data_5TDM # _model_server_result.job_id -IfzC4Vl2DvA4P4-opc1-g _model_server_result.datetime_utc '2024-11-05 22:52:20' _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 5tdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 5TDM # _exptl.entry_id 5TDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 208.123 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-C-carboxy-2-deoxy-L-threo-pentaric 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 5TDM _cell.length_a 55.379 _cell.length_b 84.814 _cell.length_c 193.869 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J,K _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 metalc ? metalc1 A O ASN 203 A ASN 203 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc2 A OD2 ASP 216 A ASP 216 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? covale ? covale1 B C GLY 273 B GLY 759 1_555 B N NEP 274 B NEP 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 B C NEP 274 B NEP 760 1_555 B N ALA 275 B ALA 761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? metalc ? metalc3 B O3P NEP 274 B NEP 760 1_555 H MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc4 D O1A ADP . A ADP 902 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 E MG MG . A MG 903 1_555 J O HOH . A HOH 1038 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc6 E MG MG . A MG 903 1_555 J O HOH . A HOH 1087 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? covale ? covale3 F C8 ADN . A ADN 904 1_555 G O1 GOL . A GOL 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? metalc ? metalc7 H MG MG . B MG 901 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc8 H MG MG . B MG 901 1_555 K O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc9 H MG MG . B MG 901 1_555 K O HOH . B HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? # _chem_comp.formula 'C6 H8 O8' _chem_comp.formula_weight 208.123 _chem_comp.id 7A2 _chem_comp.mon_nstd_flag . _chem_comp.name '3-C-carboxy-2-deoxy-L-threo-pentaric acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5TDM _atom_sites.fract_transf_matrix[1][1] 0.018057 _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] 0.011791 _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] 0.005158 _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 7A2 A 1 901 901 7A2 7A2 . D 4 ADP A 1 902 902 ADP ADP . E 5 MG A 1 903 903 MG MG . F 6 ADN A 1 904 905 ADN ADN . G 7 GOL A 1 905 907 GOL GOL . H 5 MG B 1 901 904 MG MG . I 7 GOL B 1 902 906 GOL GOL . J 8 HOH A 1 1001 1002 HOH HOH . J 8 HOH A 2 1002 1003 HOH HOH . J 8 HOH A 3 1003 1004 HOH HOH . J 8 HOH A 4 1004 1005 HOH HOH . J 8 HOH A 5 1005 1006 HOH HOH . J 8 HOH A 6 1006 1008 HOH HOH . J 8 HOH A 7 1007 1009 HOH HOH . J 8 HOH A 8 1008 1010 HOH HOH . J 8 HOH A 9 1009 1015 HOH HOH . J 8 HOH A 10 1010 1017 HOH HOH . J 8 HOH A 11 1011 1018 HOH HOH . J 8 HOH A 12 1012 1019 HOH HOH . J 8 HOH A 13 1013 1023 HOH HOH . J 8 HOH A 14 1014 1024 HOH HOH . J 8 HOH A 15 1015 1025 HOH HOH . J 8 HOH A 16 1016 1026 HOH HOH . J 8 HOH A 17 1017 1029 HOH HOH . J 8 HOH A 18 1018 1030 HOH HOH . J 8 HOH A 19 1019 1033 HOH HOH . J 8 HOH A 20 1020 1038 HOH HOH . J 8 HOH A 21 1021 1039 HOH HOH . J 8 HOH A 22 1022 1040 HOH HOH . J 8 HOH A 23 1023 1047 HOH HOH . J 8 HOH A 24 1024 1048 HOH HOH . J 8 HOH A 25 1025 1051 HOH HOH . J 8 HOH A 26 1026 1056 HOH HOH . J 8 HOH A 27 1027 1058 HOH HOH . J 8 HOH A 28 1028 1061 HOH HOH . J 8 HOH A 29 1029 1062 HOH HOH . J 8 HOH A 30 1030 1063 HOH HOH . J 8 HOH A 31 1031 1064 HOH HOH . J 8 HOH A 32 1032 1065 HOH HOH . J 8 HOH A 33 1033 1066 HOH HOH . J 8 HOH A 34 1034 1067 HOH HOH . J 8 HOH A 35 1035 1068 HOH HOH . J 8 HOH A 36 1036 1069 HOH HOH . J 8 HOH A 37 1037 1070 HOH HOH . J 8 HOH A 38 1038 1071 HOH HOH . J 8 HOH A 39 1039 1072 HOH HOH . J 8 HOH A 40 1040 1073 HOH HOH . J 8 HOH A 41 1041 1074 HOH HOH . J 8 HOH A 42 1042 1075 HOH HOH . J 8 HOH A 43 1043 1076 HOH HOH . J 8 HOH A 44 1044 1077 HOH HOH . J 8 HOH A 45 1045 1078 HOH HOH . J 8 HOH A 46 1046 1079 HOH HOH . J 8 HOH A 47 1047 1081 HOH HOH . J 8 HOH A 48 1048 1083 HOH HOH . J 8 HOH A 49 1049 1088 HOH HOH . J 8 HOH A 50 1050 1089 HOH HOH . J 8 HOH A 51 1051 1091 HOH HOH . J 8 HOH A 52 1052 1093 HOH HOH . J 8 HOH A 53 1053 1094 HOH HOH . J 8 HOH A 54 1054 1096 HOH HOH . J 8 HOH A 55 1055 1097 HOH HOH . J 8 HOH A 56 1056 1099 HOH HOH . J 8 HOH A 57 1057 1101 HOH HOH . J 8 HOH A 58 1058 1102 HOH HOH . J 8 HOH A 59 1059 1103 HOH HOH . J 8 HOH A 60 1060 1104 HOH HOH . J 8 HOH A 61 1061 1105 HOH HOH . J 8 HOH A 62 1062 1106 HOH HOH . J 8 HOH A 63 1063 1107 HOH HOH . J 8 HOH A 64 1064 1109 HOH HOH . J 8 HOH A 65 1065 1110 HOH HOH . J 8 HOH A 66 1066 1113 HOH HOH . J 8 HOH A 67 1067 1117 HOH HOH . J 8 HOH A 68 1068 1118 HOH HOH . J 8 HOH A 69 1069 1119 HOH HOH . J 8 HOH A 70 1070 1120 HOH HOH . J 8 HOH A 71 1071 1122 HOH HOH . J 8 HOH A 72 1072 1123 HOH HOH . J 8 HOH A 73 1073 1124 HOH HOH . J 8 HOH A 74 1074 1125 HOH HOH . J 8 HOH A 75 1075 1126 HOH HOH . J 8 HOH A 76 1076 1128 HOH HOH . J 8 HOH A 77 1077 1130 HOH HOH . J 8 HOH A 78 1078 1131 HOH HOH . J 8 HOH A 79 1079 1132 HOH HOH . J 8 HOH A 80 1080 1135 HOH HOH . J 8 HOH A 81 1081 1136 HOH HOH . J 8 HOH A 82 1082 1138 HOH HOH . J 8 HOH A 83 1083 1139 HOH HOH . J 8 HOH A 84 1084 1140 HOH HOH . J 8 HOH A 85 1085 1141 HOH HOH . J 8 HOH A 86 1086 1143 HOH HOH . J 8 HOH A 87 1087 1144 HOH HOH . J 8 HOH A 88 1088 1146 HOH HOH . J 8 HOH A 89 1089 1149 HOH HOH . J 8 HOH A 90 1090 1150 HOH HOH . J 8 HOH A 91 1091 1152 HOH HOH . J 8 HOH A 92 1092 1154 HOH HOH . J 8 HOH A 93 1093 1155 HOH HOH . J 8 HOH A 94 1094 1156 HOH HOH . J 8 HOH A 95 1095 1157 HOH HOH . J 8 HOH A 96 1096 1159 HOH HOH . J 8 HOH A 97 1097 1160 HOH HOH . J 8 HOH A 98 1098 1161 HOH HOH . J 8 HOH A 99 1099 1162 HOH HOH . J 8 HOH A 100 1100 1165 HOH HOH . J 8 HOH A 101 1101 1166 HOH HOH . J 8 HOH A 102 1102 1167 HOH HOH . J 8 HOH A 103 1103 1170 HOH HOH . J 8 HOH A 104 1104 1171 HOH HOH . J 8 HOH A 105 1105 1172 HOH HOH . J 8 HOH A 106 1106 1173 HOH HOH . J 8 HOH A 107 1107 1175 HOH HOH . J 8 HOH A 108 1108 1177 HOH HOH . J 8 HOH A 109 1109 1178 HOH HOH . J 8 HOH A 110 1110 1179 HOH HOH . J 8 HOH A 111 1111 1184 HOH HOH . J 8 HOH A 112 1112 1185 HOH HOH . J 8 HOH A 113 1113 1187 HOH HOH . K 8 HOH B 1 1001 1001 HOH HOH . K 8 HOH B 2 1002 1007 HOH HOH . K 8 HOH B 3 1003 1011 HOH HOH . K 8 HOH B 4 1004 1012 HOH HOH . K 8 HOH B 5 1005 1013 HOH HOH . K 8 HOH B 6 1006 1014 HOH HOH . K 8 HOH B 7 1007 1016 HOH HOH . K 8 HOH B 8 1008 1020 HOH HOH . K 8 HOH B 9 1009 1021 HOH HOH . K 8 HOH B 10 1010 1022 HOH HOH . K 8 HOH B 11 1011 1027 HOH HOH . K 8 HOH B 12 1012 1028 HOH HOH . K 8 HOH B 13 1013 1031 HOH HOH . K 8 HOH B 14 1014 1032 HOH HOH . K 8 HOH B 15 1015 1034 HOH HOH . K 8 HOH B 16 1016 1035 HOH HOH . K 8 HOH B 17 1017 1036 HOH HOH . K 8 HOH B 18 1018 1037 HOH HOH . K 8 HOH B 19 1019 1041 HOH HOH . K 8 HOH B 20 1020 1042 HOH HOH . K 8 HOH B 21 1021 1043 HOH HOH . K 8 HOH B 22 1022 1044 HOH HOH . K 8 HOH B 23 1023 1045 HOH HOH . K 8 HOH B 24 1024 1046 HOH HOH . K 8 HOH B 25 1025 1049 HOH HOH . K 8 HOH B 26 1026 1050 HOH HOH . K 8 HOH B 27 1027 1052 HOH HOH . K 8 HOH B 28 1028 1053 HOH HOH . K 8 HOH B 29 1029 1054 HOH HOH . K 8 HOH B 30 1030 1055 HOH HOH . K 8 HOH B 31 1031 1057 HOH HOH . K 8 HOH B 32 1032 1059 HOH HOH . K 8 HOH B 33 1033 1060 HOH HOH . K 8 HOH B 34 1034 1080 HOH HOH . K 8 HOH B 35 1035 1082 HOH HOH . K 8 HOH B 36 1036 1084 HOH HOH . K 8 HOH B 37 1037 1085 HOH HOH . K 8 HOH B 38 1038 1086 HOH HOH . K 8 HOH B 39 1039 1087 HOH HOH . K 8 HOH B 40 1040 1090 HOH HOH . K 8 HOH B 41 1041 1092 HOH HOH . K 8 HOH B 42 1042 1095 HOH HOH . K 8 HOH B 43 1043 1098 HOH HOH . K 8 HOH B 44 1044 1100 HOH HOH . K 8 HOH B 45 1045 1108 HOH HOH . K 8 HOH B 46 1046 1111 HOH HOH . K 8 HOH B 47 1047 1112 HOH HOH . K 8 HOH B 48 1048 1114 HOH HOH . K 8 HOH B 49 1049 1115 HOH HOH . K 8 HOH B 50 1050 1116 HOH HOH . K 8 HOH B 51 1051 1121 HOH HOH . K 8 HOH B 52 1052 1127 HOH HOH . K 8 HOH B 53 1053 1129 HOH HOH . K 8 HOH B 54 1054 1133 HOH HOH . K 8 HOH B 55 1055 1134 HOH HOH . K 8 HOH B 56 1056 1137 HOH HOH . K 8 HOH B 57 1057 1142 HOH HOH . K 8 HOH B 58 1058 1145 HOH HOH . K 8 HOH B 59 1059 1147 HOH HOH . K 8 HOH B 60 1060 1148 HOH HOH . K 8 HOH B 61 1061 1151 HOH HOH . K 8 HOH B 62 1062 1153 HOH HOH . K 8 HOH B 63 1063 1158 HOH HOH . K 8 HOH B 64 1064 1163 HOH HOH . K 8 HOH B 65 1065 1164 HOH HOH . K 8 HOH B 66 1066 1168 HOH HOH . K 8 HOH B 67 1067 1169 HOH HOH . K 8 HOH B 68 1068 1174 HOH HOH . K 8 HOH B 69 1069 1176 HOH HOH . K 8 HOH B 70 1070 1180 HOH HOH . K 8 HOH B 71 1071 1181 HOH HOH . K 8 HOH B 72 1072 1182 HOH HOH . K 8 HOH B 73 1073 1183 HOH HOH . K 8 HOH B 74 1074 1186 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 7A2 . . . C 3 23.63 -6.518 37.184 1 51.86 ? C 7A2 901 A 1 HETATM 2 O O 7A2 . . . C 3 24.841 -6.803 37.046 1 49.79 ? O 7A2 901 A 1 HETATM 3 C C1 7A2 . . . C 3 23.142 -5.131 37.505 1 70.61 ? C1 7A2 901 A 1 HETATM 4 C C2 7A2 . . . C 3 22.056 -5.107 38.592 1 85.36 ? C2 7A2 901 A 1 HETATM 5 C C3 7A2 . . . C 3 22.743 -5.856 39.741 1 91.02 ? C3 7A2 901 A 1 HETATM 6 C C4 7A2 . . . C 3 21.678 -3.693 39.093 1 96.39 ? C4 7A2 901 A 1 HETATM 7 C C5 7A2 . . . C 3 21.32 -2.716 37.976 1 80.8 ? C5 7A2 901 A 1 HETATM 8 O O1 7A2 . . . C 3 22.707 -7.358 37.051 1 44.37 ? O1 7A2 901 A 1 HETATM 9 O O2 7A2 . . . C 3 20.911 -5.825 38.167 1 75.06 ? O2 7A2 901 A 1 HETATM 10 O O3 7A2 . . . C 3 23.778 -5.434 40.271 1 98.47 ? O3 7A2 901 A 1 HETATM 11 O O4 7A2 . . . C 3 22.183 -6.923 40.072 1 92.16 ? O4 7A2 901 A 1 HETATM 12 O O5 7A2 . . . C 3 22.817 -3.196 39.776 1 107.78 ? O5 7A2 901 A 1 HETATM 13 O O6 7A2 . . . C 3 20.294 -1.997 38 1 70.74 ? O6 7A2 901 A 1 HETATM 14 O O7 7A2 . . . C 3 22.159 -2.686 37.06 1 74.3 ? O7 7A2 901 A 1 HETATM 15 H H2 7A2 . . . C 3 22.769 -4.682 36.585 1 84.74 ? H2 7A2 901 A 1 HETATM 16 H H3 7A2 . . . C 3 23.978 -4.504 37.811 1 84.74 ? H3 7A2 901 A 1 HETATM 17 H H 7A2 . . . C 3 20.855 -3.789 39.8 1 115.67 ? H 7A2 901 A 1 HETATM 18 H H4 7A2 . . . C 3 20.206 -5.751 38.863 1 90.08 ? H4 7A2 901 A 1 HETATM 19 H H6 7A2 . . . C 3 22.508 -2.472 40.381 1 129.33 ? H6 7A2 901 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 19 #