data_8X7D # _model_server_result.job_id 5M95I4fbs_vuQvd_6PwC1w _model_server_result.datetime_utc '2024-11-26 17:11:09' _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 8x7d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":403}' # _entry.id 8X7D # _exptl.entry_id 8X7D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC ACID' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.89 _cell.angle_gamma 90 _cell.entry_id 8X7D _cell.length_a 46.019 _cell.length_b 140.474 _cell.length_c 58.976 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 E N N ? 3 G N N ? 3 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 NE2 HIS 225 A HIS 225 1_555 C CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc2 A OD1 ASP 227 A ASP 227 1_555 C CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 A NE2 HIS 282 A HIS 282 1_555 C CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 C CO CO . A CO 401 1_555 D O5 AKG . A AKG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc5 C CO CO . A CO 401 1_555 D O2 AKG . A AKG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 B NE2 HIS 225 B HIS 225 1_555 F CO CO . B CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc7 B OD1 ASP 227 B ASP 227 1_555 F CO CO . B CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc8 B NE2 HIS 282 B HIS 282 1_555 F CO CO . B CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc9 F CO CO . B CO 401 1_555 G O1 AKG . B AKG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc10 F CO CO . B CO 401 1_555 G O5 AKG . B AKG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc11 F CO CO . B CO 401 1_555 J O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? # _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 8X7D _atom_sites.fract_transf_matrix[1][1] 0.02173 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008731 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007119 _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] 0.018273 _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 1 401 401 CO CO . D 3 AKG A 1 402 501 AKG LIG . E 3 AKG A 1 403 601 AKG LIG . F 2 CO B 1 401 401 CO CO . G 3 AKG B 1 402 501 AKG LIG . H 3 AKG B 1 403 601 AKG LIG . I 4 HOH A 1 501 161 HOH HOH . I 4 HOH A 2 502 50 HOH HOH . I 4 HOH A 3 503 3 HOH HOH . I 4 HOH A 4 504 184 HOH HOH . I 4 HOH A 5 505 104 HOH HOH . I 4 HOH A 6 506 66 HOH HOH . I 4 HOH A 7 507 27 HOH HOH . I 4 HOH A 8 508 15 HOH HOH . I 4 HOH A 9 509 130 HOH HOH . I 4 HOH A 10 510 90 HOH HOH . I 4 HOH A 11 511 94 HOH HOH . I 4 HOH A 12 512 29 HOH HOH . I 4 HOH A 13 513 11 HOH HOH . I 4 HOH A 14 514 2 HOH HOH . I 4 HOH A 15 515 63 HOH HOH . I 4 HOH A 16 516 4 HOH HOH . I 4 HOH A 17 517 65 HOH HOH . I 4 HOH A 18 518 142 HOH HOH . I 4 HOH A 19 519 111 HOH HOH . I 4 HOH A 20 520 30 HOH HOH . I 4 HOH A 21 521 26 HOH HOH . I 4 HOH A 22 522 6 HOH HOH . I 4 HOH A 23 523 41 HOH HOH . I 4 HOH A 24 524 46 HOH HOH . I 4 HOH A 25 525 61 HOH HOH . I 4 HOH A 26 526 99 HOH HOH . I 4 HOH A 27 527 186 HOH HOH . I 4 HOH A 28 528 36 HOH HOH . I 4 HOH A 29 529 9 HOH HOH . I 4 HOH A 30 530 44 HOH HOH . I 4 HOH A 31 531 91 HOH HOH . I 4 HOH A 32 532 134 HOH HOH . I 4 HOH A 33 533 67 HOH HOH . I 4 HOH A 34 534 13 HOH HOH . I 4 HOH A 35 535 148 HOH HOH . I 4 HOH A 36 536 133 HOH HOH . I 4 HOH A 37 537 93 HOH HOH . I 4 HOH A 38 538 1 HOH HOH . I 4 HOH A 39 539 39 HOH HOH . I 4 HOH A 40 540 10 HOH HOH . I 4 HOH A 41 541 86 HOH HOH . I 4 HOH A 42 542 189 HOH HOH . I 4 HOH A 43 543 76 HOH HOH . I 4 HOH A 44 544 5 HOH HOH . I 4 HOH A 45 545 114 HOH HOH . I 4 HOH A 46 546 81 HOH HOH . I 4 HOH A 47 547 105 HOH HOH . I 4 HOH A 48 548 139 HOH HOH . I 4 HOH A 49 549 53 HOH HOH . I 4 HOH A 50 550 12 HOH HOH . I 4 HOH A 51 551 62 HOH HOH . I 4 HOH A 52 552 151 HOH HOH . I 4 HOH A 53 553 124 HOH HOH . I 4 HOH A 54 554 21 HOH HOH . I 4 HOH A 55 555 32 HOH HOH . I 4 HOH A 56 556 120 HOH HOH . I 4 HOH A 57 557 85 HOH HOH . I 4 HOH A 58 558 110 HOH HOH . I 4 HOH A 59 559 35 HOH HOH . I 4 HOH A 60 560 33 HOH HOH . I 4 HOH A 61 561 16 HOH HOH . I 4 HOH A 62 562 117 HOH HOH . I 4 HOH A 63 563 147 HOH HOH . I 4 HOH A 64 564 180 HOH HOH . I 4 HOH A 65 565 48 HOH HOH . I 4 HOH A 66 566 145 HOH HOH . I 4 HOH A 67 567 14 HOH HOH . I 4 HOH A 68 568 183 HOH HOH . I 4 HOH A 69 569 108 HOH HOH . I 4 HOH A 70 570 25 HOH HOH . I 4 HOH A 71 571 116 HOH HOH . I 4 HOH A 72 572 95 HOH HOH . I 4 HOH A 73 573 131 HOH HOH . I 4 HOH A 74 574 28 HOH HOH . I 4 HOH A 75 575 51 HOH HOH . I 4 HOH A 76 576 87 HOH HOH . I 4 HOH A 77 577 157 HOH HOH . I 4 HOH A 78 578 60 HOH HOH . I 4 HOH A 79 579 74 HOH HOH . I 4 HOH A 80 580 119 HOH HOH . I 4 HOH A 81 581 182 HOH HOH . I 4 HOH A 82 582 158 HOH HOH . I 4 HOH A 83 583 71 HOH HOH . I 4 HOH A 84 584 103 HOH HOH . I 4 HOH A 85 585 56 HOH HOH . I 4 HOH A 86 586 128 HOH HOH . I 4 HOH A 87 587 64 HOH HOH . I 4 HOH A 88 588 121 HOH HOH . I 4 HOH A 89 589 153 HOH HOH . I 4 HOH A 90 590 141 HOH HOH . I 4 HOH A 91 591 123 HOH HOH . I 4 HOH A 92 592 155 HOH HOH . I 4 HOH A 93 593 159 HOH HOH . I 4 HOH A 94 594 54 HOH HOH . I 4 HOH A 95 595 88 HOH HOH . I 4 HOH A 96 596 57 HOH HOH . I 4 HOH A 97 597 171 HOH HOH . I 4 HOH A 98 598 79 HOH HOH . I 4 HOH A 99 599 173 HOH HOH . I 4 HOH A 100 600 152 HOH HOH . I 4 HOH A 101 601 122 HOH HOH . I 4 HOH A 102 602 149 HOH HOH . I 4 HOH A 103 603 109 HOH HOH . I 4 HOH A 104 604 164 HOH HOH . I 4 HOH A 105 605 68 HOH HOH . I 4 HOH A 106 606 127 HOH HOH . I 4 HOH A 107 607 163 HOH HOH . J 4 HOH B 1 501 146 HOH HOH . J 4 HOH B 2 502 96 HOH HOH . J 4 HOH B 3 503 40 HOH HOH . J 4 HOH B 4 504 82 HOH HOH . J 4 HOH B 5 505 8 HOH HOH . J 4 HOH B 6 506 19 HOH HOH . J 4 HOH B 7 507 24 HOH HOH . J 4 HOH B 8 508 144 HOH HOH . J 4 HOH B 9 509 70 HOH HOH . J 4 HOH B 10 510 132 HOH HOH . J 4 HOH B 11 511 169 HOH HOH . J 4 HOH B 12 512 137 HOH HOH . J 4 HOH B 13 513 7 HOH HOH . J 4 HOH B 14 514 101 HOH HOH . J 4 HOH B 15 515 49 HOH HOH . J 4 HOH B 16 516 77 HOH HOH . J 4 HOH B 17 517 58 HOH HOH . J 4 HOH B 18 518 23 HOH HOH . J 4 HOH B 19 519 106 HOH HOH . J 4 HOH B 20 520 135 HOH HOH . J 4 HOH B 21 521 177 HOH HOH . J 4 HOH B 22 522 83 HOH HOH . J 4 HOH B 23 523 172 HOH HOH . J 4 HOH B 24 524 31 HOH HOH . J 4 HOH B 25 525 73 HOH HOH . J 4 HOH B 26 526 52 HOH HOH . J 4 HOH B 27 527 38 HOH HOH . J 4 HOH B 28 528 55 HOH HOH . J 4 HOH B 29 529 138 HOH HOH . J 4 HOH B 30 530 97 HOH HOH . J 4 HOH B 31 531 37 HOH HOH . J 4 HOH B 32 532 185 HOH HOH . J 4 HOH B 33 533 187 HOH HOH . J 4 HOH B 34 534 80 HOH HOH . J 4 HOH B 35 535 47 HOH HOH . J 4 HOH B 36 536 126 HOH HOH . J 4 HOH B 37 537 18 HOH HOH . J 4 HOH B 38 538 102 HOH HOH . J 4 HOH B 39 539 42 HOH HOH . J 4 HOH B 40 540 84 HOH HOH . J 4 HOH B 41 541 22 HOH HOH . J 4 HOH B 42 542 190 HOH HOH . J 4 HOH B 43 543 72 HOH HOH . J 4 HOH B 44 544 43 HOH HOH . J 4 HOH B 45 545 92 HOH HOH . J 4 HOH B 46 546 176 HOH HOH . J 4 HOH B 47 547 118 HOH HOH . J 4 HOH B 48 548 45 HOH HOH . J 4 HOH B 49 549 17 HOH HOH . J 4 HOH B 50 550 59 HOH HOH . J 4 HOH B 51 551 98 HOH HOH . J 4 HOH B 52 552 181 HOH HOH . J 4 HOH B 53 553 20 HOH HOH . J 4 HOH B 54 554 115 HOH HOH . J 4 HOH B 55 555 78 HOH HOH . J 4 HOH B 56 556 69 HOH HOH . J 4 HOH B 57 557 75 HOH HOH . J 4 HOH B 58 558 34 HOH HOH . J 4 HOH B 59 559 156 HOH HOH . J 4 HOH B 60 560 129 HOH HOH . J 4 HOH B 61 561 107 HOH HOH . J 4 HOH B 62 562 150 HOH HOH . J 4 HOH B 63 563 154 HOH HOH . J 4 HOH B 64 564 125 HOH HOH . J 4 HOH B 65 565 140 HOH HOH . J 4 HOH B 66 566 188 HOH HOH . J 4 HOH B 67 567 162 HOH HOH . J 4 HOH B 68 568 178 HOH HOH . J 4 HOH B 69 569 170 HOH HOH . J 4 HOH B 70 570 165 HOH HOH . J 4 HOH B 71 571 167 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 . . . E 3 20.778 11.818 1.286 1 57.57 ? C1 AKG 403 A 1 HETATM 2 O O1 AKG . . . E 3 21.349 12.71 0.604 1 56.68 -1 O1 AKG 403 A 1 HETATM 3 O O2 AKG . . . E 3 20.588 11.996 2.52 1 50.68 ? O2 AKG 403 A 1 HETATM 4 C C2 AKG . . . E 3 20.321 10.524 0.615 1 48.56 ? C2 AKG 403 A 1 HETATM 5 O O5 AKG . . . E 3 20.227 9.524 1.249 1 48.68 ? O5 AKG 403 A 1 HETATM 6 C C3 AKG . . . E 3 20 10.526 -0.882 1 48.55 ? C3 AKG 403 A 1 HETATM 7 C C4 AKG . . . E 3 18.532 10.875 -1.129 1 47.23 ? C4 AKG 403 A 1 HETATM 8 C C5 AKG . . . E 3 18.398 11.604 -2.467 1 53.2 ? C5 AKG 403 A 1 HETATM 9 O O3 AKG . . . E 3 19.338 11.563 -3.305 1 51.52 -1 O3 AKG 403 A 1 HETATM 10 O O4 AKG . . . E 3 17.347 12.246 -2.734 1 41.59 ? O4 AKG 403 A 1 # _model_server_stats.io_time_ms 106 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 726 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #