data_3ESJ # _model_server_result.job_id k0jcQK8XpbJbmNMBGaYixw _model_server_result.datetime_utc '2024-11-22 11:08:04' _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 3esj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 3ESJ # _exptl.entry_id 3ESJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 305.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one _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 90 _cell.entry_id 3ESJ _cell.length_a 144.498 _cell.length_b 144.498 _cell.length_c 144.498 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ESJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 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 A OD2 ASP 14 A ASP 8 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 A NE2 HIS 16 A HIS 10 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc3 A ND1 HIS 48 A HIS 42 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 A OE1 GLU 155 A GLU 149 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc5 A OE2 GLU 155 A GLU 149 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc6 B ZN ZN . A ZN 900 1_555 F O HOH . A HOH 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? # _chem_comp.formula 'C9 H12 N3 O7 P' _chem_comp.formula_weight 305.181 _chem_comp.id CC7 _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one _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 O2 C2 CC7 doub 70 n n C2 N3 CC7 sing 71 n n C2 N1 CC7 sing 72 n n N3 C4 CC7 doub 73 n n C4 N4 CC7 sing 74 n n C4 C5 CC7 sing 75 n n C5 C6 CC7 doub 76 n n C6 N1 CC7 sing 77 n n N1 C1' CC7 sing 78 n n C1' O4' CC7 sing 79 n n C1' C2' CC7 sing 80 n n O4' C4' CC7 sing 81 n n C4' C5' CC7 sing 82 n n C4' C3' CC7 sing 83 n n C5' O5' CC7 sing 84 n n O5' P CC7 sing 85 n n P O2P CC7 sing 86 n n P O1P CC7 doub 87 n n P O3' CC7 sing 88 n n O3' C3' CC7 sing 89 n n C3' C2' CC7 sing 90 n n C2' O2' CC7 sing 91 n n N4 HN4 CC7 sing 92 n n N4 HN4A CC7 sing 93 n n C5 H5 CC7 sing 94 n n C6 H6 CC7 sing 95 n n C1' H1' CC7 sing 96 n n C4' H4' CC7 sing 97 n n C5' H5' CC7 sing 98 n n C5' "H5'A" CC7 sing 99 n n O2P HO2P CC7 sing 100 n n C3' H3' CC7 sing 101 n n C2' H2' CC7 sing 102 n n O2' HO2' CC7 sing 103 n n # _atom_sites.entry_id 3ESJ _atom_sites.fract_transf_matrix[1][1] 0.006921 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006921 _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] 0.006921 _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 ZN A 1 900 900 ZN ZN . C 3 CC7 A 1 901 901 CC7 CC7 . D 4 MG A 1 903 903 MG MG . E 5 GPP A 1 904 904 GPP GPP . F 6 HOH A 1 905 905 HOH HOH . F 6 HOH A 2 906 906 HOH HOH . F 6 HOH A 3 907 907 HOH HOH . F 6 HOH A 4 908 908 HOH HOH . F 6 HOH A 5 909 909 HOH HOH . F 6 HOH A 6 910 910 HOH HOH . F 6 HOH A 7 911 911 HOH HOH . F 6 HOH A 8 912 912 HOH HOH . F 6 HOH A 9 913 913 HOH HOH . F 6 HOH A 10 914 914 HOH HOH . F 6 HOH A 11 915 915 HOH HOH . F 6 HOH A 12 916 916 HOH HOH . F 6 HOH A 13 917 917 HOH HOH . F 6 HOH A 14 918 918 HOH HOH . F 6 HOH A 15 919 919 HOH HOH . F 6 HOH A 16 920 920 HOH HOH . F 6 HOH A 17 921 921 HOH HOH . F 6 HOH A 18 922 922 HOH HOH . F 6 HOH A 19 923 923 HOH HOH . F 6 HOH A 20 924 924 HOH HOH . F 6 HOH A 21 925 925 HOH HOH . F 6 HOH A 22 926 926 HOH HOH . F 6 HOH A 23 927 927 HOH HOH . F 6 HOH A 24 928 928 HOH HOH . F 6 HOH A 25 929 929 HOH HOH . F 6 HOH A 26 930 930 HOH HOH . F 6 HOH A 27 931 931 HOH HOH . F 6 HOH A 28 932 932 HOH HOH . F 6 HOH A 29 933 933 HOH HOH . F 6 HOH A 30 934 934 HOH HOH . F 6 HOH A 31 935 935 HOH HOH . F 6 HOH A 32 936 936 HOH HOH . F 6 HOH A 33 937 937 HOH HOH . F 6 HOH A 34 938 938 HOH HOH . F 6 HOH A 35 939 939 HOH HOH . F 6 HOH A 36 940 940 HOH HOH . F 6 HOH A 37 941 941 HOH HOH . F 6 HOH A 38 942 942 HOH HOH . F 6 HOH A 39 943 943 HOH HOH . F 6 HOH A 40 944 944 HOH HOH . F 6 HOH A 41 945 945 HOH HOH . F 6 HOH A 42 946 946 HOH HOH . F 6 HOH A 43 947 947 HOH HOH . F 6 HOH A 44 948 948 HOH HOH . F 6 HOH A 45 949 949 HOH HOH . F 6 HOH A 46 950 950 HOH HOH . F 6 HOH A 47 951 951 HOH HOH . F 6 HOH A 48 952 952 HOH HOH . F 6 HOH A 49 953 953 HOH HOH . F 6 HOH A 50 954 954 HOH HOH . F 6 HOH A 51 955 955 HOH HOH . F 6 HOH A 52 956 956 HOH HOH . F 6 HOH A 53 957 957 HOH HOH . F 6 HOH A 54 958 958 HOH HOH . F 6 HOH A 55 959 959 HOH HOH . F 6 HOH A 56 960 960 HOH HOH . F 6 HOH A 57 961 961 HOH HOH . F 6 HOH A 58 962 962 HOH HOH . F 6 HOH A 59 963 963 HOH HOH . F 6 HOH A 60 964 964 HOH HOH . F 6 HOH A 61 965 965 HOH HOH . F 6 HOH A 62 966 966 HOH HOH . F 6 HOH A 63 967 967 HOH HOH . F 6 HOH A 64 968 968 HOH HOH . F 6 HOH A 65 969 969 HOH HOH . F 6 HOH A 66 970 970 HOH HOH . F 6 HOH A 67 971 971 HOH HOH . F 6 HOH A 68 972 972 HOH HOH . F 6 HOH A 69 973 973 HOH HOH . F 6 HOH A 70 974 974 HOH HOH . F 6 HOH A 71 975 975 HOH HOH . F 6 HOH A 72 976 976 HOH HOH . F 6 HOH A 73 977 977 HOH HOH . F 6 HOH A 74 978 978 HOH HOH . F 6 HOH A 75 979 979 HOH HOH . F 6 HOH A 76 980 980 HOH HOH . F 6 HOH A 77 981 981 HOH HOH . F 6 HOH A 78 982 982 HOH HOH . F 6 HOH A 79 983 983 HOH HOH . F 6 HOH A 80 984 984 HOH HOH . F 6 HOH A 81 985 985 HOH HOH . F 6 HOH A 82 986 986 HOH HOH . F 6 HOH A 83 987 987 HOH HOH . F 6 HOH A 84 988 988 HOH HOH . F 6 HOH A 85 989 989 HOH HOH . F 6 HOH A 86 990 990 HOH HOH . F 6 HOH A 87 991 991 HOH HOH . F 6 HOH A 88 992 992 HOH HOH . F 6 HOH A 89 993 993 HOH HOH . F 6 HOH A 90 994 994 HOH HOH . F 6 HOH A 91 995 995 HOH HOH . F 6 HOH A 92 996 996 HOH HOH . F 6 HOH A 93 997 997 HOH HOH . F 6 HOH A 94 998 998 HOH HOH . F 6 HOH A 95 999 999 HOH HOH . F 6 HOH A 96 1000 1000 HOH HOH . F 6 HOH A 97 1001 1001 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 CC7 . . . C 3 7.186 31.902 13.768 1 33.47 ? O2 CC7 901 A 1 HETATM 2 C C2 CC7 . . . C 3 7.513 30.771 13.455 1 35.52 ? C2 CC7 901 A 1 HETATM 3 N N3 CC7 . . . C 3 6.753 29.722 13.782 1 35.55 ? N3 CC7 901 A 1 HETATM 4 C C4 CC7 . . . C 3 7.118 28.483 13.437 1 34.2 ? C4 CC7 901 A 1 HETATM 5 N N4 CC7 . . . C 3 6.346 27.49 13.779 1 33.77 ? N4 CC7 901 A 1 HETATM 6 C C5 CC7 . . . C 3 8.278 28.237 12.721 1 34.8 ? C5 CC7 901 A 1 HETATM 7 C C6 CC7 . . . C 3 9.079 29.309 12.353 1 36.24 ? C6 CC7 901 A 1 HETATM 8 N N1 CC7 . . . C 3 8.674 30.596 12.744 1 37.16 ? N1 CC7 901 A 1 HETATM 9 C C1' CC7 . . . C 3 9.433 31.793 12.409 1 39.27 ? C1' CC7 901 A 1 HETATM 10 O O4' CC7 . . . C 3 9.006 32.057 11.065 1 40.73 ? O4' CC7 901 A 1 HETATM 11 C C4' CC7 . . . C 3 10.134 32.557 10.409 1 42.54 ? C4' CC7 901 A 1 HETATM 12 C C5' CC7 . . . C 3 10.049 32.32 8.907 1 41.96 ? C5' CC7 901 A 1 HETATM 13 O O5' CC7 . . . C 3 11.327 32.571 8.313 1 43.25 ? O5' CC7 901 A 1 HETATM 14 P P CC7 . . . C 3 12.67 31.905 8.954 1 43.81 ? P CC7 901 A 1 HETATM 15 O O2P CC7 . . . C 3 12.517 30.336 8.781 1 43.1 ? O2P CC7 901 A 1 HETATM 16 O O1P CC7 . . . C 3 13.891 32.509 8.377 1 40.39 ? O1P CC7 901 A 1 HETATM 17 O O3' CC7 . . . C 3 12.484 32.02 10.49 1 42.77 ? O3' CC7 901 A 1 HETATM 18 C C3' CC7 . . . C 3 11.187 31.581 10.903 1 42.88 ? C3' CC7 901 A 1 HETATM 19 C C2' CC7 . . . C 3 10.943 31.645 12.385 1 40.51 ? C2' CC7 901 A 1 HETATM 20 O O2' CC7 . . . C 3 11.481 32.846 12.888 1 39.52 ? O2' CC7 901 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 424 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #