data_1DP2 # _model_server_result.job_id eD6TMlNqOAPj58CXyLCnXQ _model_server_result.datetime_utc '2025-02-26 14:51:51' _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 1dp2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":900}' # _entry.id 1DP2 # _exptl.entry_id 1DP2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.326 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid' _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 99.6 _cell.angle_gamma 90 _cell.entry_id 1DP2 _cell.length_a 154.36 _cell.length_b 49.31 _cell.length_c 41.68 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DP2 _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 ? _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 # 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 A C THR 246 A THR 246 1_555 A N CSS 247 A CSS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C CSS 247 A CSS 247 1_555 A N ARG 248 A ARG 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? # _chem_comp.formula 'C8 H14 O2 S2' _chem_comp.formula_weight 206.326 _chem_comp.id LPB _chem_comp.mon_nstd_flag . _chem_comp.name '5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid' _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 O1 C1 LPB doub 208 n n O2 C1 LPB sing 209 n n O2 HO2 LPB sing 210 n n C1 C2 LPB sing 211 n n C2 C3 LPB sing 212 n n C2 H21 LPB sing 213 n n C2 H22 LPB sing 214 n n C3 C4 LPB sing 215 n n C3 H31 LPB sing 216 n n C3 H32 LPB sing 217 n n C4 C5 LPB sing 218 n n C4 H41 LPB sing 219 n n C4 H42 LPB sing 220 n n C5 C6 LPB sing 221 n n C5 H51 LPB sing 222 n n C5 H52 LPB sing 223 n n C6 C7 LPB sing 224 n n C6 S6 LPB sing 225 n n C6 H6 LPB sing 226 n n C7 C8 LPB sing 227 n n C7 H71 LPB sing 228 n n C7 H72 LPB sing 229 n n C8 S8 LPB sing 230 n n C8 H81 LPB sing 231 n n C8 H82 LPB sing 232 n n S8 S6 LPB sing 233 n n # _atom_sites.entry_id 1DP2 _atom_sites.fract_transf_matrix[1][1] 0.006478 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001096 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02028 _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] 0.024333 _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 LPB A 1 900 900 LPB LIP . C 3 HOH A 1 901 1 HOH H2O . C 3 HOH A 2 902 2 HOH H2O . C 3 HOH A 3 903 3 HOH H2O . C 3 HOH A 4 904 4 HOH H2O . C 3 HOH A 5 905 5 HOH H2O . C 3 HOH A 6 906 6 HOH H2O . C 3 HOH A 7 907 7 HOH H2O . C 3 HOH A 8 908 8 HOH H2O . C 3 HOH A 9 909 9 HOH H2O . C 3 HOH A 10 910 10 HOH H2O . C 3 HOH A 11 911 11 HOH H2O . C 3 HOH A 12 912 12 HOH H2O . C 3 HOH A 13 913 13 HOH H2O . C 3 HOH A 14 914 14 HOH H2O . C 3 HOH A 15 915 15 HOH H2O . C 3 HOH A 16 916 16 HOH H2O . C 3 HOH A 17 917 17 HOH H2O . C 3 HOH A 18 918 18 HOH H2O . C 3 HOH A 19 919 19 HOH H2O . C 3 HOH A 20 920 20 HOH H2O . C 3 HOH A 21 921 21 HOH H2O . C 3 HOH A 22 922 22 HOH H2O . C 3 HOH A 23 923 23 HOH H2O . C 3 HOH A 24 924 24 HOH H2O . C 3 HOH A 25 925 25 HOH H2O . C 3 HOH A 26 926 26 HOH H2O . C 3 HOH A 27 927 27 HOH H2O . C 3 HOH A 28 928 28 HOH H2O . C 3 HOH A 29 929 29 HOH H2O . C 3 HOH A 30 930 30 HOH H2O . C 3 HOH A 31 931 31 HOH H2O . C 3 HOH A 32 932 32 HOH H2O . C 3 HOH A 33 933 33 HOH H2O . C 3 HOH A 34 934 34 HOH H2O . C 3 HOH A 35 935 35 HOH H2O . C 3 HOH A 36 936 36 HOH H2O . C 3 HOH A 37 937 37 HOH H2O . C 3 HOH A 38 938 38 HOH H2O . C 3 HOH A 39 939 39 HOH H2O . C 3 HOH A 40 940 40 HOH H2O . C 3 HOH A 41 941 41 HOH H2O . C 3 HOH A 42 942 42 HOH H2O . C 3 HOH A 43 943 43 HOH H2O . C 3 HOH A 44 944 44 HOH H2O . C 3 HOH A 45 945 45 HOH H2O . C 3 HOH A 46 946 46 HOH H2O . C 3 HOH A 47 947 47 HOH H2O . C 3 HOH A 48 948 48 HOH H2O . C 3 HOH A 49 949 49 HOH H2O . C 3 HOH A 50 950 50 HOH H2O . C 3 HOH A 51 951 51 HOH H2O . C 3 HOH A 52 952 52 HOH H2O . C 3 HOH A 53 953 53 HOH H2O . C 3 HOH A 54 954 54 HOH H2O . C 3 HOH A 55 955 55 HOH H2O . C 3 HOH A 56 956 56 HOH H2O . C 3 HOH A 57 957 57 HOH H2O . C 3 HOH A 58 958 58 HOH H2O . C 3 HOH A 59 959 59 HOH H2O . C 3 HOH A 60 960 60 HOH H2O . C 3 HOH A 61 961 61 HOH H2O . C 3 HOH A 62 962 62 HOH H2O . C 3 HOH A 63 963 63 HOH H2O . C 3 HOH A 64 964 64 HOH H2O . C 3 HOH A 65 965 65 HOH H2O . C 3 HOH A 66 966 66 HOH H2O . C 3 HOH A 67 967 67 HOH H2O . C 3 HOH A 68 968 68 HOH H2O . C 3 HOH A 69 969 69 HOH H2O . C 3 HOH A 70 970 70 HOH H2O . C 3 HOH A 71 971 71 HOH H2O . C 3 HOH A 72 972 72 HOH H2O . C 3 HOH A 73 973 73 HOH H2O . C 3 HOH A 74 974 74 HOH H2O . C 3 HOH A 75 975 75 HOH H2O . C 3 HOH A 76 976 76 HOH H2O . C 3 HOH A 77 977 77 HOH H2O . C 3 HOH A 78 978 78 HOH H2O . C 3 HOH A 79 979 79 HOH H2O . C 3 HOH A 80 980 80 HOH H2O . C 3 HOH A 81 981 81 HOH H2O . C 3 HOH A 82 982 82 HOH H2O . C 3 HOH A 83 983 83 HOH H2O . C 3 HOH A 84 984 84 HOH H2O . C 3 HOH A 85 985 85 HOH H2O . C 3 HOH A 86 986 86 HOH H2O . C 3 HOH A 87 987 87 HOH H2O . C 3 HOH A 88 988 88 HOH H2O . C 3 HOH A 89 989 89 HOH H2O . C 3 HOH A 90 990 90 HOH H2O . C 3 HOH A 91 991 91 HOH H2O . C 3 HOH A 92 992 92 HOH H2O . C 3 HOH A 93 993 93 HOH H2O . C 3 HOH A 94 994 94 HOH H2O . C 3 HOH A 95 995 95 HOH H2O . C 3 HOH A 96 996 96 HOH H2O . C 3 HOH A 97 997 97 HOH H2O . C 3 HOH A 98 998 98 HOH H2O . C 3 HOH A 99 999 99 HOH H2O . C 3 HOH A 100 1000 100 HOH H2O . C 3 HOH A 101 1001 101 HOH H2O . C 3 HOH A 102 1002 102 HOH H2O . C 3 HOH A 103 1003 103 HOH H2O . C 3 HOH A 104 1004 104 HOH H2O . C 3 HOH A 105 1005 105 HOH H2O . C 3 HOH A 106 1006 106 HOH H2O . C 3 HOH A 107 1007 107 HOH H2O . C 3 HOH A 108 1008 108 HOH H2O . C 3 HOH A 109 1009 109 HOH H2O . C 3 HOH A 110 1010 110 HOH H2O . C 3 HOH A 111 1011 111 HOH H2O . C 3 HOH A 112 1012 112 HOH H2O . # 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 O1 LPB . . . B 2 42.091 11.336 36.058 0.5 57.81 ? O1 LPB 900 A 1 HETATM 2 O O2 LPB . . . B 2 42.072 12.979 37.418 0.5 57.24 ? O2 LPB 900 A 1 HETATM 3 C C1 LPB . . . B 2 41.77 12.48 36.339 0.5 57.59 ? C1 LPB 900 A 1 HETATM 4 C C2 LPB . . . B 2 40.971 13.258 35.304 0.5 58.37 ? C2 LPB 900 A 1 HETATM 5 C C3 LPB . . . B 2 41.463 14.627 34.892 0.5 60.59 ? C3 LPB 900 A 1 HETATM 6 C C4 LPB . . . B 2 41.023 15.644 35.917 0.5 61.7 ? C4 LPB 900 A 1 HETATM 7 C C5 LPB . . . B 2 42.036 16.753 35.863 0.5 63.56 ? C5 LPB 900 A 1 HETATM 8 C C6 LPB . . . B 2 42.454 17.288 37.22 0.5 64.97 ? C6 LPB 900 A 1 HETATM 9 C C7 LPB . . . B 2 42.659 16.171 38.256 0.5 65.58 ? C7 LPB 900 A 1 HETATM 10 C C8 LPB . . . B 2 44.083 15.956 38.753 0.5 65.25 ? C8 LPB 900 A 1 HETATM 11 S S8 LPB . . . B 2 45.281 16.885 37.764 0.5 65.79 ? S8 LPB 900 A 1 HETATM 12 S S6 LPB . . . B 2 43.993 18.194 36.949 0.5 65.54 ? S6 LPB 900 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 12 #