data_8W0J # _model_server_result.job_id x5OcLJIMvN02n8nOAoWPvQ _model_server_result.datetime_utc '2025-07-30 15:20:39' _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 8w0j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 8W0J # _exptl.entry_id 8W0J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 385.269 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-{(S)-hydroxy[(prop-2-yn-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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8W0J _cell.length_a 139.073 _cell.length_b 139.073 _cell.length_c 544.504 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8W0J _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA _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 # 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 Q N N ? 2 AA N N # _chem_comp.formula 'C13 H16 N5 O7 P' _chem_comp.formula_weight 385.269 _chem_comp.id YHT _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-{(S)-hydroxy[(prop-2-yn-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 C11 C12 YHT sing 416 n n C11 O6 YHT sing 417 n n C12 C13 YHT trip 418 n n O7 P1 YHT doub 419 n n O6 P1 YHT sing 420 n n P1 O4 YHT sing 421 n n P1 O5 YHT sing 422 n n N2 C4 YHT doub 423 n y N2 C5 YHT sing 424 n y N5 C8 YHT sing 425 n n C4 N1 YHT sing 426 n y O4 C10 YHT sing 427 n n C5 C8 YHT sing 428 n y C5 C6 YHT doub 429 n y C8 N4 YHT doub 430 n y O2 C3 YHT sing 431 n n O2 C9 YHT sing 432 n n N1 C6 YHT sing 433 n y N1 C3 YHT sing 434 n n C6 N3 YHT sing 435 n y N4 C7 YHT sing 436 n y C10 C9 YHT sing 437 n n C3 C2 YHT sing 438 n n C9 C1 YHT sing 439 n n C7 N3 YHT doub 440 n y C2 C1 YHT sing 441 n n C2 O3 YHT sing 442 n n C1 O1 YHT sing 443 n n C1 H1 YHT sing 444 n n C2 H2 YHT sing 445 n n C3 H3 YHT sing 446 n n C4 H4 YHT sing 447 n n C13 H5 YHT sing 448 n n C10 H6 YHT sing 449 n n C10 H7 YHT sing 450 n n C11 H8 YHT sing 451 n n C11 H9 YHT sing 452 n n C7 H10 YHT sing 453 n n C9 H11 YHT sing 454 n n N5 H12 YHT sing 455 n n N5 H13 YHT sing 456 n n O1 H14 YHT sing 457 n n O3 H15 YHT sing 458 n n O5 H16 YHT sing 459 n n # _atom_sites.entry_id 8W0J _atom_sites.fract_transf_matrix[1][1] 0.00719 _atom_sites.fract_transf_matrix[1][2] 0.004151 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008303 _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] 0.001837 _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 YHT A 1 701 1 YHT 196 . E 3 GOL A 1 702 1 GOL GOL . F 3 GOL A 1 703 4 GOL GOL . G 3 GOL A 1 704 6 GOL GOL . H 3 GOL A 1 705 8 GOL GOL . I 4 PGE A 1 706 9 PGE PGE . J 4 PGE A 1 707 11 PGE PGE . K 5 SO4 A 1 708 1 SO4 SO4 . L 5 SO4 A 1 709 2 SO4 SO4 . M 5 SO4 A 1 710 3 SO4 SO4 . N 5 SO4 A 1 711 5 SO4 SO4 . O 5 SO4 A 1 712 9 SO4 SO4 . P 5 SO4 A 1 713 12 SO4 SO4 . Q 2 YHT B 1 701 2 YHT 196 . R 3 GOL B 1 702 2 GOL GOL . S 3 GOL B 1 703 5 GOL GOL . T 4 PGE B 1 704 10 PGE PGE . U 6 CL B 1 705 1 CL CL . V 6 CL B 1 706 2 CL CL . W 5 SO4 B 1 707 6 SO4 SO4 . X 5 SO4 B 1 708 10 SO4 SO4 . Y 5 SO4 B 1 709 11 SO4 SO4 . Z 5 SO4 B 1 710 13 SO4 SO4 . AA 2 YHT C 1 701 3 YHT 196 . BA 3 GOL C 1 702 3 GOL GOL . CA 3 GOL C 1 703 7 GOL GOL . DA 5 SO4 C 1 704 4 SO4 SO4 . EA 5 SO4 C 1 705 7 SO4 SO4 . FA 5 SO4 C 1 706 8 SO4 SO4 . GA 7 HOH A 1 801 139 HOH HOH . GA 7 HOH A 2 802 79 HOH HOH . GA 7 HOH A 3 803 164 HOH HOH . GA 7 HOH A 4 804 157 HOH HOH . GA 7 HOH A 5 805 5 HOH HOH . GA 7 HOH A 6 806 125 HOH HOH . GA 7 HOH A 7 807 165 HOH HOH . GA 7 HOH A 8 808 24 HOH HOH . GA 7 HOH A 9 809 66 HOH HOH . GA 7 HOH A 10 810 9 HOH HOH . GA 7 HOH A 11 811 21 HOH HOH . GA 7 HOH A 12 812 7 HOH HOH . GA 7 HOH A 13 813 46 HOH HOH . GA 7 HOH A 14 814 60 HOH HOH . GA 7 HOH A 15 815 83 HOH HOH . GA 7 HOH A 16 816 90 HOH HOH . GA 7 HOH A 17 817 67 HOH HOH . GA 7 HOH A 18 818 62 HOH HOH . GA 7 HOH A 19 819 110 HOH HOH . GA 7 HOH A 20 820 35 HOH HOH . GA 7 HOH A 21 821 173 HOH HOH . GA 7 HOH A 22 822 86 HOH HOH . GA 7 HOH A 23 823 12 HOH HOH . GA 7 HOH A 24 824 19 HOH HOH . GA 7 HOH A 25 825 87 HOH HOH . GA 7 HOH A 26 826 101 HOH HOH . GA 7 HOH A 27 827 131 HOH HOH . GA 7 HOH A 28 828 3 HOH HOH . GA 7 HOH A 29 829 112 HOH HOH . GA 7 HOH A 30 830 151 HOH HOH . GA 7 HOH A 31 831 16 HOH HOH . GA 7 HOH A 32 832 31 HOH HOH . GA 7 HOH A 33 833 156 HOH HOH . GA 7 HOH A 34 834 152 HOH HOH . GA 7 HOH A 35 835 27 HOH HOH . GA 7 HOH A 36 836 104 HOH HOH . GA 7 HOH A 37 837 40 HOH HOH . GA 7 HOH A 38 838 75 HOH HOH . GA 7 HOH A 39 839 73 HOH HOH . GA 7 HOH A 40 840 48 HOH HOH . GA 7 HOH A 41 841 100 HOH HOH . GA 7 HOH A 42 842 116 HOH HOH . GA 7 HOH A 43 843 77 HOH HOH . GA 7 HOH A 44 844 114 HOH HOH . GA 7 HOH A 45 845 20 HOH HOH . GA 7 HOH A 46 846 69 HOH HOH . GA 7 HOH A 47 847 99 HOH HOH . GA 7 HOH A 48 848 122 HOH HOH . GA 7 HOH A 49 849 158 HOH HOH . GA 7 HOH A 50 850 34 HOH HOH . GA 7 HOH A 51 851 52 HOH HOH . GA 7 HOH A 52 852 37 HOH HOH . GA 7 HOH A 53 853 172 HOH HOH . GA 7 HOH A 54 854 160 HOH HOH . GA 7 HOH A 55 855 145 HOH HOH . GA 7 HOH A 56 856 118 HOH HOH . GA 7 HOH A 57 857 4 HOH HOH . GA 7 HOH A 58 858 30 HOH HOH . GA 7 HOH A 59 859 149 HOH HOH . GA 7 HOH A 60 860 153 HOH HOH . GA 7 HOH A 61 861 6 HOH HOH . GA 7 HOH A 62 862 8 HOH HOH . GA 7 HOH A 63 863 78 HOH HOH . GA 7 HOH A 64 864 136 HOH HOH . GA 7 HOH A 65 865 147 HOH HOH . GA 7 HOH A 66 866 64 HOH HOH . GA 7 HOH A 67 867 163 HOH HOH . GA 7 HOH A 68 868 127 HOH HOH . GA 7 HOH A 69 869 25 HOH HOH . GA 7 HOH A 70 870 105 HOH HOH . GA 7 HOH A 71 871 13 HOH HOH . GA 7 HOH A 72 872 56 HOH HOH . GA 7 HOH A 73 873 1 HOH HOH . GA 7 HOH A 74 874 162 HOH HOH . GA 7 HOH A 75 875 148 HOH HOH . GA 7 HOH A 76 876 175 HOH HOH . GA 7 HOH A 77 877 161 HOH HOH . GA 7 HOH A 78 878 17 HOH HOH . GA 7 HOH A 79 879 130 HOH HOH . GA 7 HOH A 80 880 58 HOH HOH . GA 7 HOH A 81 881 141 HOH HOH . GA 7 HOH A 82 882 135 HOH HOH . GA 7 HOH A 83 883 109 HOH HOH . GA 7 HOH A 84 884 2 HOH HOH . GA 7 HOH A 85 885 115 HOH HOH . GA 7 HOH A 86 886 126 HOH HOH . GA 7 HOH A 87 887 111 HOH HOH . GA 7 HOH A 88 888 74 HOH HOH . GA 7 HOH A 89 889 26 HOH HOH . GA 7 HOH A 90 890 123 HOH HOH . GA 7 HOH A 91 891 169 HOH HOH . GA 7 HOH A 92 892 50 HOH HOH . GA 7 HOH A 93 893 168 HOH HOH . GA 7 HOH A 94 894 171 HOH HOH . HA 7 HOH B 1 801 137 HOH HOH . HA 7 HOH B 2 802 23 HOH HOH . HA 7 HOH B 3 803 22 HOH HOH . HA 7 HOH B 4 804 55 HOH HOH . HA 7 HOH B 5 805 59 HOH HOH . HA 7 HOH B 6 806 14 HOH HOH . HA 7 HOH B 7 807 97 HOH HOH . HA 7 HOH B 8 808 103 HOH HOH . HA 7 HOH B 9 809 18 HOH HOH . HA 7 HOH B 10 810 36 HOH HOH . HA 7 HOH B 11 811 166 HOH HOH . HA 7 HOH B 12 812 94 HOH HOH . HA 7 HOH B 13 813 174 HOH HOH . HA 7 HOH B 14 814 85 HOH HOH . HA 7 HOH B 15 815 63 HOH HOH . HA 7 HOH B 16 816 167 HOH HOH . HA 7 HOH B 17 817 10 HOH HOH . HA 7 HOH B 18 818 39 HOH HOH . HA 7 HOH B 19 819 129 HOH HOH . HA 7 HOH B 20 820 120 HOH HOH . HA 7 HOH B 21 821 11 HOH HOH . HA 7 HOH B 22 822 150 HOH HOH . HA 7 HOH B 23 823 92 HOH HOH . HA 7 HOH B 24 824 93 HOH HOH . HA 7 HOH B 25 825 29 HOH HOH . HA 7 HOH B 26 826 33 HOH HOH . HA 7 HOH B 27 827 91 HOH HOH . HA 7 HOH B 28 828 41 HOH HOH . HA 7 HOH B 29 829 82 HOH HOH . HA 7 HOH B 30 830 70 HOH HOH . HA 7 HOH B 31 831 42 HOH HOH . HA 7 HOH B 32 832 49 HOH HOH . HA 7 HOH B 33 833 38 HOH HOH . HA 7 HOH B 34 834 72 HOH HOH . HA 7 HOH B 35 835 108 HOH HOH . HA 7 HOH B 36 836 140 HOH HOH . HA 7 HOH B 37 837 170 HOH HOH . HA 7 HOH B 38 838 28 HOH HOH . HA 7 HOH B 39 839 121 HOH HOH . HA 7 HOH B 40 840 65 HOH HOH . HA 7 HOH B 41 841 98 HOH HOH . HA 7 HOH B 42 842 128 HOH HOH . HA 7 HOH B 43 843 134 HOH HOH . HA 7 HOH B 44 844 54 HOH HOH . HA 7 HOH B 45 845 159 HOH HOH . HA 7 HOH B 46 846 80 HOH HOH . HA 7 HOH B 47 847 45 HOH HOH . HA 7 HOH B 48 848 138 HOH HOH . HA 7 HOH B 49 849 32 HOH HOH . HA 7 HOH B 50 850 95 HOH HOH . HA 7 HOH B 51 851 57 HOH HOH . HA 7 HOH B 52 852 51 HOH HOH . HA 7 HOH B 53 853 113 HOH HOH . HA 7 HOH B 54 854 47 HOH HOH . HA 7 HOH B 55 855 133 HOH HOH . HA 7 HOH B 56 856 71 HOH HOH . HA 7 HOH B 57 857 119 HOH HOH . HA 7 HOH B 58 858 76 HOH HOH . HA 7 HOH B 59 859 15 HOH HOH . HA 7 HOH B 60 860 117 HOH HOH . HA 7 HOH B 61 861 124 HOH HOH . HA 7 HOH B 62 862 154 HOH HOH . HA 7 HOH B 63 863 96 HOH HOH . HA 7 HOH B 64 864 61 HOH HOH . HA 7 HOH B 65 865 177 HOH HOH . HA 7 HOH B 66 866 102 HOH HOH . HA 7 HOH B 67 867 84 HOH HOH . HA 7 HOH B 68 868 81 HOH HOH . HA 7 HOH B 69 869 144 HOH HOH . HA 7 HOH B 70 870 132 HOH HOH . HA 7 HOH B 71 871 142 HOH HOH . HA 7 HOH B 72 872 176 HOH HOH . HA 7 HOH B 73 873 143 HOH HOH . IA 7 HOH C 1 801 107 HOH HOH . IA 7 HOH C 2 802 53 HOH HOH . IA 7 HOH C 3 803 89 HOH HOH . IA 7 HOH C 4 804 68 HOH HOH . IA 7 HOH C 5 805 146 HOH HOH . IA 7 HOH C 6 806 88 HOH HOH . IA 7 HOH C 7 807 44 HOH HOH . IA 7 HOH C 8 808 155 HOH HOH . IA 7 HOH C 9 809 43 HOH HOH . IA 7 HOH C 10 810 106 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 YHT . . . D 2 19.942 18.306 -16.783 1 49.86 ? C1 YHT 701 A 1 HETATM 2 C C2 YHT . . . D 2 21.101 17.388 -17.173 1 47.34 ? C2 YHT 701 A 1 HETATM 3 C C3 YHT . . . D 2 20.893 17.297 -18.687 1 49.12 ? C3 YHT 701 A 1 HETATM 4 C C4 YHT . . . D 2 21.074 19.407 -20.071 1 48.41 ? C4 YHT 701 A 1 HETATM 5 C C5 YHT . . . D 2 23.152 19.474 -20.51 1 45.52 ? C5 YHT 701 A 1 HETATM 6 C C6 YHT . . . D 2 22.96 18.342 -19.74 1 46.36 ? C6 YHT 701 A 1 HETATM 7 C C12 YHT . . . D 2 17.671 21.022 -21.09 1 50.81 ? C12 YHT 701 A 1 HETATM 8 C C13 YHT . . . D 2 18.578 21.761 -21.19 1 49.76 ? C13 YHT 701 A 1 HETATM 9 C C10 YHT . . . D 2 17.663 18.676 -17.901 1 47.78 ? C10 YHT 701 A 1 HETATM 10 C C11 YHT . . . D 2 16.57 20.068 -20.919 1 47.19 ? C11 YHT 701 A 1 HETATM 11 C C7 YHT . . . D 2 25.103 17.829 -19.817 1 45.7 ? C7 YHT 701 A 1 HETATM 12 C C8 YHT . . . D 2 24.463 19.752 -20.937 1 46.4 ? C8 YHT 701 A 1 HETATM 13 C C9 YHT . . . D 2 18.832 17.751 -17.675 1 50.15 ? C9 YHT 701 A 1 HETATM 14 N N1 YHT . . . D 2 21.615 18.304 -19.463 1 43.33 ? N1 YHT 701 A 1 HETATM 15 N N2 YHT . . . D 2 21.952 20.14 -20.712 1 47.78 ? N2 YHT 701 A 1 HETATM 16 N N3 YHT . . . D 2 23.909 17.47 -19.356 1 45.98 ? N3 YHT 701 A 1 HETATM 17 N N4 YHT . . . D 2 25.438 18.887 -20.565 1 47.23 ? N4 YHT 701 A 1 HETATM 18 N N5 YHT . . . D 2 24.788 20.81 -21.677 1 46.34 ? N5 YHT 701 A 1 HETATM 19 O O1 YHT . . . D 2 19.591 18.249 -15.405 1 53.72 ? O1 YHT 701 A 1 HETATM 20 O O2 YHT . . . D 2 19.499 17.484 -18.927 1 49.38 ? O2 YHT 701 A 1 HETATM 21 O O3 YHT . . . D 2 20.894 16.118 -16.593 1 47.55 ? O3 YHT 701 A 1 HETATM 22 O O4 YHT . . . D 2 16.632 17.998 -18.649 1 43.85 ? O4 YHT 701 A 1 HETATM 23 O O5 YHT . . . D 2 14.799 19.333 -17.615 1 56.4 ? O5 YHT 701 A 1 HETATM 24 O O6 YHT . . . D 2 15.992 20.178 -19.62 1 47.36 ? O6 YHT 701 A 1 HETATM 25 O O7 YHT . . . D 2 14.425 18.233 -19.886 1 50.33 ? O7 YHT 701 A 1 HETATM 26 P P1 YHT . . . D 2 15.337 18.897 -18.925 1 46.25 ? P1 YHT 701 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #