data_8VTK # _model_server_result.job_id NlAfpNQRsX9o9MxOABAcPA _model_server_result.datetime_utc '2025-07-31 15:16:55' _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 8vtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":404}' # _entry.id 8VTK # _exptl.entry_id 8VTK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.914 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPHEROIDENE _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 8VTK _cell.length_a 140.95 _cell.length_b 140.95 _cell.length_c 186.72 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I,J,K,L,M,N,O,P,Q,R,S _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 10 _struct_asym.id N _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 covale ? covale1 C C LEU 208 M LEU 209 1_555 C N 2L5 209 M 2L5 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 C C 2L5 209 M 2L5 210 1_555 C N GLY 210 M GLY 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _chem_comp.formula 'C41 H60 O' _chem_comp.formula_weight 568.914 _chem_comp.id SPO _chem_comp.mon_nstd_flag . _chem_comp.name SPHEROIDENE _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 CM1 O1 SPO sing 908 n n CM1 HM11 SPO sing 909 n n CM1 HM12 SPO sing 910 n n CM1 HM13 SPO sing 911 n n O1 C1 SPO sing 912 n n C1 C2 SPO sing 913 n n C1 C3 SPO sing 914 n n C1 C4 SPO sing 915 n n C2 H21A SPO sing 916 n n C2 H22A SPO sing 917 n n C2 H23 SPO sing 918 n n C3 H31 SPO sing 919 n n C3 H32A SPO sing 920 n n C3 H33 SPO sing 921 n n C4 C5 SPO sing 922 n n C4 H41 SPO sing 923 n n C4 H42 SPO sing 924 n n C5 C6 SPO doub 925 e n C5 H5 SPO sing 926 n n C6 C7 SPO sing 927 n n C6 H6 SPO sing 928 n n C7 C8 SPO sing 929 n n C7 C9 SPO doub 930 e n C8 H81 SPO sing 931 n n C8 H82 SPO sing 932 n n C8 H83 SPO sing 933 n n C9 C10 SPO sing 934 n n C9 H9 SPO sing 935 n n C10 C11 SPO doub 936 e n C10 H10 SPO sing 937 n n C11 C12 SPO sing 938 n n C11 H11 SPO sing 939 n n C12 C13 SPO sing 940 n n C12 C14 SPO doub 941 e n C13 H131 SPO sing 942 n n C13 H132 SPO sing 943 n n C13 H133 SPO sing 944 n n C14 C15 SPO sing 945 n n C14 H14 SPO sing 946 n n C15 C16 SPO doub 947 e n C15 H15 SPO sing 948 n n C16 C17 SPO sing 949 n n C16 H16 SPO sing 950 n n C17 C18 SPO sing 951 n n C17 C19 SPO doub 952 z n C18 H181 SPO sing 953 n n C18 H182 SPO sing 954 n n C18 H183 SPO sing 955 n n C19 C20 SPO sing 956 n n C19 H19 SPO sing 957 n n C20 C21 SPO doub 958 e n C20 H20 SPO sing 959 n n C21 C22 SPO sing 960 n n C21 H21 SPO sing 961 n n C22 C23 SPO doub 962 e n C22 H22 SPO sing 963 n n C23 C24 SPO sing 964 n n C23 C25 SPO sing 965 n n C24 H241 SPO sing 966 n n C24 H242 SPO sing 967 n n C24 H243 SPO sing 968 n n C25 C26 SPO doub 969 e n C25 H25 SPO sing 970 n n C26 C27 SPO sing 971 n n C26 H26 SPO sing 972 n n C27 C28 SPO doub 973 e n C27 H27 SPO sing 974 n n C28 C29 SPO sing 975 n n C28 C30 SPO sing 976 n n C29 H291 SPO sing 977 n n C29 H292 SPO sing 978 n n C29 H293 SPO sing 979 n n C30 C31 SPO sing 980 n n C30 H301 SPO sing 981 n n C30 H302 SPO sing 982 n n C31 C32 SPO sing 983 n n C31 H311 SPO sing 984 n n C31 H312 SPO sing 985 n n C32 C33 SPO doub 986 e n C32 H32 SPO sing 987 n n C33 C34 SPO sing 988 n n C33 C35 SPO sing 989 n n C34 H341 SPO sing 990 n n C34 H342 SPO sing 991 n n C34 H343 SPO sing 992 n n C35 C36 SPO sing 993 n n C35 H351 SPO sing 994 n n C35 H352 SPO sing 995 n n C36 C37 SPO sing 996 n n C36 H361 SPO sing 997 n n C36 H362 SPO sing 998 n n C37 C38 SPO doub 999 n n C37 H37 SPO sing 1000 n n C38 C39 SPO sing 1001 n n C38 C40 SPO sing 1002 n n C39 H391 SPO sing 1003 n n C39 H392 SPO sing 1004 n n C39 H393 SPO sing 1005 n n C40 H401 SPO sing 1006 n n C40 H402 SPO sing 1007 n n C40 H403 SPO sing 1008 n n # _atom_sites.entry_id 8VTK _atom_sites.fract_transf_matrix[1][1] 0.007095 _atom_sites.fract_transf_matrix[1][2] 0.004096 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008192 _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] 0.005356 _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 D 4 FE L 1 301 406 FE FE . E 5 BPH L 1 302 407 BPH BPH . F 6 BCL L 1 303 301 BCL BCL . G 5 BPH L 1 304 302 BPH BPH . H 7 U10 L 1 305 303 U10 U10 . I 6 BCL L 1 306 304 BCL BCL . J 8 CL L 1 307 306 CL CL . K 6 BCL M 1 401 401 BCL BCL . L 9 LDA M 1 402 403 LDA LDA . M 9 LDA M 1 403 405 LDA LDA . N 10 SPO M 1 404 409 SPO SPO . O 11 CDL M 1 405 410 CDL CDL . P 6 BCL M 1 406 305 BCL BCL . Q 12 HOH H 1 301 3 HOH HOH . Q 12 HOH H 2 302 7 HOH HOH . Q 12 HOH H 3 303 2 HOH HOH . Q 12 HOH H 4 304 12 HOH HOH . Q 12 HOH H 5 305 9 HOH HOH . R 12 HOH L 1 401 15 HOH HOH . R 12 HOH L 2 402 6 HOH HOH . R 12 HOH L 3 403 11 HOH HOH . R 12 HOH L 4 404 1 HOH HOH . S 12 HOH M 1 501 13 HOH HOH . S 12 HOH M 2 502 8 HOH HOH . S 12 HOH M 3 503 14 HOH HOH . S 12 HOH M 4 504 17 HOH HOH . S 12 HOH M 5 505 16 HOH HOH . S 12 HOH M 6 506 19 HOH HOH . S 12 HOH M 7 507 20 HOH HOH . S 12 HOH M 8 508 10 HOH HOH . S 12 HOH M 9 509 5 HOH HOH . S 12 HOH M 10 510 18 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 CM1 SPO . . . N 10 -27.283 37.581 -24.493 1 73.81 ? CM1 SPO 404 M 1 HETATM 2 O O1 SPO . . . N 10 -26.541 36.364 -24.583 1 79.6 ? O1 SPO 404 M 1 HETATM 3 C C1 SPO . . . N 10 -25.511 36.143 -23.577 1 78.62 ? C1 SPO 404 M 1 HETATM 4 C C2 SPO . . . N 10 -24.626 37.368 -23.585 1 74.13 ? C2 SPO 404 M 1 HETATM 5 C C3 SPO . . . N 10 -24.717 34.903 -23.958 1 74.6 ? C3 SPO 404 M 1 HETATM 6 C C4 SPO . . . N 10 -26.087 36.044 -22.158 1 75.37 ? C4 SPO 404 M 1 HETATM 7 C C5 SPO . . . N 10 -27.397 35.319 -22.037 1 77.28 ? C5 SPO 404 M 1 HETATM 8 C C6 SPO . . . N 10 -27.68 34.466 -21.07 1 81.68 ? C6 SPO 404 M 1 HETATM 9 C C7 SPO . . . N 10 -28.934 33.755 -20.864 1 84.32 ? C7 SPO 404 M 1 HETATM 10 C C8 SPO . . . N 10 -29.815 33.522 -22.064 1 80.54 ? C8 SPO 404 M 1 HETATM 11 C C9 SPO . . . N 10 -29.252 33.348 -19.602 1 71.27 ? C9 SPO 404 M 1 HETATM 12 C C10 SPO . . . N 10 -30.417 32.638 -19.165 1 66.76 ? C10 SPO 404 M 1 HETATM 13 C C11 SPO . . . N 10 -30.48 31.978 -17.978 1 69.93 ? C11 SPO 404 M 1 HETATM 14 C C12 SPO . . . N 10 -31.618 31.246 -17.418 1 64.73 ? C12 SPO 404 M 1 HETATM 15 C C13 SPO . . . N 10 -32.848 31.098 -18.262 1 60.38 ? C13 SPO 404 M 1 HETATM 16 C C14 SPO . . . N 10 -31.533 30.745 -16.162 1 62.08 ? C14 SPO 404 M 1 HETATM 17 C C15 SPO . . . N 10 -32.53 30.008 -15.442 1 60.78 ? C15 SPO 404 M 1 HETATM 18 C C16 SPO . . . N 10 -32.305 29.505 -14.212 1 59.66 ? C16 SPO 404 M 1 HETATM 19 C C17 SPO . . . N 10 -33.226 28.751 -13.383 1 53.19 ? C17 SPO 404 M 1 HETATM 20 C C18 SPO . . . N 10 -34.685 28.814 -13.727 1 49.72 ? C18 SPO 404 M 1 HETATM 21 C C19 SPO . . . N 10 -32.742 28.028 -12.335 1 57.33 ? C19 SPO 404 M 1 HETATM 22 C C20 SPO . . . N 10 -33.489 27.232 -11.406 1 54.48 ? C20 SPO 404 M 1 HETATM 23 C C21 SPO . . . N 10 -32.982 26.417 -10.434 1 52.28 ? C21 SPO 404 M 1 HETATM 24 C C22 SPO . . . N 10 -31.597 26.175 -10.152 1 54.23 ? C22 SPO 404 M 1 HETATM 25 C C23 SPO . . . N 10 -31.093 25.463 -9.102 1 59.66 ? C23 SPO 404 M 1 HETATM 26 C C24 SPO . . . N 10 -31.977 24.823 -8.062 1 55.55 ? C24 SPO 404 M 1 HETATM 27 C C25 SPO . . . N 10 -29.653 25.297 -8.961 1 62.17 ? C25 SPO 404 M 1 HETATM 28 C C26 SPO . . . N 10 -29.009 24.741 -7.918 1 58.57 ? C26 SPO 404 M 1 HETATM 29 C C27 SPO . . . N 10 -27.59 24.571 -7.819 1 49.88 ? C27 SPO 404 M 1 HETATM 30 C C28 SPO . . . N 10 -26.93 24.294 -6.725 1 55.28 ? C28 SPO 404 M 1 HETATM 31 C C29 SPO . . . N 10 -27.628 24.138 -5.405 1 62.35 ? C29 SPO 404 M 1 HETATM 32 C C30 SPO . . . N 10 -25.434 24.104 -6.693 1 59.95 ? C30 SPO 404 M 1 HETATM 33 C C31 SPO . . . N 10 -25.06 22.962 -7.643 1 60.58 ? C31 SPO 404 M 1 HETATM 34 C C32 SPO . . . N 10 -23.697 22.402 -7.384 1 67.51 ? C32 SPO 404 M 1 HETATM 35 C C33 SPO . . . N 10 -23.144 21.326 -7.941 1 72.69 ? C33 SPO 404 M 1 HETATM 36 C C34 SPO . . . N 10 -23.832 20.462 -8.956 1 71.44 ? C34 SPO 404 M 1 HETATM 37 C C35 SPO . . . N 10 -21.756 20.881 -7.566 1 75.91 ? C35 SPO 404 M 1 HETATM 38 C C36 SPO . . . N 10 -20.709 21.751 -8.275 1 81.95 ? C36 SPO 404 M 1 HETATM 39 C C37 SPO . . . N 10 -19.333 21.199 -8.049 1 90.73 ? C37 SPO 404 M 1 HETATM 40 C C38 SPO . . . N 10 -18.584 21.348 -6.969 1 92.98 ? C38 SPO 404 M 1 HETATM 41 C C39 SPO . . . N 10 -19.04 22.132 -5.767 1 82.92 ? C39 SPO 404 M 1 HETATM 42 C C40 SPO . . . N 10 -17.217 20.746 -6.846 1 81.1 ? C40 SPO 404 M 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 42 #