data_5V9F # _model_server_result.job_id bU_WwuM3bgPmz2Ban4zujA _model_server_result.datetime_utc '2024-10-27 06:21:10' _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 5v9f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 5V9F # _exptl.entry_id 5V9F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 168.125 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SULFOPYRUVATE _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 107.81 _cell.angle_gamma 90 _cell.entry_id 5V9F _cell.length_a 46.285 _cell.length_b 119.506 _cell.length_c 60.707 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V9F _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 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 5 _struct_asym.id F _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 OE2 GLU 63 A GLU 63 1_555 G MN MN . A MN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc2 A O ASN 208 A ASN 208 1_555 D NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc3 A NZ LYS 244 A LYS 244 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc4 A NE2 HIS 264 A HIS 264 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc5 A OG1 THR 291 A THR 291 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc6 A OD1 ASP 311 A ASP 311 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 A NE2 HIS 502 A HIS 502 1_555 G MN MN . A MN 706 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc8 A OE2 GLU 607 A GLU 607 1_555 G MN MN . A MN 706 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc9 B MN MN . A MN 701 1_555 E O2G GTP . A GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc10 B MN MN . A MN 701 1_555 E O1B GTP . A GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc11 B MN MN . A MN 701 1_555 H O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc12 B MN MN . A MN 701 1_555 H O HOH . A HOH 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc13 B MN MN . A MN 701 1_555 H O HOH . A HOH 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc14 C MN MN . A MN 702 1_555 E O1G GTP . A GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc15 C MN MN . A MN 702 1_555 F O1 SPV . A SPV 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc16 C MN MN . A MN 702 1_555 F O2 SPV . A SPV 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc17 D NA NA . A NA 703 1_555 H O HOH . A HOH 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc18 D NA NA . A NA 703 1_555 H O HOH . A HOH 940 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.031 ? metalc ? metalc19 G MN MN . A MN 706 1_555 H O HOH . A HOH 839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc20 G MN MN . A MN 706 1_555 H O HOH . A HOH 951 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? # _chem_comp.formula 'C3 H4 O6 S' _chem_comp.formula_weight 168.125 _chem_comp.id SPV _chem_comp.mon_nstd_flag . _chem_comp.name SULFOPYRUVATE _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 C1 O1 SPV doub 340 n n C1 O2' SPV sing 341 n n C1 C2 SPV sing 342 n n O2' "H2'O" SPV sing 343 n n C2 C3 SPV sing 344 n n C2 O2 SPV doub 345 n n C3 S SPV sing 346 n n C3 H31 SPV sing 347 n n C3 H32 SPV sing 348 n n S O1S SPV doub 349 n n S O2S SPV sing 350 n n S O3S SPV doub 351 n n O2S H2SO SPV sing 352 n n # _atom_sites.entry_id 5V9F _atom_sites.fract_transf_matrix[1][1] 0.021605 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00694 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008368 _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] 0.017302 _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 MN A 1 701 700 MN MN . C 2 MN A 1 702 800 MN MN . D 3 NA A 1 703 1100 NA NA . E 4 GTP A 1 704 1000 GTP GTP . F 5 SPV A 1 705 1200 SPV SPV . G 2 MN A 1 706 1 MN MN . H 6 HOH A 1 801 96 HOH HOH . H 6 HOH A 2 802 152 HOH HOH . H 6 HOH A 3 803 93 HOH HOH . H 6 HOH A 4 804 100 HOH HOH . H 6 HOH A 5 805 2 HOH HOH . H 6 HOH A 6 806 144 HOH HOH . H 6 HOH A 7 807 22 HOH HOH . H 6 HOH A 8 808 149 HOH HOH . H 6 HOH A 9 809 180 HOH HOH . H 6 HOH A 10 810 1 HOH HOH . H 6 HOH A 11 811 159 HOH HOH . H 6 HOH A 12 812 16 HOH HOH . H 6 HOH A 13 813 151 HOH HOH . H 6 HOH A 14 814 182 HOH HOH . H 6 HOH A 15 815 86 HOH HOH . H 6 HOH A 16 816 137 HOH HOH . H 6 HOH A 17 817 44 HOH HOH . H 6 HOH A 18 818 51 HOH HOH . H 6 HOH A 19 819 61 HOH HOH . H 6 HOH A 20 820 145 HOH HOH . H 6 HOH A 21 821 188 HOH HOH . H 6 HOH A 22 822 56 HOH HOH . H 6 HOH A 23 823 88 HOH HOH . H 6 HOH A 24 824 197 HOH HOH . H 6 HOH A 25 825 118 HOH HOH . H 6 HOH A 26 826 92 HOH HOH . H 6 HOH A 27 827 131 HOH HOH . H 6 HOH A 28 828 209 HOH HOH . H 6 HOH A 29 829 60 HOH HOH . H 6 HOH A 30 830 187 HOH HOH . H 6 HOH A 31 831 124 HOH HOH . H 6 HOH A 32 832 41 HOH HOH . H 6 HOH A 33 833 190 HOH HOH . H 6 HOH A 34 834 135 HOH HOH . H 6 HOH A 35 835 156 HOH HOH . H 6 HOH A 36 836 103 HOH HOH . H 6 HOH A 37 837 17 HOH HOH . H 6 HOH A 38 838 75 HOH HOH . H 6 HOH A 39 839 163 HOH HOH . H 6 HOH A 40 840 38 HOH HOH . H 6 HOH A 41 841 45 HOH HOH . H 6 HOH A 42 842 113 HOH HOH . H 6 HOH A 43 843 73 HOH HOH . H 6 HOH A 44 844 142 HOH HOH . H 6 HOH A 45 845 203 HOH HOH . H 6 HOH A 46 846 72 HOH HOH . H 6 HOH A 47 847 34 HOH HOH . H 6 HOH A 48 848 69 HOH HOH . H 6 HOH A 49 849 3 HOH HOH . H 6 HOH A 50 850 8 HOH HOH . H 6 HOH A 51 851 63 HOH HOH . H 6 HOH A 52 852 217 HOH HOH . H 6 HOH A 53 853 87 HOH HOH . H 6 HOH A 54 854 215 HOH HOH . H 6 HOH A 55 855 147 HOH HOH . H 6 HOH A 56 856 174 HOH HOH . H 6 HOH A 57 857 68 HOH HOH . H 6 HOH A 58 858 108 HOH HOH . H 6 HOH A 59 859 74 HOH HOH . H 6 HOH A 60 860 52 HOH HOH . H 6 HOH A 61 861 202 HOH HOH . H 6 HOH A 62 862 84 HOH HOH . H 6 HOH A 63 863 173 HOH HOH . H 6 HOH A 64 864 33 HOH HOH . H 6 HOH A 65 865 200 HOH HOH . H 6 HOH A 66 866 67 HOH HOH . H 6 HOH A 67 867 177 HOH HOH . H 6 HOH A 68 868 49 HOH HOH . H 6 HOH A 69 869 146 HOH HOH . H 6 HOH A 70 870 78 HOH HOH . H 6 HOH A 71 871 71 HOH HOH . H 6 HOH A 72 872 35 HOH HOH . H 6 HOH A 73 873 172 HOH HOH . H 6 HOH A 74 874 47 HOH HOH . H 6 HOH A 75 875 70 HOH HOH . H 6 HOH A 76 876 26 HOH HOH . H 6 HOH A 77 877 148 HOH HOH . H 6 HOH A 78 878 13 HOH HOH . H 6 HOH A 79 879 54 HOH HOH . H 6 HOH A 80 880 85 HOH HOH . H 6 HOH A 81 881 112 HOH HOH . H 6 HOH A 82 882 99 HOH HOH . H 6 HOH A 83 883 105 HOH HOH . H 6 HOH A 84 884 166 HOH HOH . H 6 HOH A 85 885 90 HOH HOH . H 6 HOH A 86 886 106 HOH HOH . H 6 HOH A 87 887 161 HOH HOH . H 6 HOH A 88 888 40 HOH HOH . H 6 HOH A 89 889 102 HOH HOH . H 6 HOH A 90 890 15 HOH HOH . H 6 HOH A 91 891 58 HOH HOH . H 6 HOH A 92 892 101 HOH HOH . H 6 HOH A 93 893 7 HOH HOH . H 6 HOH A 94 894 94 HOH HOH . H 6 HOH A 95 895 5 HOH HOH . H 6 HOH A 96 896 64 HOH HOH . H 6 HOH A 97 897 46 HOH HOH . H 6 HOH A 98 898 55 HOH HOH . H 6 HOH A 99 899 48 HOH HOH . H 6 HOH A 100 900 29 HOH HOH . H 6 HOH A 101 901 66 HOH HOH . H 6 HOH A 102 902 82 HOH HOH . H 6 HOH A 103 903 27 HOH HOH . H 6 HOH A 104 904 10 HOH HOH . H 6 HOH A 105 905 20 HOH HOH . H 6 HOH A 106 906 30 HOH HOH . H 6 HOH A 107 907 111 HOH HOH . H 6 HOH A 108 908 150 HOH HOH . H 6 HOH A 109 909 43 HOH HOH . H 6 HOH A 110 910 12 HOH HOH . H 6 HOH A 111 911 50 HOH HOH . H 6 HOH A 112 912 65 HOH HOH . H 6 HOH A 113 913 129 HOH HOH . H 6 HOH A 114 914 36 HOH HOH . H 6 HOH A 115 915 95 HOH HOH . H 6 HOH A 116 916 141 HOH HOH . H 6 HOH A 117 917 37 HOH HOH . H 6 HOH A 118 918 89 HOH HOH . H 6 HOH A 119 919 109 HOH HOH . H 6 HOH A 120 920 204 HOH HOH . H 6 HOH A 121 921 14 HOH HOH . H 6 HOH A 122 922 216 HOH HOH . H 6 HOH A 123 923 19 HOH HOH . H 6 HOH A 124 924 62 HOH HOH . H 6 HOH A 125 925 175 HOH HOH . H 6 HOH A 126 926 123 HOH HOH . H 6 HOH A 127 927 59 HOH HOH . H 6 HOH A 128 928 170 HOH HOH . H 6 HOH A 129 929 154 HOH HOH . H 6 HOH A 130 930 79 HOH HOH . H 6 HOH A 131 931 143 HOH HOH . H 6 HOH A 132 932 83 HOH HOH . H 6 HOH A 133 933 206 HOH HOH . H 6 HOH A 134 934 153 HOH HOH . H 6 HOH A 135 935 110 HOH HOH . H 6 HOH A 136 936 189 HOH HOH . H 6 HOH A 137 937 31 HOH HOH . H 6 HOH A 138 938 23 HOH HOH . H 6 HOH A 139 939 77 HOH HOH . H 6 HOH A 140 940 4 HOH HOH . H 6 HOH A 141 941 42 HOH HOH . H 6 HOH A 142 942 91 HOH HOH . H 6 HOH A 143 943 39 HOH HOH . H 6 HOH A 144 944 24 HOH HOH . H 6 HOH A 145 945 28 HOH HOH . H 6 HOH A 146 946 104 HOH HOH . H 6 HOH A 147 947 140 HOH HOH . H 6 HOH A 148 948 32 HOH HOH . H 6 HOH A 149 949 195 HOH HOH . H 6 HOH A 150 950 116 HOH HOH . H 6 HOH A 151 951 81 HOH HOH . H 6 HOH A 152 952 125 HOH HOH . H 6 HOH A 153 953 57 HOH HOH . H 6 HOH A 154 954 127 HOH HOH . H 6 HOH A 155 955 132 HOH HOH . H 6 HOH A 156 956 53 HOH HOH . H 6 HOH A 157 957 139 HOH HOH . H 6 HOH A 158 958 25 HOH HOH . H 6 HOH A 159 959 168 HOH HOH . H 6 HOH A 160 960 114 HOH HOH . H 6 HOH A 161 961 214 HOH HOH . H 6 HOH A 162 962 76 HOH HOH . H 6 HOH A 163 963 11 HOH HOH . H 6 HOH A 164 964 21 HOH HOH . H 6 HOH A 165 965 210 HOH HOH . H 6 HOH A 166 966 128 HOH HOH . H 6 HOH A 167 967 198 HOH HOH . H 6 HOH A 168 968 133 HOH HOH . H 6 HOH A 169 969 120 HOH HOH . H 6 HOH A 170 970 211 HOH HOH . H 6 HOH A 171 971 181 HOH HOH . H 6 HOH A 172 972 122 HOH HOH . H 6 HOH A 173 973 107 HOH HOH . H 6 HOH A 174 974 199 HOH HOH . H 6 HOH A 175 975 162 HOH HOH . H 6 HOH A 176 976 121 HOH HOH . H 6 HOH A 177 977 138 HOH HOH . H 6 HOH A 178 978 176 HOH HOH . H 6 HOH A 179 979 194 HOH HOH . H 6 HOH A 180 980 160 HOH HOH . H 6 HOH A 181 981 98 HOH HOH . H 6 HOH A 182 982 130 HOH HOH . H 6 HOH A 183 983 155 HOH HOH . H 6 HOH A 184 984 183 HOH HOH . H 6 HOH A 185 985 171 HOH HOH . H 6 HOH A 186 986 164 HOH HOH . H 6 HOH A 187 987 186 HOH HOH . H 6 HOH A 188 988 134 HOH HOH . H 6 HOH A 189 989 208 HOH HOH . H 6 HOH A 190 990 119 HOH HOH . H 6 HOH A 191 991 158 HOH HOH . H 6 HOH A 192 992 136 HOH HOH . H 6 HOH A 193 993 169 HOH HOH . H 6 HOH A 194 994 212 HOH HOH . H 6 HOH A 195 995 115 HOH HOH . H 6 HOH A 196 996 167 HOH HOH . H 6 HOH A 197 997 207 HOH HOH . H 6 HOH A 198 998 196 HOH HOH . H 6 HOH A 199 999 157 HOH HOH . H 6 HOH A 200 1000 213 HOH HOH . H 6 HOH A 201 1001 191 HOH HOH . H 6 HOH A 202 1002 185 HOH HOH . H 6 HOH A 203 1003 201 HOH HOH . H 6 HOH A 204 1004 193 HOH HOH . H 6 HOH A 205 1005 192 HOH HOH . H 6 HOH A 206 1006 165 HOH HOH . H 6 HOH A 207 1007 184 HOH HOH . H 6 HOH A 208 1008 205 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 C C1 SPV . . . F 5 1.156 -2.132 10.015 1 34.28 ? C1 SPV 705 A 1 HETATM 2 O O1 SPV . . . F 5 0.76 -0.943 10.117 1 31.43 ? O1 SPV 705 A 1 HETATM 3 O O2' SPV . . . F 5 2.349 -2.434 10.212 1 35.12 ? O2' SPV 705 A 1 HETATM 4 C C2 SPV . . . F 5 0.198 -3.179 9.651 1 34.84 ? C2 SPV 705 A 1 HETATM 5 C C3 SPV . . . F 5 0.68 -4.605 9.403 1 34.84 ? C3 SPV 705 A 1 HETATM 6 O O2 SPV . . . F 5 -1 -2.877 9.557 1 32.94 ? O2 SPV 705 A 1 HETATM 7 S S SPV . . . F 5 1.234 -4.879 7.837 1 36.29 ? S SPV 705 A 1 HETATM 8 O O1S SPV . . . F 5 0.115 -4.874 6.942 1 35.9 ? O1S SPV 705 A 1 HETATM 9 O O2S SPV . . . F 5 2.006 -6.312 7.816 1 35.67 ? O2S SPV 705 A 1 HETATM 10 O O3S SPV . . . F 5 2.19 -3.881 7.474 1 35.92 ? O3S SPV 705 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 10 #