data_3UYJ # _model_server_result.job_id v0E2eTLuNXTx3s8m4-TsOw _model_server_result.datetime_utc '2024-11-15 01:32:15' _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 3uyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 3UYJ # _exptl.entry_id 3UYJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC 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 120 _cell.entry_id 3UYJ _cell.length_a 68.393 _cell.length_b 68.393 _cell.length_c 266.686 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 ? 3 D N N ? 3 F 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 64 A CYS 232 1_555 B SG CYS 64 B CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc1 G O HOH . A HOH 5 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc2 A NE2 HIS 153 A HIS 321 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc3 A OD2 ASP 155 A ASP 323 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? metalc ? metalc4 A NE2 HIS 232 A HIS 400 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc5 C NI NI . A NI 501 1_555 D O1 AKG . A AKG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc6 C NI NI . A NI 501 1_555 D O5 AKG . A AKG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc7 H O HOH . B HOH 19 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B NE2 HIS 153 B HIS 321 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc9 B OD2 ASP 155 B ASP 323 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc10 B NE2 HIS 232 B HIS 400 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc11 E NI NI . B NI 501 1_555 F O5 AKG . B AKG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc12 E NI NI . B NI 501 1_555 F O1 AKG . B AKG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? # _chem_comp.formula 'C5 H6 O5' _chem_comp.formula_weight 146.098 _chem_comp.id AKG _chem_comp.mon_nstd_flag . _chem_comp.name '2-OXOGLUTARIC 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 AKG doub 1 n n C1 O2 AKG sing 2 n n C1 C2 AKG sing 3 n n O2 HO2 AKG sing 4 n n C2 O5 AKG doub 5 n n C2 C3 AKG sing 6 n n C3 C4 AKG sing 7 n n C3 H31 AKG sing 8 n n C3 H32 AKG sing 9 n n C4 C5 AKG sing 10 n n C4 H41 AKG sing 11 n n C4 H42 AKG sing 12 n n C5 O3 AKG doub 13 n n C5 O4 AKG sing 14 n n O4 HO4 AKG sing 15 n n # _atom_sites.entry_id 3UYJ _atom_sites.fract_transf_matrix[1][1] 0.014621 _atom_sites.fract_transf_matrix[1][2] 0.008442 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016883 _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] 0.00375 _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 NI A 1 501 501 NI NI . D 3 AKG A 1 601 601 AKG AKG . E 2 NI B 1 501 501 NI NI . F 3 AKG B 1 601 601 AKG AKG . G 4 HOH A 1 1 1 HOH HOH . G 4 HOH A 2 2 2 HOH HOH . G 4 HOH A 3 3 3 HOH HOH . G 4 HOH A 4 5 5 HOH HOH . G 4 HOH A 5 6 6 HOH HOH . G 4 HOH A 6 7 7 HOH HOH . G 4 HOH A 7 8 8 HOH HOH . G 4 HOH A 8 11 11 HOH HOH . G 4 HOH A 9 14 14 HOH HOH . G 4 HOH A 10 18 18 HOH HOH . G 4 HOH A 11 21 21 HOH HOH . G 4 HOH A 12 22 22 HOH HOH . G 4 HOH A 13 23 23 HOH HOH . G 4 HOH A 14 24 24 HOH HOH . G 4 HOH A 15 25 25 HOH HOH . G 4 HOH A 16 27 27 HOH HOH . G 4 HOH A 17 28 28 HOH HOH . G 4 HOH A 18 30 30 HOH HOH . G 4 HOH A 19 33 33 HOH HOH . G 4 HOH A 20 34 34 HOH HOH . G 4 HOH A 21 37 37 HOH HOH . G 4 HOH A 22 38 38 HOH HOH . G 4 HOH A 23 41 41 HOH HOH . G 4 HOH A 24 43 43 HOH HOH . G 4 HOH A 25 44 44 HOH HOH . G 4 HOH A 26 45 45 HOH HOH . G 4 HOH A 27 46 46 HOH HOH . G 4 HOH A 28 50 50 HOH HOH . G 4 HOH A 29 53 53 HOH HOH . G 4 HOH A 30 54 54 HOH HOH . G 4 HOH A 31 56 56 HOH HOH . G 4 HOH A 32 57 57 HOH HOH . G 4 HOH A 33 58 58 HOH HOH . G 4 HOH A 34 59 59 HOH HOH . G 4 HOH A 35 60 60 HOH HOH . G 4 HOH A 36 62 62 HOH HOH . G 4 HOH A 37 63 63 HOH HOH . G 4 HOH A 38 64 64 HOH HOH . G 4 HOH A 39 66 66 HOH HOH . G 4 HOH A 40 69 69 HOH HOH . G 4 HOH A 41 72 72 HOH HOH . G 4 HOH A 42 77 77 HOH HOH . G 4 HOH A 43 78 78 HOH HOH . G 4 HOH A 44 79 79 HOH HOH . G 4 HOH A 45 80 80 HOH HOH . G 4 HOH A 46 81 81 HOH HOH . G 4 HOH A 47 83 83 HOH HOH . G 4 HOH A 48 84 84 HOH HOH . G 4 HOH A 49 88 88 HOH HOH . G 4 HOH A 50 89 89 HOH HOH . G 4 HOH A 51 90 90 HOH HOH . G 4 HOH A 52 91 91 HOH HOH . G 4 HOH A 53 92 92 HOH HOH . G 4 HOH A 54 93 93 HOH HOH . G 4 HOH A 55 94 94 HOH HOH . G 4 HOH A 56 95 95 HOH HOH . G 4 HOH A 57 96 96 HOH HOH . G 4 HOH A 58 97 97 HOH HOH . G 4 HOH A 59 98 98 HOH HOH . G 4 HOH A 60 99 99 HOH HOH . G 4 HOH A 61 100 100 HOH HOH . G 4 HOH A 62 105 105 HOH HOH . G 4 HOH A 63 106 106 HOH HOH . G 4 HOH A 64 107 107 HOH HOH . G 4 HOH A 65 108 108 HOH HOH . G 4 HOH A 66 110 110 HOH HOH . G 4 HOH A 67 111 111 HOH HOH . G 4 HOH A 68 112 112 HOH HOH . G 4 HOH A 69 113 113 HOH HOH . G 4 HOH A 70 115 115 HOH HOH . G 4 HOH A 71 116 116 HOH HOH . G 4 HOH A 72 119 119 HOH HOH . G 4 HOH A 73 120 120 HOH HOH . G 4 HOH A 74 121 121 HOH HOH . G 4 HOH A 75 122 122 HOH HOH . G 4 HOH A 76 123 123 HOH HOH . G 4 HOH A 77 125 125 HOH HOH . G 4 HOH A 78 126 126 HOH HOH . G 4 HOH A 79 128 128 HOH HOH . G 4 HOH A 80 130 130 HOH HOH . G 4 HOH A 81 133 133 HOH HOH . G 4 HOH A 82 134 134 HOH HOH . G 4 HOH A 83 136 136 HOH HOH . G 4 HOH A 84 137 137 HOH HOH . G 4 HOH A 85 138 138 HOH HOH . G 4 HOH A 86 139 139 HOH HOH . G 4 HOH A 87 141 141 HOH HOH . G 4 HOH A 88 143 143 HOH HOH . G 4 HOH A 89 147 147 HOH HOH . G 4 HOH A 90 148 148 HOH HOH . G 4 HOH A 91 149 149 HOH HOH . G 4 HOH A 92 152 152 HOH HOH . G 4 HOH A 93 154 154 HOH HOH . G 4 HOH A 94 156 156 HOH HOH . G 4 HOH A 95 157 157 HOH HOH . G 4 HOH A 96 158 158 HOH HOH . G 4 HOH A 97 159 159 HOH HOH . G 4 HOH A 98 162 162 HOH HOH . G 4 HOH A 99 164 164 HOH HOH . G 4 HOH A 100 417 169 HOH HOH . G 4 HOH A 101 418 170 HOH HOH . G 4 HOH A 102 419 171 HOH HOH . G 4 HOH A 103 420 172 HOH HOH . G 4 HOH A 104 421 173 HOH HOH . G 4 HOH A 105 422 174 HOH HOH . G 4 HOH A 106 423 177 HOH HOH . G 4 HOH A 107 424 179 HOH HOH . G 4 HOH A 108 425 180 HOH HOH . G 4 HOH A 109 426 181 HOH HOH . G 4 HOH A 110 427 183 HOH HOH . G 4 HOH A 111 428 184 HOH HOH . G 4 HOH A 112 429 185 HOH HOH . G 4 HOH A 113 430 188 HOH HOH . G 4 HOH A 114 431 193 HOH HOH . G 4 HOH A 115 432 194 HOH HOH . G 4 HOH A 116 433 195 HOH HOH . G 4 HOH A 117 434 196 HOH HOH . G 4 HOH A 118 435 197 HOH HOH . G 4 HOH A 119 436 198 HOH HOH . G 4 HOH A 120 437 199 HOH HOH . G 4 HOH A 121 438 200 HOH HOH . G 4 HOH A 122 439 201 HOH HOH . G 4 HOH A 123 440 202 HOH HOH . G 4 HOH A 124 441 205 HOH HOH . G 4 HOH A 125 442 206 HOH HOH . G 4 HOH A 126 443 207 HOH HOH . G 4 HOH A 127 444 209 HOH HOH . H 4 HOH B 1 4 4 HOH HOH . H 4 HOH B 2 9 9 HOH HOH . H 4 HOH B 3 10 10 HOH HOH . H 4 HOH B 4 12 12 HOH HOH . H 4 HOH B 5 13 13 HOH HOH . H 4 HOH B 6 15 15 HOH HOH . H 4 HOH B 7 16 16 HOH HOH . H 4 HOH B 8 17 17 HOH HOH . H 4 HOH B 9 19 19 HOH HOH . H 4 HOH B 10 20 20 HOH HOH . H 4 HOH B 11 26 26 HOH HOH . H 4 HOH B 12 29 29 HOH HOH . H 4 HOH B 13 31 31 HOH HOH . H 4 HOH B 14 32 32 HOH HOH . H 4 HOH B 15 35 35 HOH HOH . H 4 HOH B 16 36 36 HOH HOH . H 4 HOH B 17 39 39 HOH HOH . H 4 HOH B 18 40 40 HOH HOH . H 4 HOH B 19 42 42 HOH HOH . H 4 HOH B 20 47 47 HOH HOH . H 4 HOH B 21 48 48 HOH HOH . H 4 HOH B 22 49 49 HOH HOH . H 4 HOH B 23 51 51 HOH HOH . H 4 HOH B 24 52 52 HOH HOH . H 4 HOH B 25 55 55 HOH HOH . H 4 HOH B 26 61 61 HOH HOH . H 4 HOH B 27 65 65 HOH HOH . H 4 HOH B 28 67 67 HOH HOH . H 4 HOH B 29 68 68 HOH HOH . H 4 HOH B 30 70 70 HOH HOH . H 4 HOH B 31 71 71 HOH HOH . H 4 HOH B 32 73 73 HOH HOH . H 4 HOH B 33 74 74 HOH HOH . H 4 HOH B 34 75 75 HOH HOH . H 4 HOH B 35 76 76 HOH HOH . H 4 HOH B 36 82 82 HOH HOH . H 4 HOH B 37 85 85 HOH HOH . H 4 HOH B 38 86 86 HOH HOH . H 4 HOH B 39 87 87 HOH HOH . H 4 HOH B 40 101 101 HOH HOH . H 4 HOH B 41 102 102 HOH HOH . H 4 HOH B 42 103 103 HOH HOH . H 4 HOH B 43 104 104 HOH HOH . H 4 HOH B 44 109 109 HOH HOH . H 4 HOH B 45 114 114 HOH HOH . H 4 HOH B 46 117 117 HOH HOH . H 4 HOH B 47 118 118 HOH HOH . H 4 HOH B 48 124 124 HOH HOH . H 4 HOH B 49 127 127 HOH HOH . H 4 HOH B 50 129 129 HOH HOH . H 4 HOH B 51 131 131 HOH HOH . H 4 HOH B 52 132 132 HOH HOH . H 4 HOH B 53 135 135 HOH HOH . H 4 HOH B 54 140 140 HOH HOH . H 4 HOH B 55 142 142 HOH HOH . H 4 HOH B 56 144 144 HOH HOH . H 4 HOH B 57 145 145 HOH HOH . H 4 HOH B 58 146 146 HOH HOH . H 4 HOH B 59 150 150 HOH HOH . H 4 HOH B 60 151 151 HOH HOH . H 4 HOH B 61 153 153 HOH HOH . H 4 HOH B 62 155 155 HOH HOH . H 4 HOH B 63 160 160 HOH HOH . H 4 HOH B 64 161 161 HOH HOH . H 4 HOH B 65 163 163 HOH HOH . H 4 HOH B 66 165 165 HOH HOH . H 4 HOH B 67 166 166 HOH HOH . H 4 HOH B 68 167 167 HOH HOH . H 4 HOH B 69 168 168 HOH HOH . H 4 HOH B 70 417 175 HOH HOH . H 4 HOH B 71 418 176 HOH HOH . H 4 HOH B 72 419 178 HOH HOH . H 4 HOH B 73 420 182 HOH HOH . H 4 HOH B 74 421 186 HOH HOH . H 4 HOH B 75 422 187 HOH HOH . H 4 HOH B 76 423 189 HOH HOH . H 4 HOH B 77 424 190 HOH HOH . H 4 HOH B 78 425 191 HOH HOH . H 4 HOH B 79 426 192 HOH HOH . H 4 HOH B 80 427 203 HOH HOH . H 4 HOH B 81 428 204 HOH HOH . H 4 HOH B 82 429 208 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 AKG . . . D 3 -23.031 21.715 -2.941 1 37.35 ? C1 AKG 601 A 1 HETATM 2 O O1 AKG . . . D 3 -22.208 21.826 -3.9 1 36.84 ? O1 AKG 601 A 1 HETATM 3 O O2 AKG . . . D 3 -22.705 21.097 -1.886 1 35.83 ? O2 AKG 601 A 1 HETATM 4 C C2 AKG . . . D 3 -24.389 22.316 -3.079 1 34.51 ? C2 AKG 601 A 1 HETATM 5 O O5 AKG . . . D 3 -24.614 23.009 -4.073 1 36.6 ? O5 AKG 601 A 1 HETATM 6 C C3 AKG . . . D 3 -25.445 22.061 -2.038 1 35.82 ? C3 AKG 601 A 1 HETATM 7 C C4 AKG . . . D 3 -26.585 23.038 -2.11 1 33.16 ? C4 AKG 601 A 1 HETATM 8 C C5 AKG . . . D 3 -27.61 22.751 -1.045 1 36.07 ? C5 AKG 601 A 1 HETATM 9 O O3 AKG . . . D 3 -27.418 21.819 -0.22 1 35.59 ? O3 AKG 601 A 1 HETATM 10 O O4 AKG . . . D 3 -28.678 23.429 -0.947 1 34.04 ? O4 AKG 601 A 1 HETATM 11 H H31 AKG . . . D 3 -25.043 22.1 -1.154 1 42.98 ? H31 AKG 601 A 1 HETATM 12 H H32 AKG . . . D 3 -25.804 21.167 -2.17 1 42.98 ? H32 AKG 601 A 1 HETATM 13 H H41 AKG . . . D 3 -27.009 22.978 -2.983 1 39.8 ? H41 AKG 601 A 1 HETATM 14 H H42 AKG . . . D 3 -26.247 23.941 -1.99 1 39.8 ? H42 AKG 601 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #