data_5Y7T
#
_model_server_result.job_id            Bp0wk-UfqVWT37-T5lHA2w 
_model_server_result.datetime_utc      '2024-11-28 19:56:23' 
_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          5y7t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    5Y7T 
#
_exptl.entry_id    5Y7T 
_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    1 
_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         90 
_cell.entry_id            5Y7T 
_cell.length_a            73.471 
_cell.length_b            118.619 
_cell.length_c            66.427 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y7T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 141 B HIS 134 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc2 A OD1 ASP 143 B ASP 136 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc3 A NE2 HIS 218 B HIS 211 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc4 B FE FE . B FE 401 1_555 D O1 AKG . B AKG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc5 B FE FE . B FE 401 1_555 D O5 AKG . B AKG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc6 B FE FE . B FE 401 1_555 E O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
#
_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 40 n n 
C1 O2 AKG sing 41 n n 
C1 C2 AKG sing 42 n n 
O2 HO2 AKG sing 43 n n 
C2 O5 AKG doub 44 n n 
C2 C3 AKG sing 45 n n 
C3 C4 AKG sing 46 n n 
C3 H31 AKG sing 47 n n 
C3 H32 AKG sing 48 n n 
C4 C5 AKG sing 49 n n 
C4 H41 AKG sing 50 n n 
C4 H42 AKG sing 51 n n 
C5 O3 AKG doub 52 n n 
C5 O4 AKG sing 53 n n 
O4 HO4 AKG sing 54 n n 
#
_atom_sites.entry_id                     5Y7T 
_atom_sites.fract_transf_matrix[1][1]    0.013611 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00843 
_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]    0.015054 
_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
B 2 FE B 1 401 1 FE FE . 
C 3 8R0 B 1 402 1 8R0 58K . 
D 4 AKG B 1 403 1 AKG AKG . 
E 5 HOH B 1 501 114 HOH HOH . 
E 5 HOH B 2 502 101 HOH HOH . 
E 5 HOH B 3 503 9 HOH HOH . 
E 5 HOH B 4 504 34 HOH HOH . 
E 5 HOH B 5 505 66 HOH HOH . 
E 5 HOH B 6 506 3 HOH HOH . 
E 5 HOH B 7 507 115 HOH HOH . 
E 5 HOH B 8 508 27 HOH HOH . 
E 5 HOH B 9 509 55 HOH HOH . 
E 5 HOH B 10 510 77 HOH HOH . 
E 5 HOH B 11 511 21 HOH HOH . 
E 5 HOH B 12 512 10 HOH HOH . 
E 5 HOH B 13 513 94 HOH HOH . 
E 5 HOH B 14 514 20 HOH HOH . 
E 5 HOH B 15 515 59 HOH HOH . 
E 5 HOH B 16 516 31 HOH HOH . 
E 5 HOH B 17 517 58 HOH HOH . 
E 5 HOH B 18 518 4 HOH HOH . 
E 5 HOH B 19 519 15 HOH HOH . 
E 5 HOH B 20 520 30 HOH HOH . 
E 5 HOH B 21 521 57 HOH HOH . 
E 5 HOH B 22 522 46 HOH HOH . 
E 5 HOH B 23 523 13 HOH HOH . 
E 5 HOH B 24 524 25 HOH HOH . 
E 5 HOH B 25 525 7 HOH HOH . 
E 5 HOH B 26 526 38 HOH HOH . 
E 5 HOH B 27 527 71 HOH HOH . 
E 5 HOH B 28 528 67 HOH HOH . 
E 5 HOH B 29 529 54 HOH HOH . 
E 5 HOH B 30 530 74 HOH HOH . 
E 5 HOH B 31 531 44 HOH HOH . 
E 5 HOH B 32 532 2 HOH HOH . 
E 5 HOH B 33 533 53 HOH HOH . 
E 5 HOH B 34 534 39 HOH HOH . 
E 5 HOH B 35 535 69 HOH HOH . 
E 5 HOH B 36 536 110 HOH HOH . 
E 5 HOH B 37 537 11 HOH HOH . 
E 5 HOH B 38 538 56 HOH HOH . 
E 5 HOH B 39 539 49 HOH HOH . 
E 5 HOH B 40 540 43 HOH HOH . 
E 5 HOH B 41 541 37 HOH HOH . 
E 5 HOH B 42 542 36 HOH HOH . 
E 5 HOH B 43 543 1 HOH HOH . 
E 5 HOH B 44 544 78 HOH HOH . 
E 5 HOH B 45 545 89 HOH HOH . 
E 5 HOH B 46 546 32 HOH HOH . 
E 5 HOH B 47 547 5 HOH HOH . 
E 5 HOH B 48 548 45 HOH HOH . 
E 5 HOH B 49 549 8 HOH HOH . 
E 5 HOH B 50 550 61 HOH HOH . 
E 5 HOH B 51 551 95 HOH HOH . 
E 5 HOH B 52 552 70 HOH HOH . 
E 5 HOH B 53 553 48 HOH HOH . 
E 5 HOH B 54 554 23 HOH HOH . 
E 5 HOH B 55 555 50 HOH HOH . 
E 5 HOH B 56 556 16 HOH HOH . 
E 5 HOH B 57 557 76 HOH HOH . 
E 5 HOH B 58 558 29 HOH HOH . 
E 5 HOH B 59 559 64 HOH HOH . 
E 5 HOH B 60 560 33 HOH HOH . 
E 5 HOH B 61 561 35 HOH HOH . 
E 5 HOH B 62 562 65 HOH HOH . 
E 5 HOH B 63 563 41 HOH HOH . 
E 5 HOH B 64 564 86 HOH HOH . 
E 5 HOH B 65 565 105 HOH HOH . 
E 5 HOH B 66 566 52 HOH HOH . 
E 5 HOH B 67 567 90 HOH HOH . 
E 5 HOH B 68 568 73 HOH HOH . 
E 5 HOH B 69 569 47 HOH HOH . 
E 5 HOH B 70 570 63 HOH HOH . 
E 5 HOH B 71 571 6 HOH HOH . 
E 5 HOH B 72 572 109 HOH HOH . 
E 5 HOH B 73 573 14 HOH HOH . 
E 5 HOH B 74 574 22 HOH HOH . 
E 5 HOH B 75 575 97 HOH HOH . 
E 5 HOH B 76 576 106 HOH HOH . 
E 5 HOH B 77 577 87 HOH HOH . 
E 5 HOH B 78 578 79 HOH HOH . 
E 5 HOH B 79 579 62 HOH HOH . 
E 5 HOH B 80 580 60 HOH HOH . 
E 5 HOH B 81 581 81 HOH HOH . 
E 5 HOH B 82 582 68 HOH HOH . 
E 5 HOH B 83 583 40 HOH HOH . 
E 5 HOH B 84 584 96 HOH HOH . 
E 5 HOH B 85 585 12 HOH HOH . 
E 5 HOH B 86 586 26 HOH HOH . 
E 5 HOH B 87 587 99 HOH HOH . 
E 5 HOH B 88 588 113 HOH HOH . 
E 5 HOH B 89 589 92 HOH HOH . 
E 5 HOH B 90 590 91 HOH HOH . 
E 5 HOH B 91 591 51 HOH HOH . 
E 5 HOH B 92 592 42 HOH HOH . 
E 5 HOH B 93 593 17 HOH HOH . 
E 5 HOH B 94 594 103 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 4 -20.574 -21.944 -4.424 1 48.45 ? C1 AKG 403 B 1 
HETATM 2 O O1 AKG . . . D 4 -21.654 -22.462 -4.905 1 47 -1 O1 AKG 403 B 1 
HETATM 3 O O2 AKG . . . D 4 -20.593 -20.886 -3.711 1 49.01 ? O2 AKG 403 B 1 
HETATM 4 C C2 AKG . . . D 4 -19.19 -22.566 -4.699 1 43.89 ? C2 AKG 403 B 1 
HETATM 5 O O5 AKG . . . D 4 -19.081 -23.53 -5.396 1 51.91 ? O5 AKG 403 B 1 
HETATM 6 C C3 AKG . . . D 4 -17.958 -21.9 -4.073 1 41.72 ? C3 AKG 403 B 1 
HETATM 7 C C4 AKG . . . D 4 -16.658 -22.487 -4.64 1 49.91 ? C4 AKG 403 B 1 
HETATM 8 C C5 AKG . . . D 4 -15.422 -21.88 -3.966 1 47.47 ? C5 AKG 403 B 1 
HETATM 9 O O3 AKG . . . D 4 -14.292 -22.137 -4.435 1 46.95 ? O3 AKG 403 B 1 
HETATM 10 O O4 AKG . . . D 4 -15.494 -21.138 -2.949 1 55.6 -1 O4 AKG 403 B 1 
HETATM 11 H H31 AKG . . . D 4 -17.983 -20.948 -4.259 1 50.06 ? H31 AKG 403 B 1 
HETATM 12 H H32 AKG . . . D 4 -17.976 -22.037 -3.113 1 50.06 ? H32 AKG 403 B 1 
HETATM 13 H H41 AKG . . . D 4 -16.656 -23.447 -4.498 1 59.89 ? H41 AKG 403 B 1 
HETATM 14 H H42 AKG . . . D 4 -16.619 -22.308 -5.592 1 59.89 ? H42 AKG 403 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#