data_6JFK # _model_server_result.job_id 3nP6fz1ePPtNuPvRoOcFkA _model_server_result.datetime_utc '2024-11-24 01:24:42' _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 6jfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 6JFK # _exptl.entry_id 6JFK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 6JFK _cell.length_a 49.624 _cell.length_b 49.624 _cell.length_c 388.065 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 103 n n PB O2B GDP sing 104 n n PB O3B GDP sing 105 n n PB O3A GDP sing 106 n n O2B HOB2 GDP sing 107 n n O3B HOB3 GDP sing 108 n n O3A PA GDP sing 109 n n PA O1A GDP doub 110 n n PA O2A GDP sing 111 n n PA O5' GDP sing 112 n n O2A HOA2 GDP sing 113 n n O5' C5' GDP sing 114 n n C5' C4' GDP sing 115 n n C5' H5' GDP sing 116 n n C5' "H5''" GDP sing 117 n n C4' O4' GDP sing 118 n n C4' C3' GDP sing 119 n n C4' H4' GDP sing 120 n n O4' C1' GDP sing 121 n n C3' O3' GDP sing 122 n n C3' C2' GDP sing 123 n n C3' H3' GDP sing 124 n n O3' HO3' GDP sing 125 n n C2' O2' GDP sing 126 n n C2' C1' GDP sing 127 n n C2' H2' GDP sing 128 n n O2' HO2' GDP sing 129 n n C1' N9 GDP sing 130 n n C1' H1' GDP sing 131 n n N9 C8 GDP sing 132 n y N9 C4 GDP sing 133 n y C8 N7 GDP doub 134 n y C8 H8 GDP sing 135 n n N7 C5 GDP sing 136 n y C5 C6 GDP sing 137 n n C5 C4 GDP doub 138 n y C6 O6 GDP doub 139 n n C6 N1 GDP sing 140 n n N1 C2 GDP sing 141 n n N1 HN1 GDP sing 142 n n C2 N2 GDP sing 143 n n C2 N3 GDP doub 144 n n N2 HN21 GDP sing 145 n n N2 HN22 GDP sing 146 n n N3 C4 GDP sing 147 n n # _atom_sites.entry_id 6JFK _atom_sites.fract_transf_matrix[1][1] 0.020152 _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] 0.020152 _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] 0.002577 _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 GDP A 1 801 1 GDP GDP . C 3 CIT A 1 802 1 CIT CIT . D 4 GOL A 1 803 1 GOL GOL . E 4 GOL A 1 804 2 GOL GOL . F 4 GOL A 1 805 3 GOL GOL . G 4 GOL A 1 806 4 GOL GOL . H 5 HOH A 1 901 91 HOH HOH . H 5 HOH A 2 902 56 HOH HOH . H 5 HOH A 3 903 64 HOH HOH . H 5 HOH A 4 904 69 HOH HOH . H 5 HOH A 5 905 182 HOH HOH . H 5 HOH A 6 906 85 HOH HOH . H 5 HOH A 7 907 99 HOH HOH . H 5 HOH A 8 908 134 HOH HOH . H 5 HOH A 9 909 59 HOH HOH . H 5 HOH A 10 910 107 HOH HOH . H 5 HOH A 11 911 6 HOH HOH . H 5 HOH A 12 912 173 HOH HOH . H 5 HOH A 13 913 11 HOH HOH . H 5 HOH A 14 914 104 HOH HOH . H 5 HOH A 15 915 14 HOH HOH . H 5 HOH A 16 916 70 HOH HOH . H 5 HOH A 17 917 54 HOH HOH . H 5 HOH A 18 918 31 HOH HOH . H 5 HOH A 19 919 78 HOH HOH . H 5 HOH A 20 920 100 HOH HOH . H 5 HOH A 21 921 79 HOH HOH . H 5 HOH A 22 922 16 HOH HOH . H 5 HOH A 23 923 84 HOH HOH . H 5 HOH A 24 924 46 HOH HOH . H 5 HOH A 25 925 7 HOH HOH . H 5 HOH A 26 926 33 HOH HOH . H 5 HOH A 27 927 123 HOH HOH . H 5 HOH A 28 928 22 HOH HOH . H 5 HOH A 29 929 74 HOH HOH . H 5 HOH A 30 930 136 HOH HOH . H 5 HOH A 31 931 58 HOH HOH . H 5 HOH A 32 932 30 HOH HOH . H 5 HOH A 33 933 10 HOH HOH . H 5 HOH A 34 934 124 HOH HOH . H 5 HOH A 35 935 95 HOH HOH . H 5 HOH A 36 936 45 HOH HOH . H 5 HOH A 37 937 44 HOH HOH . H 5 HOH A 38 938 147 HOH HOH . H 5 HOH A 39 939 61 HOH HOH . H 5 HOH A 40 940 24 HOH HOH . H 5 HOH A 41 941 160 HOH HOH . H 5 HOH A 42 942 60 HOH HOH . H 5 HOH A 43 943 48 HOH HOH . H 5 HOH A 44 944 3 HOH HOH . H 5 HOH A 45 945 122 HOH HOH . H 5 HOH A 46 946 4 HOH HOH . H 5 HOH A 47 947 170 HOH HOH . H 5 HOH A 48 948 12 HOH HOH . H 5 HOH A 49 949 55 HOH HOH . H 5 HOH A 50 950 149 HOH HOH . H 5 HOH A 51 951 51 HOH HOH . H 5 HOH A 52 952 116 HOH HOH . H 5 HOH A 53 953 80 HOH HOH . H 5 HOH A 54 954 26 HOH HOH . H 5 HOH A 55 955 25 HOH HOH . H 5 HOH A 56 956 152 HOH HOH . H 5 HOH A 57 957 62 HOH HOH . H 5 HOH A 58 958 57 HOH HOH . H 5 HOH A 59 959 35 HOH HOH . H 5 HOH A 60 960 15 HOH HOH . H 5 HOH A 61 961 94 HOH HOH . H 5 HOH A 62 962 101 HOH HOH . H 5 HOH A 63 963 17 HOH HOH . H 5 HOH A 64 964 38 HOH HOH . H 5 HOH A 65 965 72 HOH HOH . H 5 HOH A 66 966 43 HOH HOH . H 5 HOH A 67 967 87 HOH HOH . H 5 HOH A 68 968 169 HOH HOH . H 5 HOH A 69 969 63 HOH HOH . H 5 HOH A 70 970 34 HOH HOH . H 5 HOH A 71 971 71 HOH HOH . H 5 HOH A 72 972 120 HOH HOH . H 5 HOH A 73 973 41 HOH HOH . H 5 HOH A 74 974 20 HOH HOH . H 5 HOH A 75 975 13 HOH HOH . H 5 HOH A 76 976 67 HOH HOH . H 5 HOH A 77 977 68 HOH HOH . H 5 HOH A 78 978 50 HOH HOH . H 5 HOH A 79 979 5 HOH HOH . H 5 HOH A 80 980 49 HOH HOH . H 5 HOH A 81 981 110 HOH HOH . H 5 HOH A 82 982 93 HOH HOH . H 5 HOH A 83 983 82 HOH HOH . H 5 HOH A 84 984 90 HOH HOH . H 5 HOH A 85 985 129 HOH HOH . H 5 HOH A 86 986 19 HOH HOH . H 5 HOH A 87 987 23 HOH HOH . H 5 HOH A 88 988 77 HOH HOH . H 5 HOH A 89 989 153 HOH HOH . H 5 HOH A 90 990 28 HOH HOH . H 5 HOH A 91 991 37 HOH HOH . H 5 HOH A 92 992 18 HOH HOH . H 5 HOH A 93 993 119 HOH HOH . H 5 HOH A 94 994 156 HOH HOH . H 5 HOH A 95 995 21 HOH HOH . H 5 HOH A 96 996 36 HOH HOH . H 5 HOH A 97 997 111 HOH HOH . H 5 HOH A 98 998 112 HOH HOH . H 5 HOH A 99 999 86 HOH HOH . H 5 HOH A 100 1000 102 HOH HOH . H 5 HOH A 101 1001 53 HOH HOH . H 5 HOH A 102 1002 115 HOH HOH . H 5 HOH A 103 1003 113 HOH HOH . H 5 HOH A 104 1004 180 HOH HOH . H 5 HOH A 105 1005 96 HOH HOH . H 5 HOH A 106 1006 133 HOH HOH . H 5 HOH A 107 1007 66 HOH HOH . H 5 HOH A 108 1008 40 HOH HOH . H 5 HOH A 109 1009 109 HOH HOH . H 5 HOH A 110 1010 139 HOH HOH . H 5 HOH A 111 1011 76 HOH HOH . H 5 HOH A 112 1012 29 HOH HOH . H 5 HOH A 113 1013 108 HOH HOH . H 5 HOH A 114 1014 145 HOH HOH . H 5 HOH A 115 1015 73 HOH HOH . H 5 HOH A 116 1016 39 HOH HOH . H 5 HOH A 117 1017 98 HOH HOH . H 5 HOH A 118 1018 121 HOH HOH . H 5 HOH A 119 1019 9 HOH HOH . H 5 HOH A 120 1020 42 HOH HOH . H 5 HOH A 121 1021 2 HOH HOH . H 5 HOH A 122 1022 154 HOH HOH . H 5 HOH A 123 1023 159 HOH HOH . H 5 HOH A 124 1024 89 HOH HOH . H 5 HOH A 125 1025 144 HOH HOH . H 5 HOH A 126 1026 27 HOH HOH . H 5 HOH A 127 1027 178 HOH HOH . H 5 HOH A 128 1028 163 HOH HOH . H 5 HOH A 129 1029 52 HOH HOH . H 5 HOH A 130 1030 146 HOH HOH . H 5 HOH A 131 1031 181 HOH HOH . H 5 HOH A 132 1032 138 HOH HOH . H 5 HOH A 133 1033 179 HOH HOH . H 5 HOH A 134 1034 75 HOH HOH . H 5 HOH A 135 1035 92 HOH HOH . H 5 HOH A 136 1036 167 HOH HOH . H 5 HOH A 137 1037 171 HOH HOH . H 5 HOH A 138 1038 157 HOH HOH . H 5 HOH A 139 1039 103 HOH HOH . H 5 HOH A 140 1040 83 HOH HOH . H 5 HOH A 141 1041 177 HOH HOH . H 5 HOH A 142 1042 155 HOH HOH . H 5 HOH A 143 1043 32 HOH HOH . H 5 HOH A 144 1044 88 HOH HOH . H 5 HOH A 145 1045 128 HOH HOH . H 5 HOH A 146 1046 141 HOH HOH . H 5 HOH A 147 1047 65 HOH HOH . H 5 HOH A 148 1048 97 HOH HOH . H 5 HOH A 149 1049 143 HOH HOH . H 5 HOH A 150 1050 47 HOH HOH . H 5 HOH A 151 1051 164 HOH HOH . H 5 HOH A 152 1052 131 HOH HOH . H 5 HOH A 153 1053 132 HOH HOH . H 5 HOH A 154 1054 166 HOH HOH . H 5 HOH A 155 1055 126 HOH HOH . H 5 HOH A 156 1056 174 HOH HOH . H 5 HOH A 157 1057 135 HOH HOH . H 5 HOH A 158 1058 165 HOH HOH . H 5 HOH A 159 1059 105 HOH HOH . H 5 HOH A 160 1060 176 HOH HOH . H 5 HOH A 161 1061 1 HOH HOH . H 5 HOH A 162 1062 8 HOH HOH . H 5 HOH A 163 1063 118 HOH HOH . H 5 HOH A 164 1064 125 HOH HOH . H 5 HOH A 165 1065 114 HOH HOH . H 5 HOH A 166 1066 172 HOH HOH . H 5 HOH A 167 1067 162 HOH HOH . H 5 HOH A 168 1068 158 HOH HOH . H 5 HOH A 169 1069 81 HOH HOH . H 5 HOH A 170 1070 175 HOH HOH . H 5 HOH A 171 1071 168 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 P PB GDP . . . B 2 -30.555 15.414 8.934 1 26.42 ? PB GDP 801 A 1 HETATM 2 O O1B GDP . . . B 2 -29.526 14.834 8.002 1 22.33 ? O1B GDP 801 A 1 HETATM 3 O O2B GDP . . . B 2 -30.233 15.116 10.406 1 27.26 ? O2B GDP 801 A 1 HETATM 4 O O3B GDP . . . B 2 -30.697 16.904 8.737 1 26.83 ? O3B GDP 801 A 1 HETATM 5 O O3A GDP . . . B 2 -31.926 14.659 8.526 1 27.22 ? O3A GDP 801 A 1 HETATM 6 P PA GDP . . . B 2 -32.983 13.887 9.461 1 26.59 ? PA GDP 801 A 1 HETATM 7 O O1A GDP . . . B 2 -32.475 12.583 10.019 1 27.81 ? O1A GDP 801 A 1 HETATM 8 O O2A GDP . . . B 2 -33.598 14.829 10.44 1 25.88 ? O2A GDP 801 A 1 HETATM 9 O O5' GDP . . . B 2 -34.101 13.526 8.352 1 29.99 ? O5' GDP 801 A 1 HETATM 10 C C5' GDP . . . B 2 -34.77 14.575 7.625 1 27.35 ? C5' GDP 801 A 1 HETATM 11 C C4' GDP . . . B 2 -36.128 14.09 7.125 1 23.13 ? C4' GDP 801 A 1 HETATM 12 O O4' GDP . . . B 2 -35.881 12.992 6.253 1 26.84 ? O4' GDP 801 A 1 HETATM 13 C C3' GDP . . . B 2 -36.965 13.561 8.267 1 30.03 ? C3' GDP 801 A 1 HETATM 14 O O3' GDP . . . B 2 -38.345 13.857 8.038 1 32.49 ? O3' GDP 801 A 1 HETATM 15 C C2' GDP . . . B 2 -36.735 12.062 8.225 1 27.46 ? C2' GDP 801 A 1 HETATM 16 O O2' GDP . . . B 2 -37.812 11.345 8.827 1 30.5 ? O2' GDP 801 A 1 HETATM 17 C C1' GDP . . . B 2 -36.546 11.823 6.74 1 24.38 ? C1' GDP 801 A 1 HETATM 18 N N9 GDP . . . B 2 -35.668 10.659 6.486 1 29.51 ? N9 GDP 801 A 1 HETATM 19 C C8 GDP . . . B 2 -34.513 10.353 7.114 1 26.51 ? C8 GDP 801 A 1 HETATM 20 N N7 GDP . . . B 2 -33.968 9.219 6.609 1 26.01 ? N7 GDP 801 A 1 HETATM 21 C C5 GDP . . . B 2 -34.792 8.793 5.637 1 26.1 ? C5 GDP 801 A 1 HETATM 22 C C6 GDP . . . B 2 -34.839 7.657 4.701 1 24.98 ? C6 GDP 801 A 1 HETATM 23 O O6 GDP . . . B 2 -33.953 6.781 4.703 1 27.77 ? O6 GDP 801 A 1 HETATM 24 N N1 GDP . . . B 2 -35.884 7.591 3.846 1 29.66 ? N1 GDP 801 A 1 HETATM 25 C C2 GDP . . . B 2 -36.873 8.499 3.812 1 28.6 ? C2 GDP 801 A 1 HETATM 26 N N2 GDP . . . B 2 -37.889 8.336 2.911 1 30.51 ? N2 GDP 801 A 1 HETATM 27 N N3 GDP . . . B 2 -36.901 9.557 4.653 1 30.28 ? N3 GDP 801 A 1 HETATM 28 C C4 GDP . . . B 2 -35.905 9.746 5.557 1 30.34 ? C4 GDP 801 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #