data_5WTD # _model_server_result.job_id i3BFUcVK7AB9gFd9V1hwMA _model_server_result.datetime_utc '2024-11-06 02:59:00' _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 5wtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 5WTD # _exptl.entry_id 5WTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.046 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONATE ION' _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 5WTD _cell.length_a 137.113 _cell.length_b 157.351 _cell.length_c 107.086 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WTD _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 ? _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 # 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 disulf ? disulf1 A SG CYS 9 A CYS 9 1_555 A SG CYS 48 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf2 A SG CYS 19 A CYS 19 1_555 A SG CYS 39 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 118 A CYS 118 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf4 A SG CYS 137 A CYS 137 1_555 A SG CYS 331 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 158 A CYS 158 1_555 A SG CYS 174 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf6 A SG CYS 161 A CYS 161 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? disulf ? disulf7 A SG CYS 171 A CYS 171 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 A SG CYS 227 A CYS 227 1_555 A SG CYS 241 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf9 A SG CYS 339 A CYS 339 1_555 A SG CYS 596 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf10 A SG CYS 345 A CYS 345 1_555 A SG CYS 377 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf11 A SG CYS 355 A CYS 355 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 A SG CYS 402 A CYS 402 1_555 A SG CYS 674 A CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf13 A SG CYS 450 A CYS 450 1_555 A SG CYS 523 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 A SG CYS 474 A CYS 474 1_555 A SG CYS 665 A CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 A SG CYS 484 A CYS 484 1_555 A SG CYS 498 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 A SG CYS 495 A CYS 495 1_555 A SG CYS 506 A CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf17 A SG CYS 563 A CYS 563 1_555 A SG CYS 577 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A NE2 HIS 14 A HIS 14 1_555 D RU RU . A RU 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc2 A NE2 HIS 289 A HIS 289 1_555 D RU RU . A RU 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc3 A OD1 ASP 392 A ASP 392 1_555 B FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc4 A OH TYR 426 A TYR 426 1_555 B FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc5 A OH TYR 517 A TYR 517 1_555 B FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc6 A NE2 HIS 585 A HIS 585 1_555 B FE FE . A FE 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc7 B FE FE . A FE 701 1_555 C O7 MLI . A MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc8 B FE FE . A FE 701 1_555 C O9 MLI . A MLI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc9 D RU RU . A RU 703 1_555 E O HOH . A HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc10 D RU RU . A RU 703 1_555 E O HOH . A HOH 946 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc11 D RU RU . A RU 703 1_555 E O HOH . A HOH 948 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? # _chem_comp.formula 'C3 H2 O4 -2' _chem_comp.formula_weight 102.046 _chem_comp.id MLI _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONATE ION' _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 C2 MLI sing 237 n n C1 C3 MLI sing 238 n n C1 H11 MLI sing 239 n n C1 H12 MLI sing 240 n n C2 O6 MLI doub 241 n n C2 O7 MLI sing 242 n n C3 O8 MLI doub 243 n n C3 O9 MLI sing 244 n n # _atom_sites.entry_id 5WTD _atom_sites.fract_transf_matrix[1][1] 0.007293 _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] 0.006355 _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] 0.009338 _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 FE A 1 701 681 FE FE . C 3 MLI A 1 702 682 MLI MLI . D 4 RU A 1 703 691 RU RU . E 5 HOH A 1 801 59 HOH HOH . E 5 HOH A 2 802 11 HOH HOH . E 5 HOH A 3 803 103 HOH HOH . E 5 HOH A 4 804 134 HOH HOH . E 5 HOH A 5 805 18 HOH HOH . E 5 HOH A 6 806 130 HOH HOH . E 5 HOH A 7 807 44 HOH HOH . E 5 HOH A 8 808 53 HOH HOH . E 5 HOH A 9 809 25 HOH HOH . E 5 HOH A 10 810 95 HOH HOH . E 5 HOH A 11 811 174 HOH HOH . E 5 HOH A 12 812 60 HOH HOH . E 5 HOH A 13 813 54 HOH HOH . E 5 HOH A 14 814 117 HOH HOH . E 5 HOH A 15 815 86 HOH HOH . E 5 HOH A 16 816 51 HOH HOH . E 5 HOH A 17 817 184 HOH HOH . E 5 HOH A 18 818 42 HOH HOH . E 5 HOH A 19 819 94 HOH HOH . E 5 HOH A 20 820 66 HOH HOH . E 5 HOH A 21 821 29 HOH HOH . E 5 HOH A 22 822 108 HOH HOH . E 5 HOH A 23 823 157 HOH HOH . E 5 HOH A 24 824 43 HOH HOH . E 5 HOH A 25 825 80 HOH HOH . E 5 HOH A 26 826 10 HOH HOH . E 5 HOH A 27 827 69 HOH HOH . E 5 HOH A 28 828 72 HOH HOH . E 5 HOH A 29 829 79 HOH HOH . E 5 HOH A 30 830 45 HOH HOH . E 5 HOH A 31 831 104 HOH HOH . E 5 HOH A 32 832 55 HOH HOH . E 5 HOH A 33 833 111 HOH HOH . E 5 HOH A 34 834 73 HOH HOH . E 5 HOH A 35 835 9 HOH HOH . E 5 HOH A 36 836 4 HOH HOH . E 5 HOH A 37 837 21 HOH HOH . E 5 HOH A 38 838 177 HOH HOH . E 5 HOH A 39 839 13 HOH HOH . E 5 HOH A 40 840 41 HOH HOH . E 5 HOH A 41 841 181 HOH HOH . E 5 HOH A 42 842 199 HOH HOH . E 5 HOH A 43 843 67 HOH HOH . E 5 HOH A 44 844 47 HOH HOH . E 5 HOH A 45 845 116 HOH HOH . E 5 HOH A 46 846 84 HOH HOH . E 5 HOH A 47 847 123 HOH HOH . E 5 HOH A 48 848 83 HOH HOH . E 5 HOH A 49 849 107 HOH HOH . E 5 HOH A 50 850 31 HOH HOH . E 5 HOH A 51 851 160 HOH HOH . E 5 HOH A 52 852 202 HOH HOH . E 5 HOH A 53 853 2 HOH HOH . E 5 HOH A 54 854 58 HOH HOH . E 5 HOH A 55 855 1 HOH HOH . E 5 HOH A 56 856 124 HOH HOH . E 5 HOH A 57 857 135 HOH HOH . E 5 HOH A 58 858 112 HOH HOH . E 5 HOH A 59 859 20 HOH HOH . E 5 HOH A 60 860 24 HOH HOH . E 5 HOH A 61 861 140 HOH HOH . E 5 HOH A 62 862 92 HOH HOH . E 5 HOH A 63 863 52 HOH HOH . E 5 HOH A 64 864 68 HOH HOH . E 5 HOH A 65 865 36 HOH HOH . E 5 HOH A 66 866 57 HOH HOH . E 5 HOH A 67 867 74 HOH HOH . E 5 HOH A 68 868 37 HOH HOH . E 5 HOH A 69 869 35 HOH HOH . E 5 HOH A 70 870 63 HOH HOH . E 5 HOH A 71 871 110 HOH HOH . E 5 HOH A 72 872 49 HOH HOH . E 5 HOH A 73 873 22 HOH HOH . E 5 HOH A 74 874 50 HOH HOH . E 5 HOH A 75 875 26 HOH HOH . E 5 HOH A 76 876 23 HOH HOH . E 5 HOH A 77 877 75 HOH HOH . E 5 HOH A 78 878 122 HOH HOH . E 5 HOH A 79 879 65 HOH HOH . E 5 HOH A 80 880 30 HOH HOH . E 5 HOH A 81 881 172 HOH HOH . E 5 HOH A 82 882 34 HOH HOH . E 5 HOH A 83 883 82 HOH HOH . E 5 HOH A 84 884 147 HOH HOH . E 5 HOH A 85 885 5 HOH HOH . E 5 HOH A 86 886 28 HOH HOH . E 5 HOH A 87 887 7 HOH HOH . E 5 HOH A 88 888 148 HOH HOH . E 5 HOH A 89 889 125 HOH HOH . E 5 HOH A 90 890 62 HOH HOH . E 5 HOH A 91 891 105 HOH HOH . E 5 HOH A 92 892 8 HOH HOH . E 5 HOH A 93 893 32 HOH HOH . E 5 HOH A 94 894 114 HOH HOH . E 5 HOH A 95 895 3 HOH HOH . E 5 HOH A 96 896 97 HOH HOH . E 5 HOH A 97 897 96 HOH HOH . E 5 HOH A 98 898 98 HOH HOH . E 5 HOH A 99 899 176 HOH HOH . E 5 HOH A 100 900 88 HOH HOH . E 5 HOH A 101 901 158 HOH HOH . E 5 HOH A 102 902 19 HOH HOH . E 5 HOH A 103 903 166 HOH HOH . E 5 HOH A 104 904 153 HOH HOH . E 5 HOH A 105 905 210 HOH HOH . E 5 HOH A 106 906 113 HOH HOH . E 5 HOH A 107 907 14 HOH HOH . E 5 HOH A 108 908 178 HOH HOH . E 5 HOH A 109 909 85 HOH HOH . E 5 HOH A 110 910 40 HOH HOH . E 5 HOH A 111 911 27 HOH HOH . E 5 HOH A 112 912 169 HOH HOH . E 5 HOH A 113 913 211 HOH HOH . E 5 HOH A 114 914 137 HOH HOH . E 5 HOH A 115 915 198 HOH HOH . E 5 HOH A 116 916 693 HOH HOH . E 5 HOH A 117 917 61 HOH HOH . E 5 HOH A 118 918 76 HOH HOH . E 5 HOH A 119 919 106 HOH HOH . E 5 HOH A 120 920 165 HOH HOH . E 5 HOH A 121 921 15 HOH HOH . E 5 HOH A 122 922 143 HOH HOH . E 5 HOH A 123 923 131 HOH HOH . E 5 HOH A 124 924 78 HOH HOH . E 5 HOH A 125 925 133 HOH HOH . E 5 HOH A 126 926 119 HOH HOH . E 5 HOH A 127 927 70 HOH HOH . E 5 HOH A 128 928 87 HOH HOH . E 5 HOH A 129 929 93 HOH HOH . E 5 HOH A 130 930 161 HOH HOH . E 5 HOH A 131 931 91 HOH HOH . E 5 HOH A 132 932 142 HOH HOH . E 5 HOH A 133 933 17 HOH HOH . E 5 HOH A 134 934 71 HOH HOH . E 5 HOH A 135 935 64 HOH HOH . E 5 HOH A 136 936 6 HOH HOH . E 5 HOH A 137 937 127 HOH HOH . E 5 HOH A 138 938 167 HOH HOH . E 5 HOH A 139 939 100 HOH HOH . E 5 HOH A 140 940 33 HOH HOH . E 5 HOH A 141 941 46 HOH HOH . E 5 HOH A 142 942 81 HOH HOH . E 5 HOH A 143 943 12 HOH HOH . E 5 HOH A 144 944 156 HOH HOH . E 5 HOH A 145 945 101 HOH HOH . E 5 HOH A 146 946 695 HOH HOH . E 5 HOH A 147 947 128 HOH HOH . E 5 HOH A 148 948 692 HOH HOH . E 5 HOH A 149 949 162 HOH HOH . E 5 HOH A 150 950 126 HOH HOH . E 5 HOH A 151 951 182 HOH HOH . E 5 HOH A 152 952 115 HOH HOH . E 5 HOH A 153 953 16 HOH HOH . E 5 HOH A 154 954 694 HOH HOH . E 5 HOH A 155 955 129 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 MLI . . . C 3 36.458 48.288 -7.729 1 23.56 ? C1 MLI 702 A 1 HETATM 2 C C2 MLI . . . C 3 35.366 49.188 -7.189 1 32.75 ? C2 MLI 702 A 1 HETATM 3 C C3 MLI . . . C 3 36.843 47.166 -6.791 1 33.1 ? C3 MLI 702 A 1 HETATM 4 O O6 MLI . . . C 3 34.617 49.738 -8.025 1 37.07 ? O6 MLI 702 A 1 HETATM 5 O O7 MLI . . . C 3 35.241 49.382 -5.955 1 40.43 ? O7 MLI 702 A 1 HETATM 6 O O8 MLI . . . C 3 36.808 45.992 -7.217 1 44.46 ? O8 MLI 702 A 1 HETATM 7 O O9 MLI . . . C 3 37.206 47.429 -5.623 1 46.07 ? O9 MLI 702 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #