data_5ILW # _model_server_result.job_id IM_y6uxBROto0hwIVVZcEA _model_server_result.datetime_utc '2024-11-05 23:12:34' _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 5ilw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":802}' # _entry.id 5ILW # _exptl.entry_id 5ILW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 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 5ILW _cell.length_a 130.115 _cell.length_b 130.115 _cell.length_c 40.632 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ILW _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id ND2 _struct_conn.ptnr1_label_comp_id ASN _struct_conn.ptnr1_label_seq_id 227 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ASN _struct_conn.ptnr1_auth_seq_id 227 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C1 _struct_conn.ptnr2_label_comp_id NAG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NAG _struct_conn.ptnr2_auth_seq_id 801 _struct_conn.ptnr2_symmetry 1_555 _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 1.448 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name 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 N1 C2 URI sing 388 n n N1 C6 URI sing 389 n n N1 C1' URI sing 390 n n C2 N3 URI sing 391 n n C2 O2 URI doub 392 n n N3 C4 URI sing 393 n n N3 H3 URI sing 394 n n C4 C5 URI sing 395 n n C4 O4 URI doub 396 n n C5 C6 URI doub 397 n n C5 H5 URI sing 398 n n C6 H6 URI sing 399 n n C1' C2' URI sing 400 n n C1' O4' URI sing 401 n n C1' H1' URI sing 402 n n C2' C3' URI sing 403 n n C2' O2' URI sing 404 n n C2' H2' URI sing 405 n n C3' C4' URI sing 406 n n C3' O3' URI sing 407 n n C3' H3' URI sing 408 n n C4' O4' URI sing 409 n n C4' C5' URI sing 410 n n C4' H4' URI sing 411 n n O2' HO2' URI sing 412 n n O3' HO3' URI sing 413 n n C5' O5' URI sing 414 n n C5' "H5'1" URI sing 415 n n C5' "H5'2" URI sing 416 n n O5' HO5' URI sing 417 n n # _atom_sites.entry_id 5ILW _atom_sites.fract_transf_matrix[1][1] 0.007686 _atom_sites.fract_transf_matrix[1][2] 0.004437 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008874 _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] 0.024611 _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 NAG A 1 801 801 NAG NAG . C 3 URI A 1 802 1 URI URI . D 4 GOL A 1 803 1 GOL GOL . E 5 HOH A 1 901 954 HOH HOH . E 5 HOH A 2 902 949 HOH HOH . E 5 HOH A 3 903 9 HOH HOH . E 5 HOH A 4 904 6 HOH HOH . E 5 HOH A 5 905 17 HOH HOH . E 5 HOH A 6 906 946 HOH HOH . E 5 HOH A 7 907 1066 HOH HOH . E 5 HOH A 8 908 1002 HOH HOH . E 5 HOH A 9 909 955 HOH HOH . E 5 HOH A 10 910 920 HOH HOH . E 5 HOH A 11 911 1054 HOH HOH . E 5 HOH A 12 912 1051 HOH HOH . E 5 HOH A 13 913 930 HOH HOH . E 5 HOH A 14 914 968 HOH HOH . E 5 HOH A 15 915 939 HOH HOH . E 5 HOH A 16 916 994 HOH HOH . E 5 HOH A 17 917 1069 HOH HOH . E 5 HOH A 18 918 924 HOH HOH . E 5 HOH A 19 919 970 HOH HOH . E 5 HOH A 20 920 958 HOH HOH . E 5 HOH A 21 921 916 HOH HOH . E 5 HOH A 22 922 907 HOH HOH . E 5 HOH A 23 923 957 HOH HOH . E 5 HOH A 24 924 2 HOH HOH . E 5 HOH A 25 925 941 HOH HOH . E 5 HOH A 26 926 956 HOH HOH . E 5 HOH A 27 927 1024 HOH HOH . E 5 HOH A 28 928 985 HOH HOH . E 5 HOH A 29 929 1041 HOH HOH . E 5 HOH A 30 930 7 HOH HOH . E 5 HOH A 31 931 925 HOH HOH . E 5 HOH A 32 932 971 HOH HOH . E 5 HOH A 33 933 11 HOH HOH . E 5 HOH A 34 934 14 HOH HOH . E 5 HOH A 35 935 927 HOH HOH . E 5 HOH A 36 936 1028 HOH HOH . E 5 HOH A 37 937 990 HOH HOH . E 5 HOH A 38 938 1006 HOH HOH . E 5 HOH A 39 939 961 HOH HOH . E 5 HOH A 40 940 932 HOH HOH . E 5 HOH A 41 941 18 HOH HOH . E 5 HOH A 42 942 1 HOH HOH . E 5 HOH A 43 943 962 HOH HOH . E 5 HOH A 44 944 935 HOH HOH . E 5 HOH A 45 945 992 HOH HOH . E 5 HOH A 46 946 901 HOH HOH . E 5 HOH A 47 947 1065 HOH HOH . E 5 HOH A 48 948 1007 HOH HOH . E 5 HOH A 49 949 945 HOH HOH . E 5 HOH A 50 950 991 HOH HOH . E 5 HOH A 51 951 1063 HOH HOH . E 5 HOH A 52 952 1068 HOH HOH . E 5 HOH A 53 953 940 HOH HOH . E 5 HOH A 54 954 16 HOH HOH . E 5 HOH A 55 955 915 HOH HOH . E 5 HOH A 56 956 963 HOH HOH . E 5 HOH A 57 957 993 HOH HOH . E 5 HOH A 58 958 934 HOH HOH . E 5 HOH A 59 959 1067 HOH HOH . E 5 HOH A 60 960 1035 HOH HOH . E 5 HOH A 61 961 1012 HOH HOH . E 5 HOH A 62 962 977 HOH HOH . E 5 HOH A 63 963 1060 HOH HOH . E 5 HOH A 64 964 1036 HOH HOH . E 5 HOH A 65 965 1053 HOH HOH . E 5 HOH A 66 966 1056 HOH HOH . E 5 HOH A 67 967 964 HOH HOH . E 5 HOH A 68 968 1059 HOH HOH . E 5 HOH A 69 969 912 HOH HOH . E 5 HOH A 70 970 973 HOH HOH . E 5 HOH A 71 971 967 HOH HOH . E 5 HOH A 72 972 947 HOH HOH . E 5 HOH A 73 973 923 HOH HOH . E 5 HOH A 74 974 942 HOH HOH . E 5 HOH A 75 975 911 HOH HOH . E 5 HOH A 76 976 1040 HOH HOH . E 5 HOH A 77 977 5 HOH HOH . E 5 HOH A 78 978 1019 HOH HOH . E 5 HOH A 79 979 978 HOH HOH . E 5 HOH A 80 980 10 HOH HOH . E 5 HOH A 81 981 926 HOH HOH . E 5 HOH A 82 982 1020 HOH HOH . E 5 HOH A 83 983 1047 HOH HOH . E 5 HOH A 84 984 1070 HOH HOH . E 5 HOH A 85 985 1021 HOH HOH . E 5 HOH A 86 986 943 HOH HOH . E 5 HOH A 87 987 4 HOH HOH . E 5 HOH A 88 988 995 HOH HOH . E 5 HOH A 89 989 972 HOH HOH . E 5 HOH A 90 990 1058 HOH HOH . E 5 HOH A 91 991 909 HOH HOH . E 5 HOH A 92 992 931 HOH HOH . E 5 HOH A 93 993 1000 HOH HOH . E 5 HOH A 94 994 15 HOH HOH . E 5 HOH A 95 995 1057 HOH HOH . E 5 HOH A 96 996 1004 HOH HOH . E 5 HOH A 97 997 922 HOH HOH . E 5 HOH A 98 998 903 HOH HOH . E 5 HOH A 99 999 928 HOH HOH . E 5 HOH A 100 1000 950 HOH HOH . E 5 HOH A 101 1001 944 HOH HOH . E 5 HOH A 102 1002 1043 HOH HOH . E 5 HOH A 103 1003 3 HOH HOH . E 5 HOH A 104 1004 1071 HOH HOH . E 5 HOH A 105 1005 921 HOH HOH . E 5 HOH A 106 1006 1061 HOH HOH . E 5 HOH A 107 1007 976 HOH HOH . E 5 HOH A 108 1008 919 HOH HOH . E 5 HOH A 109 1009 969 HOH HOH . E 5 HOH A 110 1010 1064 HOH HOH . E 5 HOH A 111 1011 1032 HOH HOH . E 5 HOH A 112 1012 938 HOH HOH . E 5 HOH A 113 1013 1055 HOH HOH . E 5 HOH A 114 1014 905 HOH HOH . E 5 HOH A 115 1015 1033 HOH HOH . E 5 HOH A 116 1016 8 HOH HOH . E 5 HOH A 117 1017 1025 HOH HOH . E 5 HOH A 118 1018 1030 HOH HOH . E 5 HOH A 119 1019 1062 HOH HOH . E 5 HOH A 120 1020 998 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 N N1 URI . . . C 3 -15.135 -16.543 -10.24 1 27.45 ? N1 URI 802 A 1 HETATM 2 C C2 URI . . . C 3 -14.945 -16.576 -11.647 1 25.44 ? C2 URI 802 A 1 HETATM 3 N N3 URI . . . C 3 -14.089 -17.491 -12.163 1 27.11 ? N3 URI 802 A 1 HETATM 4 C C4 URI . . . C 3 -13.444 -18.385 -11.386 1 26.19 ? C4 URI 802 A 1 HETATM 5 C C5 URI . . . C 3 -13.624 -18.385 -9.997 1 25.01 ? C5 URI 802 A 1 HETATM 6 C C6 URI . . . C 3 -14.49 -17.436 -9.44 1 26.21 ? C6 URI 802 A 1 HETATM 7 O O2 URI . . . C 3 -15.556 -15.771 -12.404 1 23.82 ? O2 URI 802 A 1 HETATM 8 O O4 URI . . . C 3 -12.671 -19.194 -11.925 1 27.39 ? O4 URI 802 A 1 HETATM 9 C C1' URI . . . C 3 -16.027 -15.506 -9.721 1 31.06 ? C1' URI 802 A 1 HETATM 10 C C2' URI . . . C 3 -17.517 -15.872 -9.719 1 31.19 ? C2' URI 802 A 1 HETATM 11 C C3' URI . . . C 3 -17.698 -16.338 -8.312 1 30.76 ? C3' URI 802 A 1 HETATM 12 C C4' URI . . . C 3 -16.74 -15.462 -7.527 1 32.11 ? C4' URI 802 A 1 HETATM 13 O O2' URI . . . C 3 -18.309 -14.708 -9.909 1 29.9 ? O2' URI 802 A 1 HETATM 14 O O3' URI . . . C 3 -19.045 -16.13 -7.902 1 32.8 ? O3' URI 802 A 1 HETATM 15 O O4' URI . . . C 3 -15.646 -15.169 -8.4 1 28.24 ? O4' URI 802 A 1 HETATM 16 C C5' URI . . . C 3 -16.248 -16.155 -6.254 1 32.67 ? C5' URI 802 A 1 HETATM 17 O O5' URI . . . C 3 -15.341 -15.278 -5.606 1 29.57 ? O5' URI 802 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #