data_5B47 # _model_server_result.job_id 4m9_icbKS_oN-qHHwE0QYA _model_server_result.datetime_utc '2025-03-13 21:10:43' _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 5b47 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5B47 # _exptl.entry_id 5B47 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _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 5B47 _cell.length_a 100.673 _cell.length_b 203.655 _cell.length_c 126.006 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B47 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 63.003 # _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 B SG CYS 12 B CYS 12 1_555 D FE3 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc2 B SG CYS 15 B CYS 15 1_555 D FE1 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc3 B SG CYS 46 B CYS 46 1_555 D FE2 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc4 B OD1 ASP 90 B ASP 90 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc5 B OD1 ASN 118 B ASN 118 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc6 B SG CYS 197 B CYS 197 1_555 D FE4 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc7 E O1A TPP . B TPP 402 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc8 E O3B TPP . B TPP 402 1_555 F MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC ACID' _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 C O PYR doub 277 n n C OXT PYR sing 278 n n C CA PYR sing 279 n n OXT HXT PYR sing 280 n n CA O3 PYR doub 281 n n CA CB PYR sing 282 n n CB HB1 PYR sing 283 n n CB HB2 PYR sing 284 n n CB HB3 PYR sing 285 n n # _atom_sites.entry_id 5B47 _atom_sites.fract_transf_matrix[1][1] 0.009933 _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] 0.00491 _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] 0.007936 _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 C 3 PYR A 1 701 3227 PYR PYR . D 4 SF4 B 1 401 3235 SF4 SF4 . E 5 TPP B 1 402 3236 TPP TPP . F 6 MG B 1 403 3228 MG MG . G 7 HOH A 1 801 22 HOH HOH . G 7 HOH A 2 802 11 HOH HOH . G 7 HOH A 3 803 160 HOH HOH . G 7 HOH A 4 804 87 HOH HOH . G 7 HOH A 5 805 135 HOH HOH . G 7 HOH A 6 806 139 HOH HOH . G 7 HOH A 7 807 47 HOH HOH . G 7 HOH A 8 808 4 HOH HOH . G 7 HOH A 9 809 143 HOH HOH . G 7 HOH A 10 810 66 HOH HOH . G 7 HOH A 11 811 72 HOH HOH . G 7 HOH A 12 812 145 HOH HOH . G 7 HOH A 13 813 86 HOH HOH . G 7 HOH A 14 814 75 HOH HOH . G 7 HOH A 15 815 95 HOH HOH . G 7 HOH A 16 816 172 HOH HOH . G 7 HOH A 17 817 63 HOH HOH . G 7 HOH A 18 818 121 HOH HOH . G 7 HOH A 19 819 107 HOH HOH . G 7 HOH A 20 820 32 HOH HOH . G 7 HOH A 21 821 41 HOH HOH . G 7 HOH A 22 822 46 HOH HOH . G 7 HOH A 23 823 186 HOH HOH . G 7 HOH A 24 824 188 HOH HOH . G 7 HOH A 25 825 7 HOH HOH . G 7 HOH A 26 826 115 HOH HOH . G 7 HOH A 27 827 113 HOH HOH . G 7 HOH A 28 828 67 HOH HOH . G 7 HOH A 29 829 2 HOH HOH . G 7 HOH A 30 830 124 HOH HOH . G 7 HOH A 31 831 14 HOH HOH . G 7 HOH A 32 832 44 HOH HOH . G 7 HOH A 33 833 21 HOH HOH . G 7 HOH A 34 834 131 HOH HOH . G 7 HOH A 35 835 33 HOH HOH . G 7 HOH A 36 836 39 HOH HOH . G 7 HOH A 37 837 141 HOH HOH . G 7 HOH A 38 838 6 HOH HOH . G 7 HOH A 39 839 123 HOH HOH . G 7 HOH A 40 840 26 HOH HOH . G 7 HOH A 41 841 174 HOH HOH . G 7 HOH A 42 842 99 HOH HOH . G 7 HOH A 43 843 134 HOH HOH . G 7 HOH A 44 844 191 HOH HOH . G 7 HOH A 45 845 8 HOH HOH . G 7 HOH A 46 846 10 HOH HOH . G 7 HOH A 47 847 27 HOH HOH . G 7 HOH A 48 848 176 HOH HOH . G 7 HOH A 49 849 155 HOH HOH . G 7 HOH A 50 850 56 HOH HOH . G 7 HOH A 51 851 96 HOH HOH . G 7 HOH A 52 852 69 HOH HOH . G 7 HOH A 53 853 35 HOH HOH . G 7 HOH A 54 854 89 HOH HOH . G 7 HOH A 55 855 24 HOH HOH . G 7 HOH A 56 856 3 HOH HOH . G 7 HOH A 57 857 85 HOH HOH . G 7 HOH A 58 858 156 HOH HOH . G 7 HOH A 59 859 178 HOH HOH . G 7 HOH A 60 860 29 HOH HOH . G 7 HOH A 61 861 76 HOH HOH . G 7 HOH A 62 862 38 HOH HOH . G 7 HOH A 63 863 103 HOH HOH . G 7 HOH A 64 864 108 HOH HOH . G 7 HOH A 65 865 129 HOH HOH . G 7 HOH A 66 866 168 HOH HOH . G 7 HOH A 67 867 53 HOH HOH . G 7 HOH A 68 868 185 HOH HOH . G 7 HOH A 69 869 189 HOH HOH . G 7 HOH A 70 870 15 HOH HOH . G 7 HOH A 71 871 9 HOH HOH . G 7 HOH A 72 872 13 HOH HOH . G 7 HOH A 73 873 120 HOH HOH . G 7 HOH A 74 874 1 HOH HOH . G 7 HOH A 75 875 164 HOH HOH . G 7 HOH A 76 876 5 HOH HOH . G 7 HOH A 77 877 170 HOH HOH . G 7 HOH A 78 878 17 HOH HOH . G 7 HOH A 79 879 187 HOH HOH . G 7 HOH A 80 880 110 HOH HOH . G 7 HOH A 81 881 161 HOH HOH . G 7 HOH A 82 882 61 HOH HOH . G 7 HOH A 83 883 184 HOH HOH . G 7 HOH A 84 884 128 HOH HOH . G 7 HOH A 85 885 105 HOH HOH . G 7 HOH A 86 886 137 HOH HOH . G 7 HOH A 87 887 50 HOH HOH . G 7 HOH A 88 888 146 HOH HOH . G 7 HOH A 89 889 126 HOH HOH . G 7 HOH A 90 890 62 HOH HOH . G 7 HOH A 91 891 40 HOH HOH . G 7 HOH A 92 892 36 HOH HOH . G 7 HOH A 93 893 64 HOH HOH . G 7 HOH A 94 894 163 HOH HOH . G 7 HOH A 95 895 162 HOH HOH . G 7 HOH A 96 896 166 HOH HOH . G 7 HOH A 97 897 173 HOH HOH . G 7 HOH A 98 898 182 HOH HOH . G 7 HOH A 99 899 171 HOH HOH . G 7 HOH A 100 900 91 HOH HOH . G 7 HOH A 101 901 169 HOH HOH . G 7 HOH A 102 902 49 HOH HOH . G 7 HOH A 103 903 158 HOH HOH . G 7 HOH A 104 904 57 HOH HOH . G 7 HOH A 105 905 140 HOH HOH . G 7 HOH A 106 906 30 HOH HOH . G 7 HOH A 107 907 179 HOH HOH . G 7 HOH A 108 908 175 HOH HOH . G 7 HOH A 109 909 116 HOH HOH . G 7 HOH A 110 910 19 HOH HOH . G 7 HOH A 111 911 147 HOH HOH . G 7 HOH A 112 912 78 HOH HOH . G 7 HOH A 113 913 101 HOH HOH . G 7 HOH A 114 914 18 HOH HOH . G 7 HOH A 115 915 133 HOH HOH . G 7 HOH A 116 916 31 HOH HOH . G 7 HOH A 117 917 150 HOH HOH . G 7 HOH A 118 918 104 HOH HOH . G 7 HOH A 119 919 119 HOH HOH . G 7 HOH A 120 920 82 HOH HOH . G 7 HOH A 121 921 190 HOH HOH . G 7 HOH A 122 922 65 HOH HOH . G 7 HOH A 123 923 84 HOH HOH . G 7 HOH A 124 924 159 HOH HOH . G 7 HOH A 125 925 127 HOH HOH . G 7 HOH A 126 926 79 HOH HOH . G 7 HOH A 127 927 42 HOH HOH . G 7 HOH A 128 928 23 HOH HOH . G 7 HOH A 129 929 34 HOH HOH . G 7 HOH A 130 930 94 HOH HOH . G 7 HOH A 131 931 93 HOH HOH . G 7 HOH A 132 932 81 HOH HOH . G 7 HOH A 133 933 43 HOH HOH . G 7 HOH A 134 934 25 HOH HOH . G 7 HOH A 135 935 136 HOH HOH . G 7 HOH A 136 936 111 HOH HOH . G 7 HOH A 137 937 45 HOH HOH . G 7 HOH A 138 938 144 HOH HOH . G 7 HOH A 139 939 177 HOH HOH . G 7 HOH A 140 940 58 HOH HOH . G 7 HOH A 141 941 20 HOH HOH . G 7 HOH A 142 942 181 HOH HOH . G 7 HOH A 143 943 109 HOH HOH . G 7 HOH A 144 944 68 HOH HOH . G 7 HOH A 145 945 122 HOH HOH . G 7 HOH A 146 946 55 HOH HOH . G 7 HOH A 147 947 74 HOH HOH . G 7 HOH A 148 948 148 HOH HOH . G 7 HOH A 149 949 28 HOH HOH . G 7 HOH A 150 950 90 HOH HOH . G 7 HOH A 151 951 16 HOH HOH . G 7 HOH A 152 952 51 HOH HOH . G 7 HOH A 153 953 149 HOH HOH . G 7 HOH A 154 954 98 HOH HOH . G 7 HOH A 155 955 180 HOH HOH . G 7 HOH A 156 956 142 HOH HOH . G 7 HOH A 157 957 183 HOH HOH . G 7 HOH A 158 958 59 HOH HOH . G 7 HOH A 159 959 73 HOH HOH . H 7 HOH B 1 501 12 HOH HOH . H 7 HOH B 2 502 130 HOH HOH . H 7 HOH B 3 503 157 HOH HOH . H 7 HOH B 4 504 153 HOH HOH . H 7 HOH B 5 505 132 HOH HOH . H 7 HOH B 6 506 88 HOH HOH . H 7 HOH B 7 507 165 HOH HOH . H 7 HOH B 8 508 80 HOH HOH . H 7 HOH B 9 509 138 HOH HOH . H 7 HOH B 10 510 60 HOH HOH . H 7 HOH B 11 511 114 HOH HOH . H 7 HOH B 12 512 52 HOH HOH . H 7 HOH B 13 513 70 HOH HOH . H 7 HOH B 14 514 71 HOH HOH . H 7 HOH B 15 515 97 HOH HOH . H 7 HOH B 16 516 100 HOH HOH . H 7 HOH B 17 517 37 HOH HOH . H 7 HOH B 18 518 83 HOH HOH . H 7 HOH B 19 519 167 HOH HOH . H 7 HOH B 20 520 152 HOH HOH . H 7 HOH B 21 521 48 HOH HOH . H 7 HOH B 22 522 92 HOH HOH . H 7 HOH B 23 523 54 HOH HOH . H 7 HOH B 24 524 154 HOH HOH . H 7 HOH B 25 525 117 HOH HOH . H 7 HOH B 26 526 102 HOH HOH . H 7 HOH B 27 527 151 HOH HOH . H 7 HOH B 28 528 125 HOH HOH . H 7 HOH B 29 529 106 HOH HOH . H 7 HOH B 30 530 77 HOH HOH . H 7 HOH B 31 531 112 HOH HOH . H 7 HOH B 32 532 118 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 C PYR . . . C 3 6.042 -28.251 15.086 1 85.08 ? C PYR 701 A 1 HETATM 2 O O PYR . . . C 3 6.333 -27.882 13.878 1 82.73 ? O PYR 701 A 1 HETATM 3 O OXT PYR . . . C 3 4.873 -28.646 15.331 1 58.11 ? OXT PYR 701 A 1 HETATM 4 C CA PYR . . . C 3 7.027 -28.243 16.248 1 85.51 ? CA PYR 701 A 1 HETATM 5 O O3 PYR . . . C 3 6.683 -28.604 17.396 1 67.05 ? O3 PYR 701 A 1 HETATM 6 C CB PYR . . . C 3 8.466 -27.777 16.079 1 82.96 ? CB PYR 701 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 6 #