data_1YVF # _model_server_result.job_id MmM4pJpy56jA0JXnU71GLw _model_server_result.datetime_utc '2024-12-19 10:42:45' _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 1yvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":600}' # _entry.id 1YVF # _exptl.entry_id 1YVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _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 1YVF _cell.length_a 90.879 _cell.length_b 90.879 _cell.length_c 188.516 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YVF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,B,C,D,E,F,G,H,I 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 125.677333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 1YVF _atom_sites.fract_transf_matrix[1][1] 0.011004 _atom_sites.fract_transf_matrix[1][2] 0.006353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012706 _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] 0.005305 _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 PO4 A 1 702 702 PO4 PO4 . C 3 CL A 1 701 701 CL CL . D 4 PH7 A 1 800 800 PH7 PH7 . E 5 GOL A 1 600 600 GOL GOL . F 5 GOL A 1 601 601 GOL GOL . G 5 GOL A 1 602 602 GOL GOL . H 5 GOL A 1 605 605 GOL GOL . I 6 HOH A 1 801 1 HOH HOH . I 6 HOH A 2 802 2 HOH HOH . I 6 HOH A 3 803 3 HOH HOH . I 6 HOH A 4 804 4 HOH HOH . I 6 HOH A 5 805 5 HOH HOH . I 6 HOH A 6 806 6 HOH HOH . I 6 HOH A 7 807 7 HOH HOH . I 6 HOH A 8 808 8 HOH HOH . I 6 HOH A 9 809 9 HOH HOH . I 6 HOH A 10 810 10 HOH HOH . I 6 HOH A 11 811 11 HOH HOH . I 6 HOH A 12 812 12 HOH HOH . I 6 HOH A 13 813 13 HOH HOH . I 6 HOH A 14 814 14 HOH HOH . I 6 HOH A 15 815 15 HOH HOH . I 6 HOH A 16 816 16 HOH HOH . I 6 HOH A 17 817 17 HOH HOH . I 6 HOH A 18 818 18 HOH HOH . I 6 HOH A 19 819 19 HOH HOH . I 6 HOH A 20 820 20 HOH HOH . I 6 HOH A 21 821 21 HOH HOH . I 6 HOH A 22 822 22 HOH HOH . I 6 HOH A 23 823 23 HOH HOH . I 6 HOH A 24 824 24 HOH HOH . I 6 HOH A 25 825 25 HOH HOH . I 6 HOH A 26 826 26 HOH HOH . I 6 HOH A 27 827 27 HOH HOH . I 6 HOH A 28 828 28 HOH HOH . I 6 HOH A 29 829 29 HOH HOH . I 6 HOH A 30 830 30 HOH HOH . I 6 HOH A 31 831 31 HOH HOH . I 6 HOH A 32 832 32 HOH HOH . I 6 HOH A 33 833 33 HOH HOH . I 6 HOH A 34 834 34 HOH HOH . I 6 HOH A 35 835 35 HOH HOH . I 6 HOH A 36 836 36 HOH HOH . I 6 HOH A 37 837 37 HOH HOH . I 6 HOH A 38 838 38 HOH HOH . I 6 HOH A 39 839 39 HOH HOH . I 6 HOH A 40 840 40 HOH HOH . I 6 HOH A 41 841 41 HOH HOH . I 6 HOH A 42 842 42 HOH HOH . I 6 HOH A 43 843 43 HOH HOH . I 6 HOH A 44 844 44 HOH HOH . I 6 HOH A 45 845 45 HOH HOH . I 6 HOH A 46 846 46 HOH HOH . I 6 HOH A 47 847 47 HOH HOH . I 6 HOH A 48 848 48 HOH HOH . I 6 HOH A 49 849 49 HOH HOH . I 6 HOH A 50 850 50 HOH HOH . I 6 HOH A 51 851 51 HOH HOH . I 6 HOH A 52 852 52 HOH HOH . I 6 HOH A 53 853 53 HOH HOH . I 6 HOH A 54 854 54 HOH HOH . I 6 HOH A 55 855 55 HOH HOH . I 6 HOH A 56 856 56 HOH HOH . I 6 HOH A 57 857 57 HOH HOH . I 6 HOH A 58 858 58 HOH HOH . I 6 HOH A 59 859 59 HOH HOH . I 6 HOH A 60 860 60 HOH HOH . I 6 HOH A 61 861 61 HOH HOH . I 6 HOH A 62 862 62 HOH HOH . I 6 HOH A 63 863 63 HOH HOH . I 6 HOH A 64 864 64 HOH HOH . I 6 HOH A 65 865 65 HOH HOH . I 6 HOH A 66 866 66 HOH HOH . I 6 HOH A 67 867 67 HOH HOH . I 6 HOH A 68 868 68 HOH HOH . I 6 HOH A 69 869 69 HOH HOH . I 6 HOH A 70 870 70 HOH HOH . I 6 HOH A 71 871 71 HOH HOH . I 6 HOH A 72 872 72 HOH HOH . I 6 HOH A 73 873 73 HOH HOH . I 6 HOH A 74 874 74 HOH HOH . I 6 HOH A 75 875 75 HOH HOH . I 6 HOH A 76 876 76 HOH HOH . I 6 HOH A 77 877 77 HOH HOH . I 6 HOH A 78 878 78 HOH HOH . I 6 HOH A 79 879 79 HOH HOH . I 6 HOH A 80 880 80 HOH HOH . I 6 HOH A 81 881 81 HOH HOH . I 6 HOH A 82 882 82 HOH HOH . I 6 HOH A 83 883 83 HOH HOH . I 6 HOH A 84 884 84 HOH HOH . I 6 HOH A 85 885 85 HOH HOH . I 6 HOH A 86 886 86 HOH HOH . I 6 HOH A 87 887 87 HOH HOH . I 6 HOH A 88 888 88 HOH HOH . I 6 HOH A 89 889 89 HOH HOH . I 6 HOH A 90 890 90 HOH HOH . I 6 HOH A 91 891 91 HOH HOH . I 6 HOH A 92 892 92 HOH HOH . I 6 HOH A 93 893 93 HOH HOH . I 6 HOH A 94 894 94 HOH HOH . I 6 HOH A 95 895 95 HOH HOH . I 6 HOH A 96 896 96 HOH HOH . I 6 HOH A 97 897 97 HOH HOH . I 6 HOH A 98 898 98 HOH HOH . I 6 HOH A 99 899 99 HOH HOH . I 6 HOH A 100 900 100 HOH HOH . I 6 HOH A 101 901 101 HOH HOH . I 6 HOH A 102 902 102 HOH HOH . I 6 HOH A 103 903 103 HOH HOH . I 6 HOH A 104 904 104 HOH HOH . I 6 HOH A 105 905 105 HOH HOH . I 6 HOH A 106 906 106 HOH HOH . I 6 HOH A 107 907 107 HOH HOH . I 6 HOH A 108 908 108 HOH HOH . I 6 HOH A 109 909 109 HOH HOH . I 6 HOH A 110 910 110 HOH HOH . I 6 HOH A 111 911 111 HOH HOH . I 6 HOH A 112 912 112 HOH HOH . I 6 HOH A 113 913 113 HOH HOH . I 6 HOH A 114 914 114 HOH HOH . I 6 HOH A 115 915 115 HOH HOH . I 6 HOH A 116 916 116 HOH HOH . I 6 HOH A 117 917 117 HOH HOH . I 6 HOH A 118 918 118 HOH HOH . I 6 HOH A 119 919 119 HOH HOH . I 6 HOH A 120 920 120 HOH HOH . I 6 HOH A 121 921 121 HOH HOH . I 6 HOH A 122 922 122 HOH HOH . I 6 HOH A 123 923 123 HOH HOH . I 6 HOH A 124 924 124 HOH HOH . I 6 HOH A 125 925 125 HOH HOH . I 6 HOH A 126 926 126 HOH HOH . I 6 HOH A 127 927 127 HOH HOH . I 6 HOH A 128 928 128 HOH HOH . I 6 HOH A 129 929 129 HOH HOH . I 6 HOH A 130 930 130 HOH HOH . I 6 HOH A 131 931 131 HOH HOH . I 6 HOH A 132 932 132 HOH HOH . I 6 HOH A 133 933 133 HOH HOH . I 6 HOH A 134 934 134 HOH HOH . I 6 HOH A 135 935 135 HOH HOH . I 6 HOH A 136 936 136 HOH HOH . I 6 HOH A 137 937 137 HOH HOH . I 6 HOH A 138 938 138 HOH HOH . I 6 HOH A 139 939 139 HOH HOH . I 6 HOH A 140 940 140 HOH HOH . I 6 HOH A 141 941 141 HOH HOH . I 6 HOH A 142 942 142 HOH HOH . I 6 HOH A 143 943 143 HOH HOH . I 6 HOH A 144 944 144 HOH HOH . I 6 HOH A 145 945 145 HOH HOH . I 6 HOH A 146 946 146 HOH HOH . I 6 HOH A 147 947 147 HOH HOH . I 6 HOH A 148 948 148 HOH HOH . I 6 HOH A 149 949 149 HOH HOH . I 6 HOH A 150 950 150 HOH HOH . I 6 HOH A 151 951 151 HOH HOH . I 6 HOH A 152 952 152 HOH HOH . I 6 HOH A 153 953 153 HOH HOH . I 6 HOH A 154 954 154 HOH HOH . I 6 HOH A 155 955 155 HOH HOH . I 6 HOH A 156 956 156 HOH HOH . I 6 HOH A 157 957 157 HOH HOH . I 6 HOH A 158 958 158 HOH HOH . I 6 HOH A 159 959 159 HOH HOH . I 6 HOH A 160 960 160 HOH HOH . I 6 HOH A 161 961 161 HOH HOH . I 6 HOH A 162 962 162 HOH HOH . I 6 HOH A 163 963 163 HOH HOH . I 6 HOH A 164 964 164 HOH HOH . I 6 HOH A 165 965 165 HOH HOH . I 6 HOH A 166 966 166 HOH HOH . I 6 HOH A 167 967 167 HOH HOH . I 6 HOH A 168 968 168 HOH HOH . I 6 HOH A 169 969 169 HOH HOH . I 6 HOH A 170 970 170 HOH HOH . I 6 HOH A 171 971 171 HOH HOH . I 6 HOH A 172 972 172 HOH HOH . I 6 HOH A 173 973 173 HOH HOH . I 6 HOH A 174 974 174 HOH HOH . I 6 HOH A 175 975 175 HOH HOH . I 6 HOH A 176 976 176 HOH HOH . I 6 HOH A 177 977 177 HOH HOH . I 6 HOH A 178 978 178 HOH HOH . I 6 HOH A 179 979 179 HOH HOH . I 6 HOH A 180 980 180 HOH HOH . I 6 HOH A 181 981 181 HOH HOH . I 6 HOH A 182 982 182 HOH HOH . I 6 HOH A 183 983 183 HOH HOH . I 6 HOH A 184 984 184 HOH HOH . I 6 HOH A 185 985 185 HOH HOH . I 6 HOH A 186 986 186 HOH HOH . I 6 HOH A 187 987 187 HOH HOH . I 6 HOH A 188 988 188 HOH HOH . I 6 HOH A 189 989 189 HOH HOH . I 6 HOH A 190 990 190 HOH HOH . I 6 HOH A 191 991 191 HOH HOH . I 6 HOH A 192 992 192 HOH HOH . I 6 HOH A 193 993 193 HOH HOH . I 6 HOH A 194 994 194 HOH HOH . I 6 HOH A 195 995 195 HOH HOH . I 6 HOH A 196 996 196 HOH HOH . I 6 HOH A 197 997 197 HOH HOH . I 6 HOH A 198 998 198 HOH HOH . I 6 HOH A 199 999 199 HOH HOH . I 6 HOH A 200 1000 200 HOH HOH . I 6 HOH A 201 1001 201 HOH HOH . I 6 HOH A 202 1002 202 HOH HOH . I 6 HOH A 203 1003 203 HOH HOH . I 6 HOH A 204 1004 204 HOH HOH . I 6 HOH A 205 1005 205 HOH HOH . I 6 HOH A 206 1006 206 HOH HOH . I 6 HOH A 207 1007 207 HOH HOH . I 6 HOH A 208 1008 208 HOH HOH . I 6 HOH A 209 1009 209 HOH HOH . I 6 HOH A 210 1010 210 HOH HOH . I 6 HOH A 211 1011 211 HOH HOH . I 6 HOH A 212 1012 212 HOH HOH . I 6 HOH A 213 1013 213 HOH HOH . I 6 HOH A 214 1014 214 HOH HOH . I 6 HOH A 215 1015 215 HOH HOH . I 6 HOH A 216 1016 216 HOH HOH . I 6 HOH A 217 1017 217 HOH HOH . I 6 HOH A 218 1018 218 HOH HOH . I 6 HOH A 219 1019 219 HOH HOH . I 6 HOH A 220 1020 220 HOH HOH . I 6 HOH A 221 1021 221 HOH HOH . I 6 HOH A 222 1022 222 HOH HOH . I 6 HOH A 223 1023 223 HOH HOH . I 6 HOH A 224 1024 224 HOH HOH . I 6 HOH A 225 1025 225 HOH HOH . I 6 HOH A 226 1026 226 HOH HOH . I 6 HOH A 227 1027 227 HOH HOH . I 6 HOH A 228 1028 228 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 GOL . . . E 5 6.255 48.631 44.722 1 60.86 ? C1 GOL 600 A 1 HETATM 2 O O1 GOL . . . E 5 5.37 47.646 45.295 1 60.64 ? O1 GOL 600 A 1 HETATM 3 C C2 GOL . . . E 5 6.034 49.288 43.295 1 60.88 ? C2 GOL 600 A 1 HETATM 4 O O2 GOL . . . E 5 4.723 49.481 42.786 1 59.15 ? O2 GOL 600 A 1 HETATM 5 C C3 GOL . . . E 5 6.657 50.699 43.24 1 60.51 ? C3 GOL 600 A 1 HETATM 6 O O3 GOL . . . E 5 6.247 51.273 42.021 1 60.84 ? O3 GOL 600 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #