data_5K8T # _model_server_result.job_id B106x6NgqIFCYDMpLhM3pA _model_server_result.datetime_utc '2024-11-26 04:44:58' _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 5k8t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5K8T # _exptl.entry_id 5K8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 105.04 _cell.angle_gamma 90 _cell.entry_id 5K8T _cell.length_a 63.95 _cell.length_b 53.42 _cell.length_c 65.39 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K8T _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,F _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 # 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 OG1 THR 38 A THR 201 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A OE2 GLU 123 A GLU 286 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc3 B O3G GSP . A GSP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc4 B O2B GSP . A GSP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc5 D MG MG . A MG 703 1_555 F O HOH . A HOH 823 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc6 D MG MG . A MG 703 1_555 F O HOH . A HOH 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc7 E MG MG . A MG 704 1_555 F O HOH . A HOH 801 2_957 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc8 E MG MG . A MG 704 1_555 F O HOH . A HOH 838 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc9 E MG MG . A MG 704 1_555 F O HOH . A HOH 934 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc10 E MG MG . A MG 704 1_555 F O HOH . A HOH 953 2_957 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 PG O3B GSP sing 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 5K8T _atom_sites.fract_transf_matrix[1][1] 0.015637 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004202 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01872 _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] 0.015835 _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 GSP A 1 701 1 GSP GSP . C 3 CL A 1 702 2 CL CL . D 4 MG A 1 703 3 MG MG . E 4 MG A 1 704 4 MG MG . F 5 HOH A 1 801 1 HOH HOH . F 5 HOH A 2 802 117 HOH HOH . F 5 HOH A 3 803 146 HOH HOH . F 5 HOH A 4 804 47 HOH HOH . F 5 HOH A 5 805 67 HOH HOH . F 5 HOH A 6 806 123 HOH HOH . F 5 HOH A 7 807 112 HOH HOH . F 5 HOH A 8 808 38 HOH HOH . F 5 HOH A 9 809 153 HOH HOH . F 5 HOH A 10 810 122 HOH HOH . F 5 HOH A 11 811 52 HOH HOH . F 5 HOH A 12 812 142 HOH HOH . F 5 HOH A 13 813 85 HOH HOH . F 5 HOH A 14 814 87 HOH HOH . F 5 HOH A 15 815 40 HOH HOH . F 5 HOH A 16 816 108 HOH HOH . F 5 HOH A 17 817 34 HOH HOH . F 5 HOH A 18 818 46 HOH HOH . F 5 HOH A 19 819 83 HOH HOH . F 5 HOH A 20 820 60 HOH HOH . F 5 HOH A 21 821 145 HOH HOH . F 5 HOH A 22 822 90 HOH HOH . F 5 HOH A 23 823 156 HOH HOH . F 5 HOH A 24 824 26 HOH HOH . F 5 HOH A 25 825 100 HOH HOH . F 5 HOH A 26 826 50 HOH HOH . F 5 HOH A 27 827 111 HOH HOH . F 5 HOH A 28 828 27 HOH HOH . F 5 HOH A 29 829 69 HOH HOH . F 5 HOH A 30 830 89 HOH HOH . F 5 HOH A 31 831 55 HOH HOH . F 5 HOH A 32 832 118 HOH HOH . F 5 HOH A 33 833 4 HOH HOH . F 5 HOH A 34 834 11 HOH HOH . F 5 HOH A 35 835 95 HOH HOH . F 5 HOH A 36 836 134 HOH HOH . F 5 HOH A 37 837 119 HOH HOH . F 5 HOH A 38 838 115 HOH HOH . F 5 HOH A 39 839 106 HOH HOH . F 5 HOH A 40 840 131 HOH HOH . F 5 HOH A 41 841 20 HOH HOH . F 5 HOH A 42 842 62 HOH HOH . F 5 HOH A 43 843 63 HOH HOH . F 5 HOH A 44 844 48 HOH HOH . F 5 HOH A 45 845 41 HOH HOH . F 5 HOH A 46 846 102 HOH HOH . F 5 HOH A 47 847 64 HOH HOH . F 5 HOH A 48 848 42 HOH HOH . F 5 HOH A 49 849 127 HOH HOH . F 5 HOH A 50 850 61 HOH HOH . F 5 HOH A 51 851 96 HOH HOH . F 5 HOH A 52 852 114 HOH HOH . F 5 HOH A 53 853 77 HOH HOH . F 5 HOH A 54 854 88 HOH HOH . F 5 HOH A 55 855 7 HOH HOH . F 5 HOH A 56 856 37 HOH HOH . F 5 HOH A 57 857 133 HOH HOH . F 5 HOH A 58 858 13 HOH HOH . F 5 HOH A 59 859 159 HOH HOH . F 5 HOH A 60 860 57 HOH HOH . F 5 HOH A 61 861 155 HOH HOH . F 5 HOH A 62 862 132 HOH HOH . F 5 HOH A 63 863 70 HOH HOH . F 5 HOH A 64 864 15 HOH HOH . F 5 HOH A 65 865 43 HOH HOH . F 5 HOH A 66 866 2 HOH HOH . F 5 HOH A 67 867 80 HOH HOH . F 5 HOH A 68 868 120 HOH HOH . F 5 HOH A 69 869 75 HOH HOH . F 5 HOH A 70 870 36 HOH HOH . F 5 HOH A 71 871 93 HOH HOH . F 5 HOH A 72 872 16 HOH HOH . F 5 HOH A 73 873 94 HOH HOH . F 5 HOH A 74 874 109 HOH HOH . F 5 HOH A 75 875 128 HOH HOH . F 5 HOH A 76 876 68 HOH HOH . F 5 HOH A 77 877 97 HOH HOH . F 5 HOH A 78 878 14 HOH HOH . F 5 HOH A 79 879 28 HOH HOH . F 5 HOH A 80 880 125 HOH HOH . F 5 HOH A 81 881 10 HOH HOH . F 5 HOH A 82 882 135 HOH HOH . F 5 HOH A 83 883 51 HOH HOH . F 5 HOH A 84 884 32 HOH HOH . F 5 HOH A 85 885 152 HOH HOH . F 5 HOH A 86 886 22 HOH HOH . F 5 HOH A 87 887 98 HOH HOH . F 5 HOH A 88 888 160 HOH HOH . F 5 HOH A 89 889 54 HOH HOH . F 5 HOH A 90 890 19 HOH HOH . F 5 HOH A 91 891 84 HOH HOH . F 5 HOH A 92 892 151 HOH HOH . F 5 HOH A 93 893 44 HOH HOH . F 5 HOH A 94 894 6 HOH HOH . F 5 HOH A 95 895 12 HOH HOH . F 5 HOH A 96 896 21 HOH HOH . F 5 HOH A 97 897 103 HOH HOH . F 5 HOH A 98 898 49 HOH HOH . F 5 HOH A 99 899 71 HOH HOH . F 5 HOH A 100 900 17 HOH HOH . F 5 HOH A 101 901 79 HOH HOH . F 5 HOH A 102 902 8 HOH HOH . F 5 HOH A 103 903 5 HOH HOH . F 5 HOH A 104 904 30 HOH HOH . F 5 HOH A 105 905 24 HOH HOH . F 5 HOH A 106 906 124 HOH HOH . F 5 HOH A 107 907 81 HOH HOH . F 5 HOH A 108 908 157 HOH HOH . F 5 HOH A 109 909 39 HOH HOH . F 5 HOH A 110 910 141 HOH HOH . F 5 HOH A 111 911 29 HOH HOH . F 5 HOH A 112 912 33 HOH HOH . F 5 HOH A 113 913 9 HOH HOH . F 5 HOH A 114 914 23 HOH HOH . F 5 HOH A 115 915 31 HOH HOH . F 5 HOH A 116 916 3 HOH HOH . F 5 HOH A 117 917 76 HOH HOH . F 5 HOH A 118 918 110 HOH HOH . F 5 HOH A 119 919 113 HOH HOH . F 5 HOH A 120 920 129 HOH HOH . F 5 HOH A 121 921 58 HOH HOH . F 5 HOH A 122 922 73 HOH HOH . F 5 HOH A 123 923 143 HOH HOH . F 5 HOH A 124 924 137 HOH HOH . F 5 HOH A 125 925 86 HOH HOH . F 5 HOH A 126 926 18 HOH HOH . F 5 HOH A 127 927 91 HOH HOH . F 5 HOH A 128 928 126 HOH HOH . F 5 HOH A 129 929 101 HOH HOH . F 5 HOH A 130 930 35 HOH HOH . F 5 HOH A 131 931 45 HOH HOH . F 5 HOH A 132 932 56 HOH HOH . F 5 HOH A 133 933 136 HOH HOH . F 5 HOH A 134 934 158 HOH HOH . F 5 HOH A 135 935 105 HOH HOH . F 5 HOH A 136 936 82 HOH HOH . F 5 HOH A 137 937 121 HOH HOH . F 5 HOH A 138 938 99 HOH HOH . F 5 HOH A 139 939 25 HOH HOH . F 5 HOH A 140 940 149 HOH HOH . F 5 HOH A 141 941 66 HOH HOH . F 5 HOH A 142 942 107 HOH HOH . F 5 HOH A 143 943 116 HOH HOH . F 5 HOH A 144 944 92 HOH HOH . F 5 HOH A 145 945 138 HOH HOH . F 5 HOH A 146 946 130 HOH HOH . F 5 HOH A 147 947 59 HOH HOH . F 5 HOH A 148 948 53 HOH HOH . F 5 HOH A 149 949 148 HOH HOH . F 5 HOH A 150 950 139 HOH HOH . F 5 HOH A 151 951 74 HOH HOH . F 5 HOH A 152 952 144 HOH HOH . F 5 HOH A 153 953 78 HOH HOH . F 5 HOH A 154 954 65 HOH HOH . F 5 HOH A 155 955 72 HOH HOH . F 5 HOH A 156 956 104 HOH HOH . F 5 HOH A 157 957 154 HOH HOH . F 5 HOH A 158 958 147 HOH HOH . F 5 HOH A 159 959 150 HOH HOH . F 5 HOH A 160 960 140 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 PG GSP . . . B 2 118.651 8.519 67.285 1 40.72 ? PG GSP 701 A 1 HETATM 2 O O3B GSP . . . B 2 118.489 7.663 65.984 1 35.46 ? O3B GSP 701 A 1 HETATM 3 S S1G GSP . . . B 2 118.868 10.372 67.303 1 55.81 ? S1G GSP 701 A 1 HETATM 4 O O2G GSP . . . B 2 117.256 8.201 67.995 1 40 ? O2G GSP 701 A 1 HETATM 5 O O3G GSP . . . B 2 119.556 7.757 68.369 1 32.67 ? O3G GSP 701 A 1 HETATM 6 P PB GSP . . . B 2 119.942 7.204 65.037 1 34.28 ? PB GSP 701 A 1 HETATM 7 O O1B GSP . . . B 2 120.215 8.532 64.403 1 40.28 -1 O1B GSP 701 A 1 HETATM 8 O O2B GSP . . . B 2 120.843 6.638 66.117 1 32.8 ? O2B GSP 701 A 1 HETATM 9 P PA GSP . . . B 2 119.856 4.577 64.323 1 53.63 ? PA GSP 701 A 1 HETATM 10 O O1A GSP . . . B 2 121.3 4.418 63.904 1 45.16 ? O1A GSP 701 A 1 HETATM 11 O O2A GSP . . . B 2 119.36 4.383 65.733 1 44.94 -1 O2A GSP 701 A 1 HETATM 12 O O3A GSP . . . B 2 119.491 6.092 63.972 1 35.06 ? O3A GSP 701 A 1 HETATM 13 O O5' GSP . . . B 2 118.881 3.562 63.433 1 58.45 ? O5' GSP 701 A 1 HETATM 14 C C5' GSP . . . B 2 118.163 4.372 62.545 1 54.76 ? C5' GSP 701 A 1 HETATM 15 C C4' GSP . . . B 2 116.776 3.747 62.466 1 58.92 ? C4' GSP 701 A 1 HETATM 16 O O4' GSP . . . B 2 116.733 2.805 61.371 1 74.5 ? O4' GSP 701 A 1 HETATM 17 C C3' GSP . . . B 2 116.491 2.829 63.676 1 58.43 ? C3' GSP 701 A 1 HETATM 18 O O3' GSP . . . B 2 116.26 3.58 64.81 1 56.78 ? O3' GSP 701 A 1 HETATM 19 C C2' GSP . . . B 2 115.219 2.174 63.18 1 67.98 ? C2' GSP 701 A 1 HETATM 20 O O2' GSP . . . B 2 114.14 3.043 63.196 1 53.91 ? O2' GSP 701 A 1 HETATM 21 C C1' GSP . . . B 2 115.616 1.919 61.669 1 79.09 ? C1' GSP 701 A 1 HETATM 22 N N9 GSP . . . B 2 115.967 0.47 61.415 1 79.74 ? N9 GSP 701 A 1 HETATM 23 C C8 GSP . . . B 2 116.137 -0.118 60.116 1 83.57 ? C8 GSP 701 A 1 HETATM 24 N N7 GSP . . . B 2 116.438 -1.438 60.182 1 79.3 ? N7 GSP 701 A 1 HETATM 25 C C5 GSP . . . B 2 116.462 -1.741 61.553 1 82.34 ? C5 GSP 701 A 1 HETATM 26 C C6 GSP . . . B 2 116.738 -3.028 62.128 1 77.47 ? C6 GSP 701 A 1 HETATM 27 O O6 GSP . . . B 2 117.001 -4.094 61.588 1 68.56 ? O6 GSP 701 A 1 HETATM 28 N N1 GSP . . . B 2 116.687 -3.011 63.572 1 77.94 ? N1 GSP 701 A 1 HETATM 29 C C2 GSP . . . B 2 116.392 -1.821 64.275 1 78.01 ? C2 GSP 701 A 1 HETATM 30 N N2 GSP . . . B 2 116.366 -1.906 65.656 1 69.41 ? N2 GSP 701 A 1 HETATM 31 N N3 GSP . . . B 2 116.132 -0.593 63.766 1 80.73 ? N3 GSP 701 A 1 HETATM 32 C C4 GSP . . . B 2 116.176 -0.6 62.35 1 85.04 ? C4 GSP 701 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 655 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 32 #