data_2PY4 # _model_server_result.job_id qW23DbdUdlilZREcg3Ts8A _model_server_result.datetime_utc '2024-11-23 10:47:49' _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 2py4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":777}' # _entry.id 2PY4 # _exptl.entry_id 2PY4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 2PY4 _cell.length_a 54.591 _cell.length_b 54.591 _cell.length_c 83.051 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PY4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 54.591 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 27.2955 47.277193 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 B MG MG . A MG 200 1_555 C O1A DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc2 B MG MG . A MG 200 1_555 C O1B DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc3 B MG MG . A MG 200 1_555 C O2G DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc4 B MG MG . A MG 200 1_555 E O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc5 B MG MG . A MG 200 1_555 E O HOH . A HOH 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc6 B MG MG . A MG 200 1_555 E O HOH . A HOH 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 O4 C4 DUP doub 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 2PY4 _atom_sites.fract_transf_matrix[1][1] 0.018318 _atom_sites.fract_transf_matrix[1][2] 0.010576 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021152 _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] 0.012041 _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 MG A 1 200 200 MG MG . C 3 DUP A 1 777 777 DUP DUP . D 4 TRS A 1 201 201 TRS TRS . E 5 HOH A 1 778 1 HOH HOH . E 5 HOH A 2 779 2 HOH HOH . E 5 HOH A 3 780 3 HOH HOH . E 5 HOH A 4 781 4 HOH HOH . E 5 HOH A 5 782 5 HOH HOH . E 5 HOH A 6 783 6 HOH HOH . E 5 HOH A 7 784 7 HOH HOH . E 5 HOH A 8 785 8 HOH HOH . E 5 HOH A 9 786 9 HOH HOH . E 5 HOH A 10 787 10 HOH HOH . E 5 HOH A 11 788 11 HOH HOH . E 5 HOH A 12 789 12 HOH HOH . E 5 HOH A 13 790 14 HOH HOH . E 5 HOH A 14 791 15 HOH HOH . E 5 HOH A 15 792 16 HOH HOH . E 5 HOH A 16 793 17 HOH HOH . E 5 HOH A 17 794 18 HOH HOH . E 5 HOH A 18 795 19 HOH HOH . E 5 HOH A 19 796 20 HOH HOH . E 5 HOH A 20 797 21 HOH HOH . E 5 HOH A 21 798 22 HOH HOH . E 5 HOH A 22 799 23 HOH HOH . E 5 HOH A 23 800 24 HOH HOH . E 5 HOH A 24 801 25 HOH HOH . E 5 HOH A 25 802 26 HOH HOH . E 5 HOH A 26 803 27 HOH HOH . E 5 HOH A 27 804 28 HOH HOH . E 5 HOH A 28 805 29 HOH HOH . E 5 HOH A 29 806 30 HOH HOH . E 5 HOH A 30 807 31 HOH HOH . E 5 HOH A 31 808 32 HOH HOH . E 5 HOH A 32 809 33 HOH HOH . E 5 HOH A 33 810 35 HOH HOH . E 5 HOH A 34 811 36 HOH HOH . E 5 HOH A 35 812 37 HOH HOH . E 5 HOH A 36 813 38 HOH HOH . E 5 HOH A 37 814 39 HOH HOH . E 5 HOH A 38 815 40 HOH HOH . E 5 HOH A 39 816 41 HOH HOH . E 5 HOH A 40 817 42 HOH HOH . E 5 HOH A 41 818 43 HOH HOH . E 5 HOH A 42 819 44 HOH HOH . E 5 HOH A 43 820 45 HOH HOH . E 5 HOH A 44 821 46 HOH HOH . E 5 HOH A 45 822 47 HOH HOH . E 5 HOH A 46 823 48 HOH HOH . E 5 HOH A 47 824 49 HOH HOH . E 5 HOH A 48 825 50 HOH HOH . E 5 HOH A 49 826 51 HOH HOH . E 5 HOH A 50 827 52 HOH HOH . E 5 HOH A 51 828 53 HOH HOH . E 5 HOH A 52 829 54 HOH HOH . E 5 HOH A 53 830 55 HOH HOH . E 5 HOH A 54 831 56 HOH HOH . E 5 HOH A 55 832 57 HOH HOH . E 5 HOH A 56 833 58 HOH HOH . E 5 HOH A 57 834 59 HOH HOH . E 5 HOH A 58 835 60 HOH HOH . E 5 HOH A 59 836 61 HOH HOH . E 5 HOH A 60 837 62 HOH HOH . E 5 HOH A 61 838 63 HOH HOH . E 5 HOH A 62 839 64 HOH HOH . E 5 HOH A 63 840 65 HOH HOH . E 5 HOH A 64 841 66 HOH HOH . E 5 HOH A 65 842 67 HOH HOH . E 5 HOH A 66 843 68 HOH HOH . E 5 HOH A 67 844 69 HOH HOH . E 5 HOH A 68 845 70 HOH HOH . E 5 HOH A 69 846 71 HOH HOH . E 5 HOH A 70 847 72 HOH HOH . E 5 HOH A 71 848 73 HOH HOH . E 5 HOH A 72 849 74 HOH HOH . E 5 HOH A 73 850 75 HOH HOH . E 5 HOH A 74 851 76 HOH HOH . E 5 HOH A 75 852 77 HOH HOH . E 5 HOH A 76 853 78 HOH HOH . E 5 HOH A 77 854 79 HOH HOH . E 5 HOH A 78 855 80 HOH HOH . E 5 HOH A 79 856 81 HOH HOH . E 5 HOH A 80 857 82 HOH HOH . E 5 HOH A 81 858 83 HOH HOH . E 5 HOH A 82 859 84 HOH HOH . E 5 HOH A 83 860 85 HOH HOH . E 5 HOH A 84 861 86 HOH HOH . E 5 HOH A 85 862 87 HOH HOH . E 5 HOH A 86 863 88 HOH HOH . E 5 HOH A 87 864 89 HOH HOH . E 5 HOH A 88 865 90 HOH HOH . E 5 HOH A 89 866 91 HOH HOH . E 5 HOH A 90 867 92 HOH HOH . E 5 HOH A 91 868 93 HOH HOH . E 5 HOH A 92 869 94 HOH HOH . E 5 HOH A 93 870 95 HOH HOH . E 5 HOH A 94 871 96 HOH HOH . E 5 HOH A 95 872 97 HOH HOH . E 5 HOH A 96 873 98 HOH HOH . E 5 HOH A 97 874 99 HOH HOH . E 5 HOH A 98 875 100 HOH HOH . E 5 HOH A 99 876 101 HOH HOH . E 5 HOH A 100 877 102 HOH HOH . E 5 HOH A 101 878 103 HOH HOH . E 5 HOH A 102 879 104 HOH HOH . E 5 HOH A 103 880 105 HOH HOH . E 5 HOH A 104 881 106 HOH HOH . E 5 HOH A 105 882 107 HOH HOH . E 5 HOH A 106 883 108 HOH HOH . E 5 HOH A 107 884 109 HOH HOH . E 5 HOH A 108 885 110 HOH HOH . E 5 HOH A 109 886 111 HOH HOH . E 5 HOH A 110 887 112 HOH HOH . E 5 HOH A 111 888 113 HOH HOH . E 5 HOH A 112 889 114 HOH HOH . E 5 HOH A 113 890 115 HOH HOH . E 5 HOH A 114 891 116 HOH HOH . E 5 HOH A 115 892 117 HOH HOH . E 5 HOH A 116 893 118 HOH HOH . E 5 HOH A 117 894 119 HOH HOH . E 5 HOH A 118 895 120 HOH HOH . E 5 HOH A 119 896 121 HOH HOH . E 5 HOH A 120 897 122 HOH HOH . E 5 HOH A 121 898 123 HOH HOH . E 5 HOH A 122 899 124 HOH HOH . E 5 HOH A 123 900 125 HOH HOH . E 5 HOH A 124 901 126 HOH HOH . E 5 HOH A 125 902 127 HOH HOH . E 5 HOH A 126 903 128 HOH HOH . E 5 HOH A 127 904 129 HOH HOH . E 5 HOH A 128 905 130 HOH HOH . E 5 HOH A 129 906 131 HOH HOH . E 5 HOH A 130 907 132 HOH HOH . E 5 HOH A 131 908 133 HOH HOH . E 5 HOH A 132 909 134 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 O4 DUP . . . C 3 16.709 14.967 41.477 1 12.97 ? O4 DUP 777 A 1 HETATM 2 C C4 DUP . . . C 3 15.905 14.145 41.008 1 13.57 ? C4 DUP 777 A 1 HETATM 3 C C5 DUP . . . C 3 16.274 12.899 40.501 1 13.42 ? C5 DUP 777 A 1 HETATM 4 C C6 DUP . . . C 3 15.253 12.043 40.028 1 14.63 ? C6 DUP 777 A 1 HETATM 5 N N3 DUP . . . C 3 14.58 14.538 40.984 1 14 ? N3 DUP 777 A 1 HETATM 6 C C2 DUP . . . C 3 13.587 13.723 40.454 1 14.39 ? C2 DUP 777 A 1 HETATM 7 O O2 DUP . . . C 3 12.408 14.13 40.451 1 14.56 ? O2 DUP 777 A 1 HETATM 8 N N1 DUP . . . C 3 13.945 12.485 40.003 1 12.96 ? N1 DUP 777 A 1 HETATM 9 C C1' DUP . . . C 3 12.933 11.594 39.402 1 13.07 ? C1' DUP 777 A 1 HETATM 10 C C2' DUP . . . C 3 13.072 11.692 37.88 1 12.84 ? C2' DUP 777 A 1 HETATM 11 C C3' DUP . . . C 3 13.907 10.442 37.554 1 11.36 ? C3' DUP 777 A 1 HETATM 12 O O3' DUP . . . C 3 13.66 9.949 36.211 1 14.24 ? O3' DUP 777 A 1 HETATM 13 O O4' DUP . . . C 3 13.212 10.244 39.764 1 14.91 ? O4' DUP 777 A 1 HETATM 14 C C4' DUP . . . C 3 13.425 9.479 38.575 1 11.94 ? C4' DUP 777 A 1 HETATM 15 C C5' DUP . . . C 3 14.351 8.317 38.913 1 13.79 ? C5' DUP 777 A 1 HETATM 16 O O5' DUP . . . C 3 15.604 8.9 39.292 1 13.59 ? O5' DUP 777 A 1 HETATM 17 P PA DUP . . . C 3 16.819 7.922 39.751 1 15.78 ? PA DUP 777 A 1 HETATM 18 O O1A DUP . . . C 3 16.874 6.781 38.737 1 15.93 ? O1A DUP 777 A 1 HETATM 19 O O2A DUP . . . C 3 18.037 8.832 39.778 1 16.42 ? O2A DUP 777 A 1 HETATM 20 N N3A DUP . . . C 3 16.426 7.408 41.23 1 17.47 ? N3A DUP 777 A 1 HETATM 21 P PB DUP . . . C 3 15.974 5.83 41.55 1 16.82 ? PB DUP 777 A 1 HETATM 22 O O1B DUP . . . C 3 16.737 4.817 40.753 1 13.91 ? O1B DUP 777 A 1 HETATM 23 O O2B DUP . . . C 3 15.991 5.675 43.069 1 16.72 ? O2B DUP 777 A 1 HETATM 24 O O3B DUP . . . C 3 14.463 5.677 41.079 1 17.85 ? O3B DUP 777 A 1 HETATM 25 P PG DUP . . . C 3 13.86 4.655 40.019 1 16.24 ? PG DUP 777 A 1 HETATM 26 O O2G DUP . . . C 3 14.718 4.695 38.788 1 13.51 ? O2G DUP 777 A 1 HETATM 27 O O1G DUP . . . C 3 13.908 3.361 40.764 1 17.71 ? O1G DUP 777 A 1 HETATM 28 O O3G DUP . . . C 3 12.453 5.155 39.732 1 16.77 ? O3G DUP 777 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #