data_5YBR # _model_server_result.job_id sJuJPX601K5XIFIwMgIPHg _model_server_result.datetime_utc '2024-11-12 22:14:48' _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 5ybr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5YBR # _exptl.entry_id 5YBR _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 5YBR _cell.length_a 171.382 _cell.length_b 171.382 _cell.length_c 45.696 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YBR _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc2 A OD1 ASP 148 A ASP 132 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc3 A NE2 HIS 230 A HIS 214 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 C FE FE . A FE 301 1_555 D O1 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc5 C FE FE . A FE 301 1_555 D O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc6 C FE FE . A FE 301 1_555 I O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 B NE2 HIS 146 B HIS 130 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc8 B OD1 ASP 148 B ASP 132 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc9 B NE2 HIS 230 B HIS 214 1_555 F FE FE . B FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc10 F FE FE . B FE 301 1_555 G O5 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc11 F FE FE . B FE 301 1_555 G O2 AKG . B AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc12 F FE FE . B FE 301 1_555 J O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? # _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 69 n n C1 O2 AKG sing 70 n n C1 C2 AKG sing 71 n n O2 HO2 AKG sing 72 n n C2 O5 AKG doub 73 n n C2 C3 AKG sing 74 n n C3 C4 AKG sing 75 n n C3 H31 AKG sing 76 n n C3 H32 AKG sing 77 n n C4 C5 AKG sing 78 n n C4 H41 AKG sing 79 n n C4 H42 AKG sing 80 n n C5 O3 AKG doub 81 n n C5 O4 AKG sing 82 n n O4 HO4 AKG sing 83 n n # _atom_sites.entry_id 5YBR _atom_sites.fract_transf_matrix[1][1] 0.005835 _atom_sites.fract_transf_matrix[1][2] 0.003369 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006738 _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] 0.021884 _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 3 AKG AKG . E 4 8T9 A 1 303 6 8T9 LIG . F 2 FE B 1 301 2 FE FE . G 3 AKG B 1 302 4 AKG AKG . H 4 8T9 B 1 303 5 8T9 LIG . I 5 HOH A 1 401 56 HOH HOH . I 5 HOH A 2 402 32 HOH HOH . I 5 HOH A 3 403 43 HOH HOH . I 5 HOH A 4 404 63 HOH HOH . I 5 HOH A 5 405 5 HOH HOH . I 5 HOH A 6 406 100 HOH HOH . I 5 HOH A 7 407 164 HOH HOH . I 5 HOH A 8 408 1 HOH HOH . I 5 HOH A 9 409 64 HOH HOH . I 5 HOH A 10 410 96 HOH HOH . I 5 HOH A 11 411 178 HOH HOH . I 5 HOH A 12 412 189 HOH HOH . I 5 HOH A 13 413 42 HOH HOH . I 5 HOH A 14 414 10 HOH HOH . I 5 HOH A 15 415 9 HOH HOH . I 5 HOH A 16 416 55 HOH HOH . I 5 HOH A 17 417 93 HOH HOH . I 5 HOH A 18 418 35 HOH HOH . I 5 HOH A 19 419 126 HOH HOH . I 5 HOH A 20 420 22 HOH HOH . I 5 HOH A 21 421 8 HOH HOH . I 5 HOH A 22 422 104 HOH HOH . I 5 HOH A 23 423 119 HOH HOH . I 5 HOH A 24 424 23 HOH HOH . I 5 HOH A 25 425 7 HOH HOH . I 5 HOH A 26 426 195 HOH HOH . I 5 HOH A 27 427 12 HOH HOH . I 5 HOH A 28 428 29 HOH HOH . I 5 HOH A 29 429 90 HOH HOH . I 5 HOH A 30 430 116 HOH HOH . I 5 HOH A 31 431 26 HOH HOH . I 5 HOH A 32 432 49 HOH HOH . I 5 HOH A 33 433 68 HOH HOH . I 5 HOH A 34 434 4 HOH HOH . I 5 HOH A 35 435 91 HOH HOH . I 5 HOH A 36 436 73 HOH HOH . I 5 HOH A 37 437 95 HOH HOH . I 5 HOH A 38 438 123 HOH HOH . I 5 HOH A 39 439 52 HOH HOH . I 5 HOH A 40 440 115 HOH HOH . I 5 HOH A 41 441 134 HOH HOH . I 5 HOH A 42 442 25 HOH HOH . I 5 HOH A 43 443 34 HOH HOH . I 5 HOH A 44 444 128 HOH HOH . I 5 HOH A 45 445 19 HOH HOH . I 5 HOH A 46 446 15 HOH HOH . I 5 HOH A 47 447 41 HOH HOH . I 5 HOH A 48 448 89 HOH HOH . I 5 HOH A 49 449 21 HOH HOH . I 5 HOH A 50 450 81 HOH HOH . I 5 HOH A 51 451 162 HOH HOH . I 5 HOH A 52 452 85 HOH HOH . I 5 HOH A 53 453 133 HOH HOH . I 5 HOH A 54 454 99 HOH HOH . I 5 HOH A 55 455 61 HOH HOH . I 5 HOH A 56 456 130 HOH HOH . I 5 HOH A 57 457 122 HOH HOH . I 5 HOH A 58 458 121 HOH HOH . I 5 HOH A 59 459 66 HOH HOH . I 5 HOH A 60 460 113 HOH HOH . I 5 HOH A 61 461 117 HOH HOH . I 5 HOH A 62 462 65 HOH HOH . I 5 HOH A 63 463 44 HOH HOH . I 5 HOH A 64 464 86 HOH HOH . I 5 HOH A 65 465 106 HOH HOH . I 5 HOH A 66 466 146 HOH HOH . I 5 HOH A 67 467 214 HOH HOH . I 5 HOH A 68 468 37 HOH HOH . I 5 HOH A 69 469 72 HOH HOH . I 5 HOH A 70 470 188 HOH HOH . I 5 HOH A 71 471 170 HOH HOH . I 5 HOH A 72 472 174 HOH HOH . I 5 HOH A 73 473 219 HOH HOH . I 5 HOH A 74 474 226 HOH HOH . I 5 HOH A 75 475 235 HOH HOH . I 5 HOH A 76 476 184 HOH HOH . I 5 HOH A 77 477 224 HOH HOH . I 5 HOH A 78 478 36 HOH HOH . I 5 HOH A 79 479 78 HOH HOH . I 5 HOH A 80 480 181 HOH HOH . I 5 HOH A 81 481 150 HOH HOH . I 5 HOH A 82 482 158 HOH HOH . I 5 HOH A 83 483 191 HOH HOH . I 5 HOH A 84 484 62 HOH HOH . I 5 HOH A 85 485 200 HOH HOH . I 5 HOH A 86 486 215 HOH HOH . I 5 HOH A 87 487 138 HOH HOH . I 5 HOH A 88 488 177 HOH HOH . I 5 HOH A 89 489 203 HOH HOH . I 5 HOH A 90 490 152 HOH HOH . I 5 HOH A 91 491 84 HOH HOH . I 5 HOH A 92 492 216 HOH HOH . I 5 HOH A 93 493 145 HOH HOH . I 5 HOH A 94 494 208 HOH HOH . I 5 HOH A 95 495 141 HOH HOH . I 5 HOH A 96 496 157 HOH HOH . I 5 HOH A 97 497 193 HOH HOH . I 5 HOH A 98 498 237 HOH HOH . J 5 HOH B 1 401 101 HOH HOH . J 5 HOH B 2 402 82 HOH HOH . J 5 HOH B 3 403 30 HOH HOH . J 5 HOH B 4 404 13 HOH HOH . J 5 HOH B 5 405 240 HOH HOH . J 5 HOH B 6 406 71 HOH HOH . J 5 HOH B 7 407 16 HOH HOH . J 5 HOH B 8 408 165 HOH HOH . J 5 HOH B 9 409 77 HOH HOH . J 5 HOH B 10 410 137 HOH HOH . J 5 HOH B 11 411 28 HOH HOH . J 5 HOH B 12 412 39 HOH HOH . J 5 HOH B 13 413 18 HOH HOH . J 5 HOH B 14 414 14 HOH HOH . J 5 HOH B 15 415 46 HOH HOH . J 5 HOH B 16 416 2 HOH HOH . J 5 HOH B 17 417 192 HOH HOH . J 5 HOH B 18 418 38 HOH HOH . J 5 HOH B 19 419 76 HOH HOH . J 5 HOH B 20 420 33 HOH HOH . J 5 HOH B 21 421 102 HOH HOH . J 5 HOH B 22 422 40 HOH HOH . J 5 HOH B 23 423 3 HOH HOH . J 5 HOH B 24 424 118 HOH HOH . J 5 HOH B 25 425 129 HOH HOH . J 5 HOH B 26 426 74 HOH HOH . J 5 HOH B 27 427 48 HOH HOH . J 5 HOH B 28 428 220 HOH HOH . J 5 HOH B 29 429 87 HOH HOH . J 5 HOH B 30 430 124 HOH HOH . J 5 HOH B 31 431 135 HOH HOH . J 5 HOH B 32 432 58 HOH HOH . J 5 HOH B 33 433 80 HOH HOH . J 5 HOH B 34 434 229 HOH HOH . J 5 HOH B 35 435 69 HOH HOH . J 5 HOH B 36 436 51 HOH HOH . J 5 HOH B 37 437 31 HOH HOH . J 5 HOH B 38 438 17 HOH HOH . J 5 HOH B 39 439 131 HOH HOH . J 5 HOH B 40 440 98 HOH HOH . J 5 HOH B 41 441 92 HOH HOH . J 5 HOH B 42 442 53 HOH HOH . J 5 HOH B 43 443 67 HOH HOH . J 5 HOH B 44 444 79 HOH HOH . J 5 HOH B 45 445 175 HOH HOH . J 5 HOH B 46 446 57 HOH HOH . J 5 HOH B 47 447 109 HOH HOH . J 5 HOH B 48 448 103 HOH HOH . J 5 HOH B 49 449 183 HOH HOH . J 5 HOH B 50 450 111 HOH HOH . J 5 HOH B 51 451 24 HOH HOH . J 5 HOH B 52 452 110 HOH HOH . J 5 HOH B 53 453 97 HOH HOH . J 5 HOH B 54 454 168 HOH HOH . J 5 HOH B 55 455 209 HOH HOH . J 5 HOH B 56 456 114 HOH HOH . J 5 HOH B 57 457 231 HOH HOH . J 5 HOH B 58 458 180 HOH HOH . J 5 HOH B 59 459 94 HOH HOH . J 5 HOH B 60 460 59 HOH HOH . J 5 HOH B 61 461 211 HOH HOH . J 5 HOH B 62 462 147 HOH HOH . J 5 HOH B 63 463 163 HOH HOH . J 5 HOH B 64 464 239 HOH HOH . J 5 HOH B 65 465 155 HOH HOH . J 5 HOH B 66 466 172 HOH HOH . J 5 HOH B 67 467 166 HOH HOH . J 5 HOH B 68 468 105 HOH HOH . J 5 HOH B 69 469 108 HOH HOH . J 5 HOH B 70 470 160 HOH HOH . J 5 HOH B 71 471 60 HOH HOH . J 5 HOH B 72 472 202 HOH HOH . J 5 HOH B 73 473 161 HOH HOH . J 5 HOH B 74 474 198 HOH HOH . J 5 HOH B 75 475 225 HOH HOH . J 5 HOH B 76 476 234 HOH HOH . J 5 HOH B 77 477 149 HOH HOH . J 5 HOH B 78 478 45 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 33.714 189.587 1.571 1 43.22 ? C1 AKG 302 A 1 HETATM 2 O O1 AKG . . . D 3 33.731 188.549 0.853 1 42.54 ? O1 AKG 302 A 1 HETATM 3 O O2 AKG . . . D 3 32.809 189.798 2.442 1 41.88 ? O2 AKG 302 A 1 HETATM 4 C C2 AKG . . . D 3 34.836 190.596 1.391 1 33.17 ? C2 AKG 302 A 1 HETATM 5 O O5 AKG . . . D 3 35.823 190.325 0.794 1 32.81 ? O5 AKG 302 A 1 HETATM 6 C C3 AKG . . . D 3 34.67 191.954 2.029 1 31.88 ? C3 AKG 302 A 1 HETATM 7 C C4 AKG . . . D 3 35.944 192.748 1.84 1 29.5 ? C4 AKG 302 A 1 HETATM 8 C C5 AKG . . . D 3 35.657 194.123 2.422 1 32.75 ? C5 AKG 302 A 1 HETATM 9 O O3 AKG . . . D 3 36.536 195.008 2.38 1 33.04 ? O3 AKG 302 A 1 HETATM 10 O O4 AKG . . . D 3 34.544 194.375 2.959 1 33.42 ? O4 AKG 302 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #