH HOH . C 3 HOH A 58 658 38 HOH HOH . C 3 HOH A 59 659 5 HOH HOH . C 3 HOH A 60 660 42 HOH HOH . C 3 HOH A 61 661 61 HOH HOH . C 3 HOH A 62 662 25 HOH HOH . C 3 HOH A 63 663 55 HOH HOH . C 3 HOH A 64 664 4 HOH HOH . C 3 HOH A 65 665 71 HOH HOH . C 3 HOH A 66 666 64 HOH HOH . C 3 HOH A 67 667 69 HOH HOH . C 3 HOH A 68 668 59 HOH HOH . C 3 HOH A 69 669 31 HOH HOH . C 3 HOH A 70 670 68 HOH HOH . C 3 HOH A 71 671 34 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 C4 2KB . . . B 2 -12.003 -0.709 33.634 1 12.94 ? C4 2KB 501 A 1 HETATM 2 C C5 2KB . . . B 2 -11.609 -1.213 32.228 1 12.2 ? C5 2KB 501 A 1 HETATM 3 C C6 2KB . . . B 2 -12.874 -1.663 31.478 1 12.07 ? C6 2KB 501 A 1 HETATM 4 C C7 2KB . . . B 2 -12.422 -1.865 30.023 1 12.1 ? C7 2KB 501 A 1 HETATM 5 C C8 2KB . . . B 2 -11.284 -0.826 29.855 1 13.39 ? C8 2KB 501 A 1 HETATM 6 C C10 2KB . . . B 2 -13.835 -3.939 31.741 1 11.68 ? C10 2KB 501 A 1 HETATM 7 C C13 2KB . . . B 2 -15.217 -7.268 33.056 1 11.29 ? C13 2KB 501 A 1 HETATM 8 C C15 2KB . . . B 2 -14.828 -9.031 31.364 1 14.35 ? C15 2KB 501 A 1 HETATM 9 C C17 2KB . . . B 2 -13.57 -6.962 31.182 1 12.16 ? C17 2KB 501 A 1 HETATM 10 C C20 2KB . . . B 2 -10.694 -2.435 32.329 1 12.55 ? C20 2KB 501 A 1 HETATM 11 C C21 2KB . . . B 2 -9.603 0.314 31.457 1 13.69 ? C21 2KB 501 A 1 HETATM 12 C C22 2KB . . . B 2 -9.436 1.694 30.795 1 15.24 ? C22 2KB 501 A 1 HETATM 13 C C24 2KB . . . B 2 -7.074 -0.037 31.659 1 14.18 ? C24 2KB 501 A 1 HETATM 14 C C26 2KB . . . B 2 -4.568 -0.536 31.672 1 14.79 ? C26 2KB 501 A 1 HETATM 15 C C28 2KB . . . B 2 -3.621 -1.639 31.257 1 16.2 ? C28 2KB 501 A 1 HETATM 16 N N35 2KB . . . B 2 -16.288 -13.943 31.999 1 38.54 ? N35 2KB 501 A 1 HETATM 17 C C34 2KB . . . B 2 -15.987 -12.892 31.98 1 26.07 ? C34 2KB 501 A 1 HETATM 18 C C33 2KB . . . B 2 -15.609 -11.727 31.926 1 32.3 ? C33 2KB 501 A 1 HETATM 19 C C32 2KB . . . B 2 -14.178 -11.57 31.473 1 29.83 ? C32 2KB 501 A 1 HETATM 20 C C31 2KB . . . B 2 -13.425 -10.806 32.507 1 24.32 ? C31 2KB 501 A 1 HETATM 21 O O19 2KB . . . B 2 -14.082 -9.563 32.48 1 16.71 ? O19 2KB 501 A 1 HETATM 22 C C14 2KB . . . B 2 -15.884 -8.335 32.191 1 11.55 ? C14 2KB 501 A 1 HETATM 23 O O30 2KB . . . B 2 -16.989 -7.787 31.402 1 11.36 ? O30 2KB 501 A 1 HETATM 24 C C16 2KB . . . B 2 -14.081 -8.133 30.44 1 12.39 ? C16 2KB 501 A 1 HETATM 25 O O18 2KB . . . B 2 -13.063 -8.812 29.716 1 14.1 ? O18 2KB 501 A 1 HETATM 26 C C29 2KB . . . B 2 -12.277 -6.555 31.212 1 11.48 ? C29 2KB 501 A 1 HETATM 27 C C12 2KB . . . B 2 -14.421 -6.321 32.188 1 11.26 ? C12 2KB 501 A 1 HETATM 28 C C11 2KB . . . B 2 -14.527 -4.994 32.416 1 11.81 ? C11 2KB 501 A 1 HETATM 29 C C3 2KB . . . B 2 -13.627 -2.707 32.221 1 12.23 ? C3 2KB 501 A 1 HETATM 30 C C2 2KB . . . B 2 -14.101 -2.253 33.596 1 12.74 ? C2 2KB 501 A 1 HETATM 31 C C9 2KB . . . B 2 -11.052 -0.206 31.218 1 12.38 ? C9 2KB 501 A 1 HETATM 32 C C1 2KB . . . B 2 -12.883 -1.695 34.384 1 12.79 ? C1 2KB 501 A 1 HETATM 33 C C23 2KB . . . B 2 -8.405 -0.5 30.99 1 13.02 ? C23 2KB 501 A 1 HETATM 34 C C25 2KB . . . B 2 -5.974 -0.989 31.284 1 14.81 ? C25 2KB 501 A 1 HETATM 35 O O36 2KB . . . B 2 -4.236 0.663 30.942 1 13.73 ? O36 2KB 501 A 1 HETATM 36 C C27 2KB . . . B 2 -4.466 -0.154 33.112 1 16.44 ? C27 2KB 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #