data_4LB9 # _model_server_result.job_id eO7GfpbrNTzenR2yy-ynzQ _model_server_result.datetime_utc '2024-11-25 16:18:11' _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 4lb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 4LB9 # _exptl.entry_id 4LB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 588.557 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside" _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 104.56 _cell.angle_gamma 90 _cell.entry_id 4LB9 _cell.length_a 172.543 _cell.length_b 38.677 _cell.length_c 99.221 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LB9 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G _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 F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C29 H32 O13' _chem_comp.formula_weight 588.557 _chem_comp.id EVP _chem_comp.mon_nstd_flag . _chem_comp.name "(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Etoposide;VP-16 # 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 O1 EVP sing 83 n n C1 O2 EVP sing 84 n n O1 C13 EVP sing 85 n n C2 O2 EVP sing 86 n n C2 C3 EVP doub 87 n y C2 C13 EVP sing 88 n y C3 C4 EVP sing 89 n y O3 C7 EVP sing 90 n n O3 C8 EVP sing 91 n n C4 C5 EVP sing 92 n n C4 C11 EVP doub 93 n y O4 C7 EVP doub 94 n n C5 C6 EVP sing 95 n n C5 C14 EVP sing 96 n n O5 C16 EVP sing 97 n n O5 C20 EVP sing 98 n n C6 C7 EVP sing 99 n n C6 C9 EVP sing 100 n n O6 C17 EVP sing 101 n n O7 C18 EVP sing 102 n n O7 C21 EVP sing 103 n n C8 C9 EVP sing 104 n n O8 C10 EVP sing 105 n n O8 C22 EVP sing 106 n n C9 C10 EVP sing 107 n n O9 C22 EVP sing 108 n n O9 C23 EVP sing 109 n n C10 C11 EVP sing 110 n n O10 C24 EVP sing 111 n n O10 C25 EVP sing 112 n n C11 C12 EVP sing 113 n y O11 C25 EVP sing 114 n n O11 C26 EVP sing 115 n n C12 C13 EVP doub 116 n y O12 C27 EVP sing 117 n n O13 C28 EVP sing 118 n n C14 C15 EVP doub 119 n y C14 C19 EVP sing 120 n y C15 C16 EVP sing 121 n y C16 C17 EVP doub 122 n y C17 C18 EVP sing 123 n y C18 C19 EVP doub 124 n y C22 C28 EVP sing 125 n n C23 C24 EVP sing 126 n n C23 C26 EVP sing 127 n n C25 C29 EVP sing 128 n n C26 C27 EVP sing 129 n n C27 C28 EVP sing 130 n n C1 H1 EVP sing 131 n n C1 H1A EVP sing 132 n n C3 H3 EVP sing 133 n n C5 H5 EVP sing 134 n n C6 H6 EVP sing 135 n n O6 HO6 EVP sing 136 n n C8 H8 EVP sing 137 n n C8 H8A EVP sing 138 n n C9 H9 EVP sing 139 n n C10 H10 EVP sing 140 n n C12 H12 EVP sing 141 n n O12 HO12 EVP sing 142 n n O13 HO13 EVP sing 143 n n C15 H15 EVP sing 144 n n C19 H19 EVP sing 145 n n C20 H20 EVP sing 146 n n C20 H20A EVP sing 147 n n C20 H20B EVP sing 148 n n C21 H21 EVP sing 149 n n C21 H21A EVP sing 150 n n C21 H21B EVP sing 151 n n C22 H22 EVP sing 152 n n C23 H23 EVP sing 153 n n C24 H24 EVP sing 154 n n C24 H24A EVP sing 155 n n C25 H25 EVP sing 156 n n C26 H26 EVP sing 157 n n C27 H27 EVP sing 158 n n C28 H28 EVP sing 159 n n C29 H29 EVP sing 160 n n C29 H29A EVP sing 161 n n C29 H29B EVP sing 162 n n # _atom_sites.entry_id 4LB9 _atom_sites.fract_transf_matrix[1][1] 0.005796 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001506 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025855 _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] 0.010413 _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 MYR A 1 601 1002 MYR MYR . C 2 MYR A 1 602 1003 MYR MYR . D 2 MYR A 1 603 1004 MYR MYR . E 2 MYR A 1 604 1005 MYR MYR . F 3 EVP A 1 605 600 EVP EVP . G 4 HOH A 1 701 1 HOH HOH . G 4 HOH A 2 702 2 HOH HOH . G 4 HOH A 3 703 3 HOH HOH . G 4 HOH A 4 704 4 HOH HOH . G 4 HOH A 5 705 5 HOH HOH . G 4 HOH A 6 706 6 HOH HOH . G 4 HOH A 7 707 7 HOH HOH . G 4 HOH A 8 708 8 HOH HOH . G 4 HOH A 9 709 9 HOH HOH . G 4 HOH A 10 710 10 HOH HOH . G 4 HOH A 11 711 11 HOH HOH . G 4 HOH A 12 712 12 HOH HOH . G 4 HOH A 13 713 13 HOH HOH . G 4 HOH A 14 714 14 HOH HOH . G 4 HOH A 15 715 15 HOH HOH . G 4 HOH A 16 716 16 HOH HOH . G 4 HOH A 17 717 17 HOH HOH . G 4 HOH A 18 718 18 HOH HOH . G 4 HOH A 19 719 19 HOH HOH . G 4 HOH A 20 720 20 HOH HOH . G 4 HOH A 21 721 21 HOH HOH . G 4 HOH A 22 722 22 HOH HOH . G 4 HOH A 23 723 23 HOH HOH . G 4 HOH A 24 724 24 HOH HOH . G 4 HOH A 25 725 25 HOH HOH . G 4 HOH A 26 726 26 HOH HOH . G 4 HOH A 27 727 27 HOH HOH . G 4 HOH A 28 728 28 HOH HOH . G 4 HOH A 29 729 29 HOH HOH . G 4 HOH A 30 730 30 HOH HOH . G 4 HOH A 31 731 31 HOH HOH . G 4 HOH A 32 732 32 HOH HOH . G 4 HOH A 33 733 33 HOH HOH . G 4 HOH A 34 734 34 HOH HOH . G 4 HOH A 35 735 35 HOH HOH . G 4 HOH A 36 736 36 HOH HOH . G 4 HOH A 37 737 37 HOH HOH . G 4 HOH A 38 738 38 HOH HOH . G 4 HOH A 39 739 39 HOH HOH . G 4 HOH A 40 740 40 HOH HOH . G 4 HOH A 41 741 41 HOH HOH . G 4 HOH A 42 742 42 HOH HOH . G 4 HOH A 43 743 43 HOH HOH . G 4 HOH A 44 744 44 HOH HOH . G 4 HOH A 45 745 45 HOH HOH . G 4 HOH A 46 746 46 HOH HOH . G 4 HOH A 47 747 47 HOH HOH . G 4 HOH A 48 748 48 HOH HOH . G 4 HOH A 49 749 49 HOH HOH . G 4 HOH A 50 750 50 HOH HOH . G 4 HOH A 51 751 51 HOH HOH . G 4 HOH A 52 752 52 HOH HOH . G 4 HOH A 53 753 53 HOH HOH . G 4 HOH A 54 754 54 HOH HOH . G 4 HOH A 55 755 55 HOH HOH . G 4 HOH A 56 756 56 HOH HOH . G 4 HOH A 57 757 57 HOH HOH . G 4 HOH A 58 758 58 HOH HOH . G 4 HOH A 59 759 59 HOH HOH . G 4 HOH A 60 760 60 HOH HOH . G 4 HOH A 61 761 61 HOH HOH . G 4 HOH A 62 762 62 HOH HOH . G 4 HOH A 63 763 63 HOH HOH . G 4 HOH A 64 764 64 HOH HOH . G 4 HOH A 65 765 65 HOH HOH . G 4 HOH A 66 766 66 HOH HOH . G 4 HOH A 67 767 67 HOH HOH . G 4 HOH A 68 768 68 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 C1 EVP . . . F 3 28.92 -7.757 16.79 1 43.26 ? C1 EVP 605 A 1 HETATM 2 O O1 EVP . . . F 3 28.663 -6.671 17.69 1 44.07 ? O1 EVP 605 A 1 HETATM 3 C C2 EVP . . . F 3 30.851 -7.238 17.812 1 40.31 ? C2 EVP 605 A 1 HETATM 4 O O2 EVP . . . F 3 30.217 -8.281 17.21 1 46.9 ? O2 EVP 605 A 1 HETATM 5 C C3 EVP . . . F 3 32.207 -7.025 18.154 1 39.71 ? C3 EVP 605 A 1 HETATM 6 O O3 EVP . . . F 3 35.232 -1.975 19.292 1 35.01 ? O3 EVP 605 A 1 HETATM 7 C C4 EVP . . . F 3 32.611 -5.867 18.75 1 40.11 ? C4 EVP 605 A 1 HETATM 8 O O4 EVP . . . F 3 36.614 -3.869 18.496 1 47.69 ? O4 EVP 605 A 1 HETATM 9 C C5 EVP . . . F 3 34.114 -5.66 19.136 1 33.28 ? C5 EVP 605 A 1 HETATM 10 O O5 EVP . . . F 3 38.742 -7.471 18.696 1 37.97 ? O5 EVP 605 A 1 HETATM 11 C C6 EVP . . . F 3 34.354 -4.185 19.455 1 32.88 ? C6 EVP 605 A 1 HETATM 12 O O6 EVP . . . F 3 38.389 -8.216 16.052 1 26.38 ? O6 EVP 605 A 1 HETATM 13 C C7 EVP . . . F 3 35.557 -3.482 19 1 37.94 ? C7 EVP 605 A 1 HETATM 14 O O7 EVP . . . F 3 36.208 -7.833 14.816 1 35.99 ? O7 EVP 605 A 1 HETATM 15 C C8 EVP . . . F 3 33.662 -1.816 19.005 1 35.59 ? C8 EVP 605 A 1 HETATM 16 O O8 EVP . . . F 3 32.308 -3.795 21.116 1 49.32 ? O8 EVP 605 A 1 HETATM 17 C C9 EVP . . . F 3 33.195 -3.268 18.991 1 36.11 ? C9 EVP 605 A 1 HETATM 18 O O9 EVP . . . F 3 31.054 -3.693 23.05 1 44.95 ? O9 EVP 605 A 1 HETATM 19 C C10 EVP . . . F 3 32.006 -3.498 19.772 1 37.33 ? C10 EVP 605 A 1 HETATM 20 O O10 EVP . . . F 3 28.764 -2.989 25.801 1 45.77 ? O10 EVP 605 A 1 HETATM 21 C C11 EVP . . . F 3 31.581 -4.844 19.07 1 39.68 ? C11 EVP 605 A 1 HETATM 22 O O11 EVP . . . F 3 29.821 -0.997 25.205 1 63.17 ? O11 EVP 605 A 1 HETATM 23 C C12 EVP . . . F 3 30.284 -5.042 18.734 1 39.2 ? C12 EVP 605 A 1 HETATM 24 O O12 EVP . . . F 3 31.435 0.426 23.337 1 37.67 ? O12 EVP 605 A 1 HETATM 25 C C13 EVP . . . F 3 29.885 -6.241 18.104 1 39.97 ? C13 EVP 605 A 1 HETATM 26 O O13 EVP . . . F 3 32.217 -0.682 21.247 1 41.69 ? O13 EVP 605 A 1 HETATM 27 C C14 EVP . . . F 3 35.195 -6.35 18.234 1 27.43 ? C14 EVP 605 A 1 HETATM 28 C C15 EVP . . . F 3 36.546 -6.695 18.729 1 25.26 ? C15 EVP 605 A 1 HETATM 29 C C16 EVP . . . F 3 37.518 -7.28 18.023 1 28.39 ? C16 EVP 605 A 1 HETATM 30 C C17 EVP . . . F 3 37.36 -7.601 16.811 1 37.17 ? C17 EVP 605 A 1 HETATM 31 C C18 EVP . . . F 3 36.251 -7.404 16.192 1 34.6 ? C18 EVP 605 A 1 HETATM 32 C C19 EVP . . . F 3 35.061 -6.787 16.751 1 33.76 ? C19 EVP 605 A 1 HETATM 33 C C20 EVP . . . F 3 39.398 -8.712 18.728 1 30.27 ? C20 EVP 605 A 1 HETATM 34 C C21 EVP . . . F 3 36.566 -6.805 13.888 1 39.21 ? C21 EVP 605 A 1 HETATM 35 C C22 EVP . . . F 3 31.956 -2.976 22.204 1 41.95 ? C22 EVP 605 A 1 HETATM 36 C C23 EVP . . . F 3 30.571 -3.049 24.251 1 47.32 ? C23 EVP 605 A 1 HETATM 37 C C24 EVP . . . F 3 29.281 -3.678 24.681 1 49.95 ? C24 EVP 605 A 1 HETATM 38 C C25 EVP . . . F 3 28.594 -1.558 25.665 1 48.28 ? C25 EVP 605 A 1 HETATM 39 C C26 EVP . . . F 3 30.256 -1.63 24.01 1 54.51 ? C26 EVP 605 A 1 HETATM 40 C C27 EVP . . . F 3 31.455 -0.983 23.372 1 38.78 ? C27 EVP 605 A 1 HETATM 41 C C28 EVP . . . F 3 31.411 -1.538 21.977 1 36.95 ? C28 EVP 605 A 1 HETATM 42 C C29 EVP . . . F 3 28.214 -0.951 26.97 1 53.01 ? C29 EVP 605 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 42 #