data_8EPS # _model_server_result.job_id lrU4uQrSKpbx7X0k6_QRmg _model_server_result.datetime_utc '2024-10-25 20:36:17' _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 8eps # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 8EPS # _exptl.entry_id 8EPS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 387.285 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-{(S)-hydroxy[(prop-2-en-1-yl)oxy]phosphoryl}adenosine" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 66.22 _cell.angle_beta 73.16 _cell.angle_gamma 89.32 _cell.entry_id 8EPS _cell.length_a 63.138 _cell.length_b 86.889 _cell.length_c 105.861 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EPS _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C13 H18 N5 O7 P' _chem_comp.formula_weight 387.285 _chem_comp.id WPO _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-{(S)-hydroxy[(prop-2-en-1-yl)oxy]phosphoryl}adenosine" _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 C3P C2P WPO doub 376 n n C2P C1P WPO sing 377 n n C1P O3P WPO sing 378 n n O1P P WPO doub 379 n n O3P P WPO sing 380 n n N6 C6 WPO sing 381 n n N7 C8 WPO doub 382 n y N7 C5 WPO sing 383 n y P O2P WPO sing 384 n n P O5' WPO sing 385 n n C8 N9 WPO sing 386 n y C6 C5 WPO doub 387 n y C6 N1 WPO sing 388 n y C5 C4 WPO sing 389 n y O5' C5' WPO sing 390 n n N1 C2 WPO doub 391 n y N9 C4 WPO sing 392 n y N9 C1' WPO sing 393 n n C4 N3 WPO doub 394 n y O4' C1' WPO sing 395 n n O4' C4' WPO sing 396 n n C5' C4' WPO sing 397 n n C1' C2' WPO sing 398 n n C2 N3 WPO sing 399 n y C4' C3' WPO sing 400 n n C2' C3' WPO sing 401 n n C2' O2' WPO sing 402 n n C3' O3' WPO sing 403 n n O2' H1 WPO sing 404 n n C2' H2 WPO sing 405 n n C1' H3 WPO sing 406 n n C4' H4 WPO sing 407 n n C5' H5 WPO sing 408 n n C5' H6 WPO sing 409 n n O2P H7 WPO sing 410 n n C1P H8 WPO sing 411 n n C1P H9 WPO sing 412 n n C2P H10 WPO sing 413 n n C3P H11 WPO sing 414 n n C3P H12 WPO sing 415 n n C3' H13 WPO sing 416 n n O3' H14 WPO sing 417 n n C8 H15 WPO sing 418 n n C2 H16 WPO sing 419 n n N6 H17 WPO sing 420 n n N6 H18 WPO sing 421 n n # _atom_sites.entry_id 8EPS _atom_sites.fract_transf_matrix[1][1] 0.015838 _atom_sites.fract_transf_matrix[1][2] -0.000188 _atom_sites.fract_transf_matrix[1][3] -0.00519 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01151 _atom_sites.fract_transf_matrix[2][3] -0.005292 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010863 _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 2 WPO A 1 701 1 WPO 194 . E 2 WPO B 1 701 2 WPO 194 . F 2 WPO C 1 701 3 WPO 194 . G 3 HOH A 1 801 182 HOH HOH . G 3 HOH A 2 802 53 HOH HOH . G 3 HOH A 3 803 154 HOH HOH . G 3 HOH A 4 804 119 HOH HOH . G 3 HOH A 5 805 34 HOH HOH . G 3 HOH A 6 806 132 HOH HOH . G 3 HOH A 7 807 1 HOH HOH . G 3 HOH A 8 808 147 HOH HOH . G 3 HOH A 9 809 188 HOH HOH . G 3 HOH A 10 810 177 HOH HOH . G 3 HOH A 11 811 152 HOH HOH . G 3 HOH A 12 812 92 HOH HOH . G 3 HOH A 13 813 114 HOH HOH . G 3 HOH A 14 814 164 HOH HOH . G 3 HOH A 15 815 5 HOH HOH . G 3 HOH A 16 816 141 HOH HOH . G 3 HOH A 17 817 112 HOH HOH . G 3 HOH A 18 818 166 HOH HOH . G 3 HOH A 19 819 95 HOH HOH . G 3 HOH A 20 820 117 HOH HOH . G 3 HOH A 21 821 49 HOH HOH . G 3 HOH A 22 822 127 HOH HOH . G 3 HOH A 23 823 175 HOH HOH . G 3 HOH A 24 824 163 HOH HOH . G 3 HOH A 25 825 90 HOH HOH . G 3 HOH A 26 826 96 HOH HOH . G 3 HOH A 27 827 162 HOH HOH . G 3 HOH A 28 828 70 HOH HOH . G 3 HOH A 29 829 41 HOH HOH . G 3 HOH A 30 830 80 HOH HOH . G 3 HOH A 31 831 155 HOH HOH . G 3 HOH A 32 832 27 HOH HOH . G 3 HOH A 33 833 8 HOH HOH . G 3 HOH A 34 834 68 HOH HOH . G 3 HOH A 35 835 105 HOH HOH . G 3 HOH A 36 836 15 HOH HOH . G 3 HOH A 37 837 35 HOH HOH . G 3 HOH A 38 838 128 HOH HOH . G 3 HOH A 39 839 57 HOH HOH . G 3 HOH A 40 840 126 HOH HOH . G 3 HOH A 41 841 61 HOH HOH . G 3 HOH A 42 842 39 HOH HOH . G 3 HOH A 43 843 133 HOH HOH . G 3 HOH A 44 844 137 HOH HOH . G 3 HOH A 45 845 200 HOH HOH . G 3 HOH A 46 846 172 HOH HOH . G 3 HOH A 47 847 150 HOH HOH . G 3 HOH A 48 848 17 HOH HOH . G 3 HOH A 49 849 176 HOH HOH . G 3 HOH A 50 850 130 HOH HOH . G 3 HOH A 51 851 125 HOH HOH . G 3 HOH A 52 852 110 HOH HOH . G 3 HOH A 53 853 108 HOH HOH . G 3 HOH A 54 854 59 HOH HOH . G 3 HOH A 55 855 46 HOH HOH . G 3 HOH A 56 856 11 HOH HOH . G 3 HOH A 57 857 87 HOH HOH . G 3 HOH A 58 858 102 HOH HOH . G 3 HOH A 59 859 18 HOH HOH . G 3 HOH A 60 860 99 HOH HOH . G 3 HOH A 61 861 197 HOH HOH . G 3 HOH A 62 862 156 HOH HOH . G 3 HOH A 63 863 103 HOH HOH . G 3 HOH A 64 864 187 HOH HOH . G 3 HOH A 65 865 148 HOH HOH . G 3 HOH A 66 866 7 HOH HOH . G 3 HOH A 67 867 189 HOH HOH . G 3 HOH A 68 868 123 HOH HOH . G 3 HOH A 69 869 120 HOH HOH . G 3 HOH A 70 870 184 HOH HOH . G 3 HOH A 71 871 55 HOH HOH . G 3 HOH A 72 872 201 HOH HOH . G 3 HOH A 73 873 118 HOH HOH . G 3 HOH A 74 874 19 HOH HOH . G 3 HOH A 75 875 116 HOH HOH . G 3 HOH A 76 876 64 HOH HOH . G 3 HOH A 77 877 193 HOH HOH . G 3 HOH A 78 878 168 HOH HOH . G 3 HOH A 79 879 149 HOH HOH . G 3 HOH A 80 880 140 HOH HOH . G 3 HOH A 81 881 67 HOH HOH . G 3 HOH A 82 882 33 HOH HOH . H 3 HOH B 1 801 6 HOH HOH . H 3 HOH B 2 802 21 HOH HOH . H 3 HOH B 3 803 89 HOH HOH . H 3 HOH B 4 804 100 HOH HOH . H 3 HOH B 5 805 136 HOH HOH . H 3 HOH B 6 806 192 HOH HOH . H 3 HOH B 7 807 47 HOH HOH . H 3 HOH B 8 808 38 HOH HOH . H 3 HOH B 9 809 151 HOH HOH . H 3 HOH B 10 810 54 HOH HOH . H 3 HOH B 11 811 157 HOH HOH . H 3 HOH B 12 812 178 HOH HOH . H 3 HOH B 13 813 198 HOH HOH . H 3 HOH B 14 814 32 HOH HOH . H 3 HOH B 15 815 98 HOH HOH . H 3 HOH B 16 816 26 HOH HOH . H 3 HOH B 17 817 76 HOH HOH . H 3 HOH B 18 818 20 HOH HOH . H 3 HOH B 19 819 171 HOH HOH . H 3 HOH B 20 820 81 HOH HOH . H 3 HOH B 21 821 170 HOH HOH . H 3 HOH B 22 822 88 HOH HOH . H 3 HOH B 23 823 10 HOH HOH . H 3 HOH B 24 824 101 HOH HOH . H 3 HOH B 25 825 131 HOH HOH . H 3 HOH B 26 826 191 HOH HOH . H 3 HOH B 27 827 142 HOH HOH . H 3 HOH B 28 828 62 HOH HOH . H 3 HOH B 29 829 45 HOH HOH . H 3 HOH B 30 830 194 HOH HOH . H 3 HOH B 31 831 93 HOH HOH . H 3 HOH B 32 832 115 HOH HOH . H 3 HOH B 33 833 23 HOH HOH . H 3 HOH B 34 834 60 HOH HOH . H 3 HOH B 35 835 106 HOH HOH . H 3 HOH B 36 836 48 HOH HOH . H 3 HOH B 37 837 77 HOH HOH . H 3 HOH B 38 838 153 HOH HOH . H 3 HOH B 39 839 135 HOH HOH . H 3 HOH B 40 840 30 HOH HOH . H 3 HOH B 41 841 37 HOH HOH . H 3 HOH B 42 842 185 HOH HOH . H 3 HOH B 43 843 28 HOH HOH . H 3 HOH B 44 844 109 HOH HOH . H 3 HOH B 45 845 180 HOH HOH . H 3 HOH B 46 846 146 HOH HOH . H 3 HOH B 47 847 161 HOH HOH . H 3 HOH B 48 848 129 HOH HOH . H 3 HOH B 49 849 138 HOH HOH . I 3 HOH C 1 801 22 HOH HOH . I 3 HOH C 2 802 139 HOH HOH . I 3 HOH C 3 803 4 HOH HOH . I 3 HOH C 4 804 25 HOH HOH . I 3 HOH C 5 805 69 HOH HOH . I 3 HOH C 6 806 183 HOH HOH . I 3 HOH C 7 807 58 HOH HOH . I 3 HOH C 8 808 124 HOH HOH . I 3 HOH C 9 809 31 HOH HOH . I 3 HOH C 10 810 83 HOH HOH . I 3 HOH C 11 811 75 HOH HOH . I 3 HOH C 12 812 74 HOH HOH . I 3 HOH C 13 813 91 HOH HOH . I 3 HOH C 14 814 78 HOH HOH . I 3 HOH C 15 815 16 HOH HOH . I 3 HOH C 16 816 173 HOH HOH . I 3 HOH C 17 817 2 HOH HOH . I 3 HOH C 18 818 121 HOH HOH . I 3 HOH C 19 819 174 HOH HOH . I 3 HOH C 20 820 199 HOH HOH . I 3 HOH C 21 821 107 HOH HOH . I 3 HOH C 22 822 195 HOH HOH . I 3 HOH C 23 823 44 HOH HOH . I 3 HOH C 24 824 40 HOH HOH . I 3 HOH C 25 825 165 HOH HOH . I 3 HOH C 26 826 113 HOH HOH . I 3 HOH C 27 827 97 HOH HOH . I 3 HOH C 28 828 29 HOH HOH . I 3 HOH C 29 829 111 HOH HOH . I 3 HOH C 30 830 24 HOH HOH . I 3 HOH C 31 831 73 HOH HOH . I 3 HOH C 32 832 85 HOH HOH . I 3 HOH C 33 833 72 HOH HOH . I 3 HOH C 34 834 143 HOH HOH . I 3 HOH C 35 835 9 HOH HOH . I 3 HOH C 36 836 14 HOH HOH . I 3 HOH C 37 837 186 HOH HOH . I 3 HOH C 38 838 51 HOH HOH . I 3 HOH C 39 839 181 HOH HOH . I 3 HOH C 40 840 169 HOH HOH . I 3 HOH C 41 841 159 HOH HOH . I 3 HOH C 42 842 65 HOH HOH . I 3 HOH C 43 843 158 HOH HOH . I 3 HOH C 44 844 104 HOH HOH . I 3 HOH C 45 845 63 HOH HOH . I 3 HOH C 46 846 42 HOH HOH . I 3 HOH C 47 847 179 HOH HOH . I 3 HOH C 48 848 190 HOH HOH . I 3 HOH C 49 849 144 HOH HOH . I 3 HOH C 50 850 43 HOH HOH . I 3 HOH C 51 851 82 HOH HOH . I 3 HOH C 52 852 145 HOH HOH . I 3 HOH C 53 853 52 HOH HOH . I 3 HOH C 54 854 71 HOH HOH . I 3 HOH C 55 855 94 HOH HOH . I 3 HOH C 56 856 196 HOH HOH . I 3 HOH C 57 857 160 HOH HOH . I 3 HOH C 58 858 79 HOH HOH . I 3 HOH C 59 859 167 HOH HOH . I 3 HOH C 60 860 13 HOH HOH . I 3 HOH C 61 861 66 HOH HOH . I 3 HOH C 62 862 56 HOH HOH . I 3 HOH C 63 863 12 HOH HOH . I 3 HOH C 64 864 122 HOH HOH . I 3 HOH C 65 865 134 HOH HOH . I 3 HOH C 66 866 50 HOH HOH . I 3 HOH C 67 867 84 HOH HOH . I 3 HOH C 68 868 3 HOH HOH . I 3 HOH C 69 869 36 HOH HOH . I 3 HOH C 70 870 203 HOH HOH . I 3 HOH C 71 871 86 HOH HOH . I 3 HOH C 72 872 204 HOH HOH . I 3 HOH C 73 873 202 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 O O2' WPO . . . D 2 14.301 -27.074 10.706 1 30.76 ? O2' WPO 701 A 1 HETATM 2 C C2' WPO . . . D 2 14.912 -26.012 10.004 1 35.22 ? C2' WPO 701 A 1 HETATM 3 C C1' WPO . . . D 2 14.947 -26.319 8.505 1 34.11 ? C1' WPO 701 A 1 HETATM 4 O O4' WPO . . . D 2 13.735 -25.805 7.951 1 37.67 ? O4' WPO 701 A 1 HETATM 5 C C4' WPO . . . D 2 12.959 -25.202 9.011 1 39.85 ? C4' WPO 701 A 1 HETATM 6 C C5' WPO . . . D 2 12.091 -24.097 8.472 1 34.4 ? C5' WPO 701 A 1 HETATM 7 O O5' WPO . . . D 2 11.031 -24.658 7.67 1 41.86 ? O5' WPO 701 A 1 HETATM 8 P P WPO . . . D 2 10.359 -23.602 6.672 1 40.97 ? P WPO 701 A 1 HETATM 9 O O1P WPO . . . D 2 9.446 -24.333 5.759 1 33.61 -1 O1P WPO 701 A 1 HETATM 10 O O2P WPO . . . D 2 9.868 -22.44 7.455 1 36.45 ? O2P WPO 701 A 1 HETATM 11 O O3P WPO . . . D 2 11.705 -23.176 5.915 1 43.58 ? O3P WPO 701 A 1 HETATM 12 C C1P WPO . . . D 2 11.729 -21.988 5.131 1 39.5 ? C1P WPO 701 A 1 HETATM 13 C C2P WPO . . . D 2 13.137 -21.524 5.076 1 38.11 ? C2P WPO 701 A 1 HETATM 14 C C3P WPO . . . D 2 14.139 -22.249 4.673 1 42 ? C3P WPO 701 A 1 HETATM 15 C C3' WPO . . . D 2 14.023 -24.769 10.021 1 35.24 ? C3' WPO 701 A 1 HETATM 16 O O3' WPO . . . D 2 13.412 -24.449 11.262 1 40.27 ? O3' WPO 701 A 1 HETATM 17 N N9 WPO . . . D 2 16.067 -25.695 7.797 1 33.57 ? N9 WPO 701 A 1 HETATM 18 C C8 WPO . . . D 2 16.005 -24.668 6.89 1 32.04 ? C8 WPO 701 A 1 HETATM 19 N N7 WPO . . . D 2 17.173 -24.312 6.413 1 39.69 ? N7 WPO 701 A 1 HETATM 20 C C5 WPO . . . D 2 18.067 -25.161 7.052 1 36.71 ? C5 WPO 701 A 1 HETATM 21 C C4 WPO . . . D 2 17.399 -26.017 7.907 1 33.59 ? C4 WPO 701 A 1 HETATM 22 N N3 WPO . . . D 2 17.957 -26.965 8.68 1 33.64 ? N3 WPO 701 A 1 HETATM 23 C C2 WPO . . . D 2 19.277 -26.99 8.528 1 41.6 ? C2 WPO 701 A 1 HETATM 24 N N1 WPO . . . D 2 20.052 -26.231 7.745 1 47.98 ? N1 WPO 701 A 1 HETATM 25 C C6 WPO . . . D 2 19.467 -25.285 6.973 1 37.2 ? C6 WPO 701 A 1 HETATM 26 N N6 WPO . . . D 2 20.238 -24.529 6.194 1 38.81 ? N6 WPO 701 A 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #