data_2HRM # _model_server_result.job_id JYg0HMF_i_k1MtO53hMw-Q _model_server_result.datetime_utc '2024-11-24 06:00:36' _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 2hrm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":777}' # _entry.id 2HRM # _exptl.entry_id 2HRM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 386.189 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE" _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 2HRM _cell.length_a 75.65 _cell.length_b 75.65 _cell.length_c 101.558 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HRM _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _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 75.65 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 37.825 65.514822 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 # _chem_comp.formula 'C10 H16 N2 O10 P2' _chem_comp.formula_weight 386.189 _chem_comp.id UC5 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE" _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 UC5 doub 367 n n C4 C5 UC5 sing 368 n n C4 N3 UC5 sing 369 n n C5 C6 UC5 doub 370 n n C5 H5 UC5 sing 371 n n C6 N1 UC5 sing 372 n n C6 H6 UC5 sing 373 n n N3 C2 UC5 sing 374 n n N3 HN3 UC5 sing 375 n n C2 O2 UC5 doub 376 n n C2 N1 UC5 sing 377 n n N1 C1' UC5 sing 378 n n C1' C2' UC5 sing 379 n n C1' O4' UC5 sing 380 n n C1' H1' UC5 sing 381 n n C2' C3' UC5 sing 382 n n C2' "H2'1" UC5 sing 383 n n C2' "H2'2" UC5 sing 384 n n C3' O3' UC5 sing 385 n n C3' C4' UC5 sing 386 n n C3' H3' UC5 sing 387 n n O3' HO3' UC5 sing 388 n n O4' C4' UC5 sing 389 n n C4' C5' UC5 sing 390 n n C4' H4' UC5 sing 391 n n C5' O5' UC5 sing 392 n n C5' "H5'1" UC5 sing 393 n n C5' "H5'2" UC5 sing 394 n n O5' PA UC5 sing 395 n n PA O1A UC5 doub 396 n n PA O2A UC5 sing 397 n n PA C3A UC5 sing 398 n n O2A HO2A UC5 sing 399 n n C3A PB UC5 sing 400 n n C3A H3A1 UC5 sing 401 n n C3A H3A2 UC5 sing 402 n n PB O1B UC5 sing 403 n n PB O2B UC5 sing 404 n n PB O3B UC5 doub 405 n n O1B HO1B UC5 sing 406 n n O2B HO2B UC5 sing 407 n n # _atom_sites.entry_id 2HRM _atom_sites.fract_transf_matrix[1][1] 0.013219 _atom_sites.fract_transf_matrix[1][2] 0.007632 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015264 _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] 0.009847 _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 UC5 A 1 777 777 UC5 UC5 . C 3 EDO A 1 301 301 EDO EDO . D 4 HOH A 1 778 1 HOH HOH . D 4 HOH A 2 779 2 HOH HOH . D 4 HOH A 3 780 3 HOH HOH . D 4 HOH A 4 781 4 HOH HOH . D 4 HOH A 5 782 5 HOH HOH . D 4 HOH A 6 783 6 HOH HOH . D 4 HOH A 7 784 7 HOH HOH . D 4 HOH A 8 785 8 HOH HOH . D 4 HOH A 9 786 9 HOH HOH . D 4 HOH A 10 787 10 HOH HOH . D 4 HOH A 11 788 11 HOH HOH . D 4 HOH A 12 789 12 HOH HOH . D 4 HOH A 13 790 13 HOH HOH . D 4 HOH A 14 791 14 HOH HOH . D 4 HOH A 15 792 15 HOH HOH . D 4 HOH A 16 793 16 HOH HOH . D 4 HOH A 17 794 17 HOH HOH . D 4 HOH A 18 795 18 HOH HOH . D 4 HOH A 19 796 19 HOH HOH . D 4 HOH A 20 797 20 HOH HOH . D 4 HOH A 21 798 21 HOH HOH . D 4 HOH A 22 799 22 HOH HOH . D 4 HOH A 23 800 23 HOH HOH . D 4 HOH A 24 801 24 HOH HOH . D 4 HOH A 25 802 25 HOH HOH . D 4 HOH A 26 803 26 HOH HOH . D 4 HOH A 27 804 28 HOH HOH . D 4 HOH A 28 805 29 HOH HOH . D 4 HOH A 29 806 30 HOH HOH . D 4 HOH A 30 807 31 HOH HOH . D 4 HOH A 31 808 32 HOH HOH . D 4 HOH A 32 809 33 HOH HOH . D 4 HOH A 33 810 34 HOH HOH . D 4 HOH A 34 811 35 HOH HOH . D 4 HOH A 35 812 36 HOH HOH . D 4 HOH A 36 813 37 HOH HOH . D 4 HOH A 37 814 38 HOH HOH . D 4 HOH A 38 815 39 HOH HOH . D 4 HOH A 39 816 40 HOH HOH . D 4 HOH A 40 817 41 HOH HOH . D 4 HOH A 41 818 42 HOH HOH . D 4 HOH A 42 819 43 HOH HOH . D 4 HOH A 43 820 44 HOH HOH . D 4 HOH A 44 821 45 HOH HOH . D 4 HOH A 45 822 46 HOH HOH . D 4 HOH A 46 823 47 HOH HOH . D 4 HOH A 47 824 48 HOH HOH . D 4 HOH A 48 825 49 HOH HOH . D 4 HOH A 49 826 50 HOH HOH . D 4 HOH A 50 827 51 HOH HOH . D 4 HOH A 51 828 52 HOH HOH . D 4 HOH A 52 829 53 HOH HOH . D 4 HOH A 53 830 54 HOH HOH . D 4 HOH A 54 831 56 HOH HOH . D 4 HOH A 55 832 57 HOH HOH . D 4 HOH A 56 833 58 HOH HOH . D 4 HOH A 57 834 59 HOH HOH . D 4 HOH A 58 835 60 HOH HOH . D 4 HOH A 59 836 61 HOH HOH . D 4 HOH A 60 837 62 HOH HOH . D 4 HOH A 61 838 63 HOH HOH . D 4 HOH A 62 839 64 HOH HOH . D 4 HOH A 63 840 65 HOH HOH . D 4 HOH A 64 841 66 HOH HOH . D 4 HOH A 65 842 67 HOH HOH . D 4 HOH A 66 843 69 HOH HOH . D 4 HOH A 67 844 70 HOH HOH . D 4 HOH A 68 845 71 HOH HOH . D 4 HOH A 69 846 72 HOH HOH . D 4 HOH A 70 847 73 HOH HOH . D 4 HOH A 71 848 74 HOH HOH . D 4 HOH A 72 849 75 HOH HOH . D 4 HOH A 73 850 76 HOH HOH . D 4 HOH A 74 851 77 HOH HOH . D 4 HOH A 75 852 78 HOH HOH . D 4 HOH A 76 853 79 HOH HOH . D 4 HOH A 77 854 80 HOH HOH . D 4 HOH A 78 855 81 HOH HOH . D 4 HOH A 79 856 82 HOH HOH . D 4 HOH A 80 857 83 HOH HOH . D 4 HOH A 81 858 84 HOH HOH . D 4 HOH A 82 859 85 HOH HOH . D 4 HOH A 83 860 86 HOH HOH . D 4 HOH A 84 861 88 HOH HOH . D 4 HOH A 85 862 89 HOH HOH . D 4 HOH A 86 863 90 HOH HOH . D 4 HOH A 87 864 91 HOH HOH . D 4 HOH A 88 865 92 HOH HOH . D 4 HOH A 89 866 93 HOH HOH . D 4 HOH A 90 867 94 HOH HOH . D 4 HOH A 91 868 95 HOH HOH . D 4 HOH A 92 869 97 HOH HOH . D 4 HOH A 93 870 98 HOH HOH . D 4 HOH A 94 871 99 HOH HOH . D 4 HOH A 95 872 101 HOH HOH . D 4 HOH A 96 873 102 HOH HOH . D 4 HOH A 97 874 104 HOH HOH . D 4 HOH A 98 875 106 HOH HOH . D 4 HOH A 99 876 108 HOH HOH . D 4 HOH A 100 877 109 HOH HOH . D 4 HOH A 101 878 110 HOH HOH . D 4 HOH A 102 879 112 HOH HOH . D 4 HOH A 103 880 114 HOH HOH . D 4 HOH A 104 881 116 HOH HOH . D 4 HOH A 105 882 118 HOH HOH . D 4 HOH A 106 883 119 HOH HOH . D 4 HOH A 107 884 120 HOH HOH . D 4 HOH A 108 885 121 HOH HOH . D 4 HOH A 109 886 123 HOH HOH . D 4 HOH A 110 887 124 HOH HOH . D 4 HOH A 111 888 127 HOH HOH . D 4 HOH A 112 889 128 HOH HOH . D 4 HOH A 113 890 130 HOH HOH . D 4 HOH A 114 891 131 HOH HOH . D 4 HOH A 115 892 133 HOH HOH . D 4 HOH A 116 893 134 HOH HOH . D 4 HOH A 117 894 135 HOH HOH . D 4 HOH A 118 895 136 HOH HOH . D 4 HOH A 119 896 137 HOH HOH . D 4 HOH A 120 897 138 HOH HOH . D 4 HOH A 121 898 139 HOH HOH . D 4 HOH A 122 899 142 HOH HOH . D 4 HOH A 123 900 144 HOH HOH . D 4 HOH A 124 901 145 HOH HOH . D 4 HOH A 125 902 148 HOH HOH . D 4 HOH A 126 903 152 HOH HOH . D 4 HOH A 127 904 153 HOH HOH . D 4 HOH A 128 905 154 HOH HOH . D 4 HOH A 129 906 155 HOH HOH . D 4 HOH A 130 907 156 HOH HOH . D 4 HOH A 131 908 158 HOH HOH . D 4 HOH A 132 909 160 HOH HOH . D 4 HOH A 133 910 161 HOH HOH . D 4 HOH A 134 911 162 HOH HOH . D 4 HOH A 135 912 163 HOH HOH . D 4 HOH A 136 913 164 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 UC5 . . . B 2 26.501 20.997 2.495 1 20.54 ? O4 UC5 777 A 1 HETATM 2 C C4 UC5 . . . B 2 25.61 21.482 3.211 1 24.75 ? C4 UC5 777 A 1 HETATM 3 C C5 UC5 . . . B 2 25.748 22.739 3.828 1 20.17 ? C5 UC5 777 A 1 HETATM 4 C C6 UC5 . . . B 2 24.713 23.236 4.631 1 20.52 ? C6 UC5 777 A 1 HETATM 5 N N3 UC5 . . . B 2 24.448 20.779 3.4 1 19.88 ? N3 UC5 777 A 1 HETATM 6 C C2 UC5 . . . B 2 23.404 21.241 4.232 1 22.9 ? C2 UC5 777 A 1 HETATM 7 O O2 UC5 . . . B 2 22.383 20.529 4.421 1 20.51 ? O2 UC5 777 A 1 HETATM 8 N N1 UC5 . . . B 2 23.537 22.481 4.821 1 18.99 ? N1 UC5 777 A 1 HETATM 9 C C1' UC5 . . . B 2 22.528 23.063 5.726 1 20.24 ? C1' UC5 777 A 1 HETATM 10 C C2' UC5 . . . B 2 23.143 23.182 7.145 1 20.27 ? C2' UC5 777 A 1 HETATM 11 C C3' UC5 . . . B 2 23.299 24.654 7.408 1 22.84 ? C3' UC5 777 A 1 HETATM 12 O O3' UC5 . . . B 2 23.165 25.072 8.773 1 23.56 ? O3' UC5 777 A 1 HETATM 13 O O4' UC5 . . . B 2 22.158 24.396 5.342 1 21.74 ? O4' UC5 777 A 1 HETATM 14 C C4' UC5 . . . B 2 22.297 25.271 6.452 1 22.28 ? C4' UC5 777 A 1 HETATM 15 C C5' UC5 . . . B 2 22.857 26.635 6.023 1 31.12 ? C5' UC5 777 A 1 HETATM 16 O O5' UC5 . . . B 2 21.923 27.255 5.222 1 46.77 ? O5' UC5 777 A 1 HETATM 17 P PA UC5 . . . B 2 22.245 28.783 4.782 1 56.54 ? PA UC5 777 A 1 HETATM 18 O O1A UC5 . . . B 2 20.897 29.313 4.343 1 60.43 ? O1A UC5 777 A 1 HETATM 19 O O2A UC5 . . . B 2 22.939 29.57 5.876 1 51.66 ? O2A UC5 777 A 1 HETATM 20 C C3A UC5 . . . B 2 23.427 28.537 3.42 1 55.63 ? C3A UC5 777 A 1 HETATM 21 P PB UC5 . . . B 2 23.715 29.896 2.274 1 51.46 ? PB UC5 777 A 1 HETATM 22 O O1B UC5 . . . B 2 23.889 31.155 3.093 1 66.82 ? O1B UC5 777 A 1 HETATM 23 O O2B UC5 . . . B 2 24.91 29.755 1.431 1 33.91 ? O2B UC5 777 A 1 HETATM 24 O O3B UC5 . . . B 2 22.481 30.034 1.242 1 46.37 ? O3B UC5 777 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 24 #