data_3IVU # _model_server_result.job_id Iw2ec1nQ6ZxZd7sre-qpSQ _model_server_result.datetime_utc '2024-11-29 07:17:25' _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 3ivu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1000}' # _entry.id 3IVU # _exptl.entry_id 3IVU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 4 _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 3IVU _cell.length_a 133.798 _cell.length_b 133.798 _cell.length_c 125.657 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IVU _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 ? 4 E 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 metalc ? metalc1 A OE1 GLU 49 A GLU 44 1_555 C CO CO . A CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 A O ARG 219 A ARG 214 1_555 D NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc3 A NE2 HIS 229 A HIS 224 1_555 C CO CO . A CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc4 A NE2 HIS 231 A HIS 226 1_555 C CO CO . A CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc5 I O HOH . A HOH 465 1_555 C CO CO . A CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 C CO CO . A CO 500 1_555 E O1 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc7 C CO CO . A CO 500 1_555 E O5 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc8 C CO CO . A CO 500 1_555 E C1 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc9 C CO CO . A CO 500 1_555 E C2 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc10 B OE1 GLU 49 B GLU 44 1_555 F CO CO . B CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc11 B O ARG 219 B ARG 214 1_555 G NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc12 B O VAL 222 B VAL 217 1_555 G NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc13 B NE2 HIS 229 B HIS 224 1_555 F CO CO . B CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc14 B NE2 HIS 231 B HIS 226 1_555 F CO CO . B CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc15 J O HOH . B HOH 422 1_555 F CO CO . B CO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc16 F CO CO . B CO 500 1_555 H O5 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc17 F CO CO . B CO 500 1_555 H O1 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc18 F CO CO . B CO 500 1_555 H C2 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc19 F CO CO . B CO 500 1_555 H C1 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? # _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 3IVU _atom_sites.fract_transf_matrix[1][1] 0.007474 _atom_sites.fract_transf_matrix[1][2] 0.004315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00863 _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] 0.007958 _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 CO A 1 500 500 CO CO . D 3 NA A 1 503 503 NA NA . E 4 AKG A 1 1000 1000 AKG AKG . F 2 CO B 1 500 500 CO CO . G 3 NA B 1 503 503 NA NA . H 4 AKG B 1 1000 1000 AKG AKG . I 5 HOH A 1 419 2 HOH HOH . I 5 HOH A 2 420 4 HOH HOH . I 5 HOH A 3 421 5 HOH HOH . I 5 HOH A 4 422 13 HOH HOH . I 5 HOH A 5 423 16 HOH HOH . I 5 HOH A 6 424 19 HOH HOH . I 5 HOH A 7 425 20 HOH HOH . I 5 HOH A 8 426 21 HOH HOH . I 5 HOH A 9 427 22 HOH HOH . I 5 HOH A 10 428 26 HOH HOH . I 5 HOH A 11 429 28 HOH HOH . I 5 HOH A 12 430 29 HOH HOH . I 5 HOH A 13 431 33 HOH HOH . I 5 HOH A 14 432 34 HOH HOH . I 5 HOH A 15 433 42 HOH HOH . I 5 HOH A 16 434 45 HOH HOH . I 5 HOH A 17 435 49 HOH HOH . I 5 HOH A 18 436 52 HOH HOH . I 5 HOH A 19 437 53 HOH HOH . I 5 HOH A 20 438 57 HOH HOH . I 5 HOH A 21 439 58 HOH HOH . I 5 HOH A 22 440 60 HOH HOH . I 5 HOH A 23 441 61 HOH HOH . I 5 HOH A 24 442 62 HOH HOH . I 5 HOH A 25 443 63 HOH HOH . I 5 HOH A 26 444 64 HOH HOH . I 5 HOH A 27 445 66 HOH HOH . I 5 HOH A 28 446 72 HOH HOH . I 5 HOH A 29 447 76 HOH HOH . I 5 HOH A 30 448 77 HOH HOH . I 5 HOH A 31 449 82 HOH HOH . I 5 HOH A 32 450 89 HOH HOH . I 5 HOH A 33 451 92 HOH HOH . I 5 HOH A 34 452 111 HOH HOH . I 5 HOH A 35 453 117 HOH HOH . I 5 HOH A 36 454 127 HOH HOH . I 5 HOH A 37 455 132 HOH HOH . I 5 HOH A 38 456 137 HOH HOH . I 5 HOH A 39 457 138 HOH HOH . I 5 HOH A 40 458 141 HOH HOH . I 5 HOH A 41 459 142 HOH HOH . I 5 HOH A 42 460 148 HOH HOH . I 5 HOH A 43 461 156 HOH HOH . I 5 HOH A 44 462 172 HOH HOH . I 5 HOH A 45 463 174 HOH HOH . I 5 HOH A 46 464 176 HOH HOH . I 5 HOH A 47 465 178 HOH HOH . I 5 HOH A 48 466 213 HOH HOH . I 5 HOH A 49 467 220 HOH HOH . I 5 HOH A 50 468 232 HOH HOH . I 5 HOH A 51 469 238 HOH HOH . I 5 HOH A 52 470 243 HOH HOH . J 5 HOH B 1 419 1 HOH HOH . J 5 HOH B 2 420 6 HOH HOH . J 5 HOH B 3 421 7 HOH HOH . J 5 HOH B 4 422 11 HOH HOH . J 5 HOH B 5 423 12 HOH HOH . J 5 HOH B 6 424 14 HOH HOH . J 5 HOH B 7 425 15 HOH HOH . J 5 HOH B 8 426 17 HOH HOH . J 5 HOH B 9 427 18 HOH HOH . J 5 HOH B 10 428 23 HOH HOH . J 5 HOH B 11 429 31 HOH HOH . J 5 HOH B 12 430 36 HOH HOH . J 5 HOH B 13 431 37 HOH HOH . J 5 HOH B 14 432 38 HOH HOH . J 5 HOH B 15 433 39 HOH HOH . J 5 HOH B 16 434 40 HOH HOH . J 5 HOH B 17 435 41 HOH HOH . J 5 HOH B 18 436 44 HOH HOH . J 5 HOH B 19 437 47 HOH HOH . J 5 HOH B 20 438 50 HOH HOH . J 5 HOH B 21 439 51 HOH HOH . J 5 HOH B 22 440 54 HOH HOH . J 5 HOH B 23 441 59 HOH HOH . J 5 HOH B 24 442 65 HOH HOH . J 5 HOH B 25 443 71 HOH HOH . J 5 HOH B 26 444 78 HOH HOH . J 5 HOH B 27 445 81 HOH HOH . J 5 HOH B 28 446 84 HOH HOH . J 5 HOH B 29 447 88 HOH HOH . J 5 HOH B 30 448 90 HOH HOH . J 5 HOH B 31 449 91 HOH HOH . J 5 HOH B 32 450 93 HOH HOH . J 5 HOH B 33 451 96 HOH HOH . J 5 HOH B 34 452 100 HOH HOH . J 5 HOH B 35 453 104 HOH HOH . J 5 HOH B 36 454 106 HOH HOH . J 5 HOH B 37 455 108 HOH HOH . J 5 HOH B 38 456 109 HOH HOH . J 5 HOH B 39 457 110 HOH HOH . J 5 HOH B 40 458 112 HOH HOH . J 5 HOH B 41 459 113 HOH HOH . J 5 HOH B 42 460 118 HOH HOH . J 5 HOH B 43 461 119 HOH HOH . J 5 HOH B 44 462 121 HOH HOH . J 5 HOH B 45 463 124 HOH HOH . J 5 HOH B 46 464 129 HOH HOH . J 5 HOH B 47 465 131 HOH HOH . J 5 HOH B 48 466 136 HOH HOH . J 5 HOH B 49 467 146 HOH HOH . J 5 HOH B 50 468 157 HOH HOH . J 5 HOH B 51 469 161 HOH HOH . J 5 HOH B 52 470 165 HOH HOH . J 5 HOH B 53 471 166 HOH HOH . J 5 HOH B 54 472 175 HOH HOH . J 5 HOH B 55 473 177 HOH HOH . J 5 HOH B 56 474 180 HOH HOH . J 5 HOH B 57 475 185 HOH HOH . J 5 HOH B 58 476 194 HOH HOH . J 5 HOH B 59 477 195 HOH HOH . J 5 HOH B 60 478 204 HOH HOH . J 5 HOH B 61 479 206 HOH HOH . J 5 HOH B 62 480 207 HOH HOH . J 5 HOH B 63 481 208 HOH HOH . J 5 HOH B 64 482 210 HOH HOH . J 5 HOH B 65 483 244 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 . . . H 4 -13.421 43.859 -14.727 1 75.44 ? C1 AKG 1000 B 1 HETATM 2 O O1 AKG . . . H 4 -13.225 43.276 -13.611 1 72.19 ? O1 AKG 1000 B 1 HETATM 3 O O2 AKG . . . H 4 -13.514 45.106 -14.854 1 74.31 ? O2 AKG 1000 B 1 HETATM 4 C C2 AKG . . . H 4 -13.543 43.085 -15.808 1 76.59 ? C2 AKG 1000 B 1 HETATM 5 O O5 AKG . . . H 4 -13.453 41.877 -15.629 1 74.77 ? O5 AKG 1000 B 1 HETATM 6 C C3 AKG . . . H 4 -13.807 43.665 -17.185 1 79.4 ? C3 AKG 1000 B 1 HETATM 7 C C4 AKG . . . H 4 -15.314 43.52 -17.475 1 83.34 ? C4 AKG 1000 B 1 HETATM 8 C C5 AKG . . . H 4 -15.948 44.717 -18.189 1 85.72 ? C5 AKG 1000 B 1 HETATM 9 O O3 AKG . . . H 4 -15.618 44.999 -19.37 1 86.38 ? O3 AKG 1000 B 1 HETATM 10 O O4 AKG . . . H 4 -16.802 45.409 -17.585 1 86.6 ? O4 AKG 1000 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #