data_1XKD # _model_server_result.job_id LQ6HV0zSitwgtd95Z8bc7Q _model_server_result.datetime_utc '2024-11-29 14:00:50' _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 1xkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1002}' # _entry.id 1XKD # _exptl.entry_id 1XKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ISOCITRIC ACID' _entity.pdbx_number_of_molecules 2 _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 1XKD _cell.length_a 107.575 _cell.length_b 107.575 _cell.length_c 171.045 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N 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 87 A CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 9 B CYS 9 1_555 B SG CYS 87 B CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OD2 ASP 287 A ASP 287 1_555 C CA CA . A CA 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc2 A OD2 ASP 311 A ASP 311 1_555 D CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc3 A OD1 ASP 315 A ASP 315 1_555 D CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc4 F O2 ICT . A ICT 1002 1_555 D CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc5 F O7 ICT . A ICT 1002 1_555 D CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc6 C CA CA . A CA 1005 1_555 B OD2 ASP 311 B ASP 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc7 C CA CA . A CA 1005 1_555 H O2 ICT . B ICT 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc8 C CA CA . A CA 1005 1_555 H O7 ICT . B ICT 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc9 C CA CA . A CA 1005 1_555 J O HOH . B HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc10 C CA CA . A CA 1005 1_555 J O HOH . B HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc11 D CA CA . A CA 1006 1_555 I O HOH . A HOH 1135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc12 D CA CA . A CA 1006 1_555 I O HOH . A HOH 1136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc13 D CA CA . A CA 1006 1_555 I O HOH . A HOH 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc14 D CA CA . A CA 1006 1_555 B OD2 ASP 287 B ASP 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _chem_comp.formula 'C6 H8 O7' _chem_comp.formula_weight 192.124 _chem_comp.id ICT _chem_comp.mon_nstd_flag . _chem_comp.name 'ISOCITRIC 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 C1 O1 ICT doub 152 n n C1 O2 ICT sing 153 n n C1 C2 ICT sing 154 n n O2 HO2 ICT sing 155 n n C2 O7 ICT sing 156 n n C2 C3 ICT sing 157 n n C2 H2 ICT sing 158 n n O7 HO7 ICT sing 159 n n C3 C4 ICT sing 160 n n C3 C6 ICT sing 161 n n C3 H3 ICT sing 162 n n C4 C5 ICT sing 163 n n C4 H41 ICT sing 164 n n C4 H42 ICT sing 165 n n C5 O3 ICT doub 166 n n C5 O4 ICT sing 167 n n O4 HO4 ICT sing 168 n n C6 O5 ICT doub 169 n n C6 O6 ICT sing 170 n n O6 HO6 ICT sing 171 n n # _atom_sites.entry_id 1XKD _atom_sites.fract_transf_matrix[1][1] 0.009296 _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] 0.009296 _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] 0.005846 _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 2 CA A 1 1005 1005 CA CA . D 2 CA A 1 1006 1006 CA CA . E 3 NAP A 1 1001 1001 NAP NAP . F 4 ICT A 1 1002 1002 ICT ICI . G 3 NAP B 1 1003 1003 NAP NAP . H 4 ICT B 1 1004 1004 ICT ICI . I 5 HOH A 1 1007 8 HOH HOH . I 5 HOH A 2 1008 9 HOH HOH . I 5 HOH A 3 1009 12 HOH HOH . I 5 HOH A 4 1010 13 HOH HOH . I 5 HOH A 5 1011 14 HOH HOH . I 5 HOH A 6 1012 15 HOH HOH . I 5 HOH A 7 1013 16 HOH HOH . I 5 HOH A 8 1014 17 HOH HOH . I 5 HOH A 9 1015 18 HOH HOH . I 5 HOH A 10 1016 19 HOH HOH . I 5 HOH A 11 1017 21 HOH HOH . I 5 HOH A 12 1018 22 HOH HOH . I 5 HOH A 13 1019 23 HOH HOH . I 5 HOH A 14 1020 24 HOH HOH . I 5 HOH A 15 1021 25 HOH HOH . I 5 HOH A 16 1022 26 HOH HOH . I 5 HOH A 17 1023 27 HOH HOH . I 5 HOH A 18 1024 29 HOH HOH . I 5 HOH A 19 1025 30 HOH HOH . I 5 HOH A 20 1026 31 HOH HOH . I 5 HOH A 21 1027 32 HOH HOH . I 5 HOH A 22 1028 33 HOH HOH . I 5 HOH A 23 1029 36 HOH HOH . I 5 HOH A 24 1030 37 HOH HOH . I 5 HOH A 25 1031 38 HOH HOH . I 5 HOH A 26 1032 39 HOH HOH . I 5 HOH A 27 1033 40 HOH HOH . I 5 HOH A 28 1034 41 HOH HOH . I 5 HOH A 29 1035 42 HOH HOH . I 5 HOH A 30 1036 43 HOH HOH . I 5 HOH A 31 1037 44 HOH HOH . I 5 HOH A 32 1038 45 HOH HOH . I 5 HOH A 33 1039 46 HOH HOH . I 5 HOH A 34 1040 47 HOH HOH . I 5 HOH A 35 1041 48 HOH HOH . I 5 HOH A 36 1042 49 HOH HOH . I 5 HOH A 37 1043 50 HOH HOH . I 5 HOH A 38 1044 51 HOH HOH . I 5 HOH A 39 1045 52 HOH HOH . I 5 HOH A 40 1046 53 HOH HOH . I 5 HOH A 41 1047 54 HOH HOH . I 5 HOH A 42 1048 55 HOH HOH . I 5 HOH A 43 1049 57 HOH HOH . I 5 HOH A 44 1050 58 HOH HOH . I 5 HOH A 45 1051 59 HOH HOH . I 5 HOH A 46 1052 60 HOH HOH . I 5 HOH A 47 1053 61 HOH HOH . I 5 HOH A 48 1054 62 HOH HOH . I 5 HOH A 49 1055 63 HOH HOH . I 5 HOH A 50 1056 64 HOH HOH . I 5 HOH A 51 1057 65 HOH HOH . I 5 HOH A 52 1058 66 HOH HOH . I 5 HOH A 53 1059 67 HOH HOH . I 5 HOH A 54 1060 68 HOH HOH . I 5 HOH A 55 1061 69 HOH HOH . I 5 HOH A 56 1062 70 HOH HOH . I 5 HOH A 57 1063 71 HOH HOH . I 5 HOH A 58 1064 72 HOH HOH . I 5 HOH A 59 1065 75 HOH HOH . I 5 HOH A 60 1066 76 HOH HOH . I 5 HOH A 61 1067 77 HOH HOH . I 5 HOH A 62 1068 78 HOH HOH . I 5 HOH A 63 1069 79 HOH HOH . I 5 HOH A 64 1070 80 HOH HOH . I 5 HOH A 65 1071 81 HOH HOH . I 5 HOH A 66 1072 82 HOH HOH . I 5 HOH A 67 1073 83 HOH HOH . I 5 HOH A 68 1074 84 HOH HOH . I 5 HOH A 69 1075 85 HOH HOH . I 5 HOH A 70 1076 86 HOH HOH . I 5 HOH A 71 1077 87 HOH HOH . I 5 HOH A 72 1078 88 HOH HOH . I 5 HOH A 73 1079 89 HOH HOH . I 5 HOH A 74 1080 90 HOH HOH . I 5 HOH A 75 1081 91 HOH HOH . I 5 HOH A 76 1082 92 HOH HOH . I 5 HOH A 77 1083 93 HOH HOH . I 5 HOH A 78 1084 94 HOH HOH . I 5 HOH A 79 1085 95 HOH HOH . I 5 HOH A 80 1086 96 HOH HOH . I 5 HOH A 81 1087 97 HOH HOH . I 5 HOH A 82 1088 98 HOH HOH . I 5 HOH A 83 1089 99 HOH HOH . I 5 HOH A 84 1090 100 HOH HOH . I 5 HOH A 85 1091 101 HOH HOH . I 5 HOH A 86 1092 102 HOH HOH . I 5 HOH A 87 1093 103 HOH HOH . I 5 HOH A 88 1094 104 HOH HOH . I 5 HOH A 89 1095 105 HOH HOH . I 5 HOH A 90 1096 106 HOH HOH . I 5 HOH A 91 1097 107 HOH HOH . I 5 HOH A 92 1098 108 HOH HOH . I 5 HOH A 93 1099 109 HOH HOH . I 5 HOH A 94 1100 110 HOH HOH . I 5 HOH A 95 1101 111 HOH HOH . I 5 HOH A 96 1102 112 HOH HOH . I 5 HOH A 97 1103 114 HOH HOH . I 5 HOH A 98 1104 115 HOH HOH . I 5 HOH A 99 1105 116 HOH HOH . I 5 HOH A 100 1106 117 HOH HOH . I 5 HOH A 101 1107 118 HOH HOH . I 5 HOH A 102 1108 119 HOH HOH . I 5 HOH A 103 1109 120 HOH HOH . I 5 HOH A 104 1110 121 HOH HOH . I 5 HOH A 105 1111 122 HOH HOH . I 5 HOH A 106 1112 123 HOH HOH . I 5 HOH A 107 1113 124 HOH HOH . I 5 HOH A 108 1114 125 HOH HOH . I 5 HOH A 109 1115 126 HOH HOH . I 5 HOH A 110 1116 127 HOH HOH . I 5 HOH A 111 1117 128 HOH HOH . I 5 HOH A 112 1118 129 HOH HOH . I 5 HOH A 113 1119 130 HOH HOH . I 5 HOH A 114 1120 131 HOH HOH . I 5 HOH A 115 1121 132 HOH HOH . I 5 HOH A 116 1122 133 HOH HOH . I 5 HOH A 117 1123 134 HOH HOH . I 5 HOH A 118 1124 135 HOH HOH . I 5 HOH A 119 1125 137 HOH HOH . I 5 HOH A 120 1126 138 HOH HOH . I 5 HOH A 121 1127 139 HOH HOH . I 5 HOH A 122 1128 140 HOH HOH . I 5 HOH A 123 1129 141 HOH HOH . I 5 HOH A 124 1130 142 HOH HOH . I 5 HOH A 125 1131 143 HOH HOH . I 5 HOH A 126 1132 183 HOH HOH . I 5 HOH A 127 1133 187 HOH HOH . I 5 HOH A 128 1134 1 HOH HOH . I 5 HOH A 129 1135 2 HOH HOH . I 5 HOH A 130 1136 3 HOH HOH . I 5 HOH A 131 1137 4 HOH HOH . J 5 HOH B 1 1005 1 HOH HOH . J 5 HOH B 2 1006 2 HOH HOH . J 5 HOH B 3 1007 3 HOH HOH . J 5 HOH B 4 1008 4 HOH HOH . J 5 HOH B 5 1009 5 HOH HOH . J 5 HOH B 6 1010 6 HOH HOH . J 5 HOH B 7 1011 7 HOH HOH . J 5 HOH B 8 1012 10 HOH HOH . J 5 HOH B 9 1013 11 HOH HOH . J 5 HOH B 10 1014 20 HOH HOH . J 5 HOH B 11 1015 34 HOH HOH . J 5 HOH B 12 1016 35 HOH HOH . J 5 HOH B 13 1017 56 HOH HOH . J 5 HOH B 14 1018 74 HOH HOH . J 5 HOH B 15 1019 113 HOH HOH . J 5 HOH B 16 1020 136 HOH HOH . J 5 HOH B 17 1021 144 HOH HOH . J 5 HOH B 18 1022 145 HOH HOH . J 5 HOH B 19 1023 146 HOH HOH . J 5 HOH B 20 1024 147 HOH HOH . J 5 HOH B 21 1025 148 HOH HOH . J 5 HOH B 22 1026 149 HOH HOH . J 5 HOH B 23 1027 150 HOH HOH . J 5 HOH B 24 1028 151 HOH HOH . J 5 HOH B 25 1029 152 HOH HOH . J 5 HOH B 26 1030 153 HOH HOH . J 5 HOH B 27 1031 154 HOH HOH . J 5 HOH B 28 1032 155 HOH HOH . J 5 HOH B 29 1033 156 HOH HOH . J 5 HOH B 30 1034 157 HOH HOH . J 5 HOH B 31 1035 158 HOH HOH . J 5 HOH B 32 1036 159 HOH HOH . J 5 HOH B 33 1037 160 HOH HOH . J 5 HOH B 34 1038 161 HOH HOH . J 5 HOH B 35 1039 162 HOH HOH . J 5 HOH B 36 1040 163 HOH HOH . J 5 HOH B 37 1041 164 HOH HOH . J 5 HOH B 38 1042 165 HOH HOH . J 5 HOH B 39 1043 166 HOH HOH . J 5 HOH B 40 1044 167 HOH HOH . J 5 HOH B 41 1045 168 HOH HOH . J 5 HOH B 42 1046 169 HOH HOH . J 5 HOH B 43 1047 170 HOH HOH . J 5 HOH B 44 1048 171 HOH HOH . J 5 HOH B 45 1049 172 HOH HOH . J 5 HOH B 46 1050 173 HOH HOH . J 5 HOH B 47 1051 174 HOH HOH . J 5 HOH B 48 1052 175 HOH HOH . J 5 HOH B 49 1053 176 HOH HOH . J 5 HOH B 50 1054 177 HOH HOH . J 5 HOH B 51 1055 178 HOH HOH . J 5 HOH B 52 1056 179 HOH HOH . J 5 HOH B 53 1057 180 HOH HOH . J 5 HOH B 54 1058 181 HOH HOH . J 5 HOH B 55 1059 182 HOH HOH . J 5 HOH B 56 1060 184 HOH HOH . J 5 HOH B 57 1061 185 HOH HOH . J 5 HOH B 58 1062 186 HOH HOH . J 5 HOH B 59 1063 188 HOH HOH . J 5 HOH B 60 1064 189 HOH HOH . J 5 HOH B 61 1065 190 HOH HOH . J 5 HOH B 62 1066 191 HOH HOH . J 5 HOH B 63 1067 192 HOH HOH . J 5 HOH B 64 1068 193 HOH HOH . J 5 HOH B 65 1069 194 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 ICT . . . F 4 250.697 87.44 -156.239 1 28.36 ? C1 ICT 1002 A 1 HETATM 2 O O1 ICT . . . F 4 251.333 87.534 -155.177 1 29.49 ? O1 ICT 1002 A 1 HETATM 3 O O2 ICT . . . F 4 249.904 88.315 -156.635 1 27.89 ? O2 ICT 1002 A 1 HETATM 4 C C2 ICT . . . F 4 250.873 86.224 -157.095 1 30.12 ? C2 ICT 1002 A 1 HETATM 5 O O7 ICT . . . F 4 250.176 86.502 -158.303 1 30.16 ? O7 ICT 1002 A 1 HETATM 6 C C3 ICT . . . F 4 250.198 85.039 -156.413 1 29.35 ? C3 ICT 1002 A 1 HETATM 7 C C4 ICT . . . F 4 250.443 83.645 -156.991 1 29.6 ? C4 ICT 1002 A 1 HETATM 8 C C5 ICT . . . F 4 251.396 83.572 -158.164 1 30.74 ? C5 ICT 1002 A 1 HETATM 9 O O3 ICT . . . F 4 250.947 83.615 -159.336 1 29.76 ? O3 ICT 1002 A 1 HETATM 10 O O4 ICT . . . F 4 252.613 83.432 -157.913 1 32.77 ? O4 ICT 1002 A 1 HETATM 11 C C6 ICT . . . F 4 248.744 85.348 -156.552 1 29.18 ? C6 ICT 1002 A 1 HETATM 12 O O5 ICT . . . F 4 248.142 85.792 -155.56 1 25.48 ? O5 ICT 1002 A 1 HETATM 13 O O6 ICT . . . F 4 248.23 85.183 -157.683 1 31.43 ? O6 ICT 1002 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 13 #