data_5YBT # _model_server_result.job_id uMnxU6W2wuGqw8HlYo5zSQ _model_server_result.datetime_utc '2024-10-20 01:34:13' _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 5ybt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":302}' # _entry.id 5YBT # _exptl.entry_id 5YBT _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 5YBT _cell.length_a 171.569 _cell.length_b 171.569 _cell.length_c 45.605 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _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 ? 3 D N N ? 3 G 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 metalc ? metalc1 A NE2 HIS 146 A HIS 130 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc2 A OD1 ASP 148 A ASP 132 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc3 A NE2 HIS 230 A HIS 214 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc4 C FE FE . A FE 301 1_555 D O2 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc5 C FE FE . A FE 301 1_555 D O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc6 C FE FE . A FE 301 1_555 I O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc7 B NE2 HIS 146 B HIS 130 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc8 B OD1 ASP 148 B ASP 132 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc9 B NE2 HIS 230 B HIS 214 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc10 F FE FE . B FE 301 1_555 G O1 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 F FE FE . B FE 301 1_555 G O5 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc12 F FE FE . B FE 301 1_555 J O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? # _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 74 n n C1 O2 AKG sing 75 n n C1 C2 AKG sing 76 n n O2 HO2 AKG sing 77 n n C2 O5 AKG doub 78 n n C2 C3 AKG sing 79 n n C3 C4 AKG sing 80 n n C3 H31 AKG sing 81 n n C3 H32 AKG sing 82 n n C4 C5 AKG sing 83 n n C4 H41 AKG sing 84 n n C4 H42 AKG sing 85 n n C5 O3 AKG doub 86 n n C5 O4 AKG sing 87 n n O4 HO4 AKG sing 88 n n # _atom_sites.entry_id 5YBT _atom_sites.fract_transf_matrix[1][1] 0.005829 _atom_sites.fract_transf_matrix[1][2] 0.003365 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00673 _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] 0.021927 _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 FE A 1 301 1 FE FE . D 3 AKG A 1 302 1 AKG AKG . E 4 8TC A 1 303 3 8TC LIG . F 2 FE B 1 301 2 FE FE . G 3 AKG B 1 302 2 AKG AKG . H 4 8TC B 1 303 4 8TC LIG . I 5 HOH A 1 401 18 HOH HOH . I 5 HOH A 2 402 53 HOH HOH . I 5 HOH A 3 403 105 HOH HOH . I 5 HOH A 4 404 81 HOH HOH . I 5 HOH A 5 405 83 HOH HOH . I 5 HOH A 6 406 72 HOH HOH . I 5 HOH A 7 407 44 HOH HOH . I 5 HOH A 8 408 1 HOH HOH . I 5 HOH A 9 409 111 HOH HOH . I 5 HOH A 10 410 20 HOH HOH . I 5 HOH A 11 411 15 HOH HOH . I 5 HOH A 12 412 46 HOH HOH . I 5 HOH A 13 413 112 HOH HOH . I 5 HOH A 14 414 113 HOH HOH . I 5 HOH A 15 415 181 HOH HOH . I 5 HOH A 16 416 100 HOH HOH . I 5 HOH A 17 417 180 HOH HOH . I 5 HOH A 18 418 128 HOH HOH . I 5 HOH A 19 419 8 HOH HOH . I 5 HOH A 20 420 115 HOH HOH . I 5 HOH A 21 421 35 HOH HOH . I 5 HOH A 22 422 13 HOH HOH . I 5 HOH A 23 423 177 HOH HOH . I 5 HOH A 24 424 30 HOH HOH . I 5 HOH A 25 425 10 HOH HOH . I 5 HOH A 26 426 172 HOH HOH . I 5 HOH A 27 427 19 HOH HOH . I 5 HOH A 28 428 55 HOH HOH . I 5 HOH A 29 429 157 HOH HOH . I 5 HOH A 30 430 4 HOH HOH . I 5 HOH A 31 431 106 HOH HOH . I 5 HOH A 32 432 27 HOH HOH . I 5 HOH A 33 433 96 HOH HOH . I 5 HOH A 34 434 186 HOH HOH . I 5 HOH A 35 435 94 HOH HOH . I 5 HOH A 36 436 37 HOH HOH . I 5 HOH A 37 437 82 HOH HOH . I 5 HOH A 38 438 97 HOH HOH . I 5 HOH A 39 439 48 HOH HOH . I 5 HOH A 40 440 23 HOH HOH . I 5 HOH A 41 441 24 HOH HOH . I 5 HOH A 42 442 29 HOH HOH . I 5 HOH A 43 443 171 HOH HOH . I 5 HOH A 44 444 16 HOH HOH . I 5 HOH A 45 445 89 HOH HOH . I 5 HOH A 46 446 52 HOH HOH . I 5 HOH A 47 447 127 HOH HOH . I 5 HOH A 48 448 50 HOH HOH . I 5 HOH A 49 449 45 HOH HOH . I 5 HOH A 50 450 107 HOH HOH . I 5 HOH A 51 451 195 HOH HOH . I 5 HOH A 52 452 65 HOH HOH . I 5 HOH A 53 453 28 HOH HOH . I 5 HOH A 54 454 57 HOH HOH . I 5 HOH A 55 455 149 HOH HOH . I 5 HOH A 56 456 84 HOH HOH . I 5 HOH A 57 457 49 HOH HOH . I 5 HOH A 58 458 175 HOH HOH . I 5 HOH A 59 459 58 HOH HOH . I 5 HOH A 60 460 76 HOH HOH . I 5 HOH A 61 461 174 HOH HOH . I 5 HOH A 62 462 108 HOH HOH . I 5 HOH A 63 463 140 HOH HOH . I 5 HOH A 64 464 93 HOH HOH . I 5 HOH A 65 465 87 HOH HOH . I 5 HOH A 66 466 139 HOH HOH . I 5 HOH A 67 467 7 HOH HOH . I 5 HOH A 68 468 161 HOH HOH . I 5 HOH A 69 469 119 HOH HOH . I 5 HOH A 70 470 40 HOH HOH . I 5 HOH A 71 471 122 HOH HOH . I 5 HOH A 72 472 160 HOH HOH . I 5 HOH A 73 473 116 HOH HOH . I 5 HOH A 74 474 135 HOH HOH . I 5 HOH A 75 475 148 HOH HOH . I 5 HOH A 76 476 173 HOH HOH . I 5 HOH A 77 477 153 HOH HOH . I 5 HOH A 78 478 147 HOH HOH . I 5 HOH A 79 479 163 HOH HOH . I 5 HOH A 80 480 56 HOH HOH . I 5 HOH A 81 481 164 HOH HOH . I 5 HOH A 82 482 151 HOH HOH . I 5 HOH A 83 483 67 HOH HOH . I 5 HOH A 84 484 187 HOH HOH . I 5 HOH A 85 485 101 HOH HOH . I 5 HOH A 86 486 189 HOH HOH . I 5 HOH A 87 487 145 HOH HOH . I 5 HOH A 88 488 185 HOH HOH . I 5 HOH A 89 489 104 HOH HOH . I 5 HOH A 90 490 162 HOH HOH . I 5 HOH A 91 491 178 HOH HOH . J 5 HOH B 1 401 11 HOH HOH . J 5 HOH B 2 402 9 HOH HOH . J 5 HOH B 3 403 150 HOH HOH . J 5 HOH B 4 404 34 HOH HOH . J 5 HOH B 5 405 74 HOH HOH . J 5 HOH B 6 406 68 HOH HOH . J 5 HOH B 7 407 3 HOH HOH . J 5 HOH B 8 408 47 HOH HOH . J 5 HOH B 9 409 26 HOH HOH . J 5 HOH B 10 410 5 HOH HOH . J 5 HOH B 11 411 66 HOH HOH . J 5 HOH B 12 412 21 HOH HOH . J 5 HOH B 13 413 39 HOH HOH . J 5 HOH B 14 414 6 HOH HOH . J 5 HOH B 15 415 138 HOH HOH . J 5 HOH B 16 416 170 HOH HOH . J 5 HOH B 17 417 31 HOH HOH . J 5 HOH B 18 418 132 HOH HOH . J 5 HOH B 19 419 120 HOH HOH . J 5 HOH B 20 420 99 HOH HOH . J 5 HOH B 21 421 90 HOH HOH . J 5 HOH B 22 422 64 HOH HOH . J 5 HOH B 23 423 165 HOH HOH . J 5 HOH B 24 424 12 HOH HOH . J 5 HOH B 25 425 141 HOH HOH . J 5 HOH B 26 426 2 HOH HOH . J 5 HOH B 27 427 129 HOH HOH . J 5 HOH B 28 428 80 HOH HOH . J 5 HOH B 29 429 92 HOH HOH . J 5 HOH B 30 430 61 HOH HOH . J 5 HOH B 31 431 59 HOH HOH . J 5 HOH B 32 432 38 HOH HOH . J 5 HOH B 33 433 109 HOH HOH . J 5 HOH B 34 434 69 HOH HOH . J 5 HOH B 35 435 121 HOH HOH . J 5 HOH B 36 436 42 HOH HOH . J 5 HOH B 37 437 79 HOH HOH . J 5 HOH B 38 438 88 HOH HOH . J 5 HOH B 39 439 102 HOH HOH . J 5 HOH B 40 440 176 HOH HOH . J 5 HOH B 41 441 169 HOH HOH . J 5 HOH B 42 442 117 HOH HOH . J 5 HOH B 43 443 194 HOH HOH . J 5 HOH B 44 444 130 HOH HOH . J 5 HOH B 45 445 125 HOH HOH . J 5 HOH B 46 446 142 HOH HOH . J 5 HOH B 47 447 159 HOH HOH . J 5 HOH B 48 448 63 HOH HOH . J 5 HOH B 49 449 62 HOH HOH . J 5 HOH B 50 450 166 HOH HOH . J 5 HOH B 51 451 17 HOH HOH . J 5 HOH B 52 452 75 HOH HOH . J 5 HOH B 53 453 33 HOH HOH . J 5 HOH B 54 454 103 HOH HOH . J 5 HOH B 55 455 152 HOH HOH . J 5 HOH B 56 456 131 HOH HOH . J 5 HOH B 57 457 144 HOH HOH . J 5 HOH B 58 458 126 HOH HOH . J 5 HOH B 59 459 51 HOH HOH . J 5 HOH B 60 460 168 HOH HOH . J 5 HOH B 61 461 85 HOH HOH . J 5 HOH B 62 462 114 HOH HOH . J 5 HOH B 63 463 188 HOH HOH . J 5 HOH B 64 464 70 HOH HOH . J 5 HOH B 65 465 22 HOH HOH . J 5 HOH B 66 466 25 HOH HOH . J 5 HOH B 67 467 143 HOH HOH . J 5 HOH B 68 468 155 HOH HOH . J 5 HOH B 69 469 134 HOH HOH . J 5 HOH B 70 470 77 HOH HOH . J 5 HOH B 71 471 78 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 . . . G 3 105.709 214.79 19.265 1 51.22 ? C1 AKG 302 B 1 HETATM 2 O O1 AKG . . . G 3 104.763 214.229 18.669 1 51.84 ? O1 AKG 302 B 1 HETATM 3 O O2 AKG . . . G 3 105.513 215.898 19.835 1 49.86 ? O2 AKG 302 B 1 HETATM 4 C C2 AKG . . . G 3 107.069 214.098 19.289 1 52.94 ? C2 AKG 302 B 1 HETATM 5 O O5 AKG . . . G 3 107.136 212.927 19.151 1 49.94 ? O5 AKG 302 B 1 HETATM 6 C C3 AKG . . . G 3 108.353 214.889 19.503 1 54.47 ? C3 AKG 302 B 1 HETATM 7 C C4 AKG . . . G 3 109.456 213.898 19.881 1 55.62 ? C4 AKG 302 B 1 HETATM 8 C C5 AKG . . . G 3 110.657 214.625 20.491 1 58.17 ? C5 AKG 302 B 1 HETATM 9 O O3 AKG . . . G 3 111.765 214.016 20.525 1 56.48 ? O3 AKG 302 B 1 HETATM 10 O O4 AKG . . . G 3 110.524 215.8 20.96 1 56.22 ? O4 AKG 302 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #