data_6YPV
#
_model_server_result.job_id            DRBnLoIVetjR9Y4doU3L5A 
_model_server_result.datetime_utc      '2024-11-25 09:24:57' 
_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          6ypv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6YPV 
#
_exptl.entry_id    6YPV 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         78.14 
_cell.angle_beta          76.04 
_cell.angle_gamma         66.51 
_cell.entry_id            6YPV 
_cell.length_a            37.037 
_cell.length_b            39.107 
_cell.length_c            40.86 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YPV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
_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 
_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                      3 
_struct_asym.id                             C 
_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 131 A HIS 131 1_555 B FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc2 A OD2 ASP 133 A ASP 133 1_555 B FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc3 A NE2 HIS 187 A HIS 187 1_555 B FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc4 B FE FE . A FE 301 1_555 C O2 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc5 B FE FE . A FE 301 1_555 C O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
#
_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                     6YPV 
_atom_sites.fract_transf_matrix[1][1]    0.027 
_atom_sites.fract_transf_matrix[1][2]    -0.011734 
_atom_sites.fract_transf_matrix[1][3]    -0.00531 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.027881 
_atom_sites.fract_transf_matrix[2][3]    -0.003452 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.025411 
_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 A 1 301 1 FE FE . 
C 3 AKG A 1 302 1 AKG AKG . 
D 4 HOH A 1 401 29 HOH HOH . 
D 4 HOH A 2 402 30 HOH HOH . 
D 4 HOH A 3 403 24 HOH HOH . 
D 4 HOH A 4 404 13 HOH HOH . 
D 4 HOH A 5 405 52 HOH HOH . 
D 4 HOH A 6 406 15 HOH HOH . 
D 4 HOH A 7 407 40 HOH HOH . 
D 4 HOH A 8 408 47 HOH HOH . 
D 4 HOH A 9 409 22 HOH HOH . 
D 4 HOH A 10 410 14 HOH HOH . 
D 4 HOH A 11 411 4 HOH HOH . 
D 4 HOH A 12 412 16 HOH HOH . 
D 4 HOH A 13 413 21 HOH HOH . 
D 4 HOH A 14 414 91 HOH HOH . 
D 4 HOH A 15 415 27 HOH HOH . 
D 4 HOH A 16 416 19 HOH HOH . 
D 4 HOH A 17 417 31 HOH HOH . 
D 4 HOH A 18 418 6 HOH HOH . 
D 4 HOH A 19 419 35 HOH HOH . 
D 4 HOH A 20 420 2 HOH HOH . 
D 4 HOH A 21 421 28 HOH HOH . 
D 4 HOH A 22 422 53 HOH HOH . 
D 4 HOH A 23 423 5 HOH HOH . 
D 4 HOH A 24 424 26 HOH HOH . 
D 4 HOH A 25 425 17 HOH HOH . 
D 4 HOH A 26 426 45 HOH HOH . 
D 4 HOH A 27 427 39 HOH HOH . 
D 4 HOH A 28 428 7 HOH HOH . 
D 4 HOH A 29 429 3 HOH HOH . 
D 4 HOH A 30 430 20 HOH HOH . 
D 4 HOH A 31 431 65 HOH HOH . 
D 4 HOH A 32 432 1 HOH HOH . 
D 4 HOH A 33 433 73 HOH HOH . 
D 4 HOH A 34 434 8 HOH HOH . 
D 4 HOH A 35 435 56 HOH HOH . 
D 4 HOH A 36 436 76 HOH HOH . 
D 4 HOH A 37 437 12 HOH HOH . 
D 4 HOH A 38 438 37 HOH HOH . 
D 4 HOH A 39 439 32 HOH HOH . 
D 4 HOH A 40 440 70 HOH HOH . 
D 4 HOH A 41 441 68 HOH HOH . 
D 4 HOH A 42 442 74 HOH HOH . 
D 4 HOH A 43 443 10 HOH HOH . 
D 4 HOH A 44 444 84 HOH HOH . 
D 4 HOH A 45 445 18 HOH HOH . 
D 4 HOH A 46 446 89 HOH HOH . 
D 4 HOH A 47 447 38 HOH HOH . 
D 4 HOH A 48 448 11 HOH HOH . 
D 4 HOH A 49 449 66 HOH HOH . 
D 4 HOH A 50 450 25 HOH HOH . 
D 4 HOH A 51 451 46 HOH HOH . 
D 4 HOH A 52 452 87 HOH HOH . 
D 4 HOH A 53 453 63 HOH HOH . 
D 4 HOH A 54 454 49 HOH HOH . 
D 4 HOH A 55 455 23 HOH HOH . 
D 4 HOH A 56 456 62 HOH HOH . 
D 4 HOH A 57 457 41 HOH HOH . 
D 4 HOH A 58 458 92 HOH HOH . 
D 4 HOH A 59 459 86 HOH HOH . 
D 4 HOH A 60 460 67 HOH HOH . 
D 4 HOH A 61 461 36 HOH HOH . 
D 4 HOH A 62 462 88 HOH HOH . 
D 4 HOH A 63 463 57 HOH HOH . 
D 4 HOH A 64 464 79 HOH HOH . 
D 4 HOH A 65 465 75 HOH HOH . 
D 4 HOH A 66 466 71 HOH HOH . 
D 4 HOH A 67 467 9 HOH HOH . 
D 4 HOH A 68 468 77 HOH HOH . 
D 4 HOH A 69 469 50 HOH HOH . 
D 4 HOH A 70 470 72 HOH HOH . 
D 4 HOH A 71 471 51 HOH HOH . 
D 4 HOH A 72 472 90 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 . . . C 3 -2.597 -1.235 2.341 1 37.93 ? C1 AKG 302 A 1 
HETATM 2 O O1 AKG . . . C 3 -2.356 -2.083 1.439 1 38.63 ? O1 AKG 302 A 1 
HETATM 3 O O2 AKG . . . C 3 -2.177 -1.415 3.517 1 38.64 ? O2 AKG 302 A 1 
HETATM 4 C C2 AKG . . . C 3 -3.408 0.015 2.008 1 35.62 ? C2 AKG 302 A 1 
HETATM 5 O O5 AKG . . . C 3 -3.903 0.646 2.875 1 33.76 ? O5 AKG 302 A 1 
HETATM 6 C C3 AKG . . . C 3 -3.578 0.442 0.552 1 35.09 ? C3 AKG 302 A 1 
HETATM 7 C C4 AKG . . . C 3 -4.261 1.808 0.505 1 33.78 ? C4 AKG 302 A 1 
HETATM 8 C C5 AKG . . . C 3 -4.478 2.204 -0.954 1 30.45 ? C5 AKG 302 A 1 
HETATM 9 O O3 AKG . . . C 3 -4.803 1.323 -1.794 1 29.29 ? O3 AKG 302 A 1 
HETATM 10 O O4 AKG . . . C 3 -4.333 3.4 -1.308 1 28.61 ? O4 AKG 302 A 1 
HETATM 11 H H31 AKG . . . C 3 -2.708 0.5 0.127 1 42.13 ? H31 AKG 302 A 1 
HETATM 12 H H32 AKG . . . C 3 -4.123 -0.21 0.085 1 42.13 ? H32 AKG 302 A 1 
HETATM 13 H H41 AKG . . . C 3 -5.117 1.759 0.96 1 40.57 ? H41 AKG 302 A 1 
HETATM 14 H H42 AKG . . . C 3 -3.7 2.468 0.942 1 40.57 ? H42 AKG 302 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#