data_5Y2V
#
_model_server_result.job_id            uD2ZpKjV8AxSHD_X69J4tw 
_model_server_result.datetime_utc      '2025-08-05 11:23:20' 
_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          5y2v 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
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_entry.id    5Y2V 
#
_exptl.entry_id    5Y2V 
_exptl.method      'X-RAY DIFFRACTION' 
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_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                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5Y2V 
_cell.length_a            90.766 
_cell.length_b            109.16 
_cell.length_c            178.226 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y2V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
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_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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 F N N 
? 3 H N N 
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_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     ? 
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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                     5Y2V 
_atom_sites.fract_transf_matrix[1][1]    0.011017 
_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]    0.009161 
_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]    0.005611 
_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
E 2 PO4 A 1 401 2 PO4 PO4 . 
F 3 AKG B 1 401 1 AKG AKG . 
G 2 PO4 C 1 401 1 PO4 PO4 . 
H 3 AKG D 1 401 2 AKG AKG . 
I 4 HOH A 1 501 103 HOH HOH . 
I 4 HOH A 2 502 20 HOH HOH . 
I 4 HOH A 3 503 26 HOH HOH . 
I 4 HOH A 4 504 105 HOH HOH . 
I 4 HOH A 5 505 19 HOH HOH . 
I 4 HOH A 6 506 9 HOH HOH . 
I 4 HOH A 7 507 55 HOH HOH . 
I 4 HOH A 8 508 97 HOH HOH . 
I 4 HOH A 9 509 4 HOH HOH . 
I 4 HOH A 10 510 107 HOH HOH . 
I 4 HOH A 11 511 91 HOH HOH . 
I 4 HOH A 12 512 23 HOH HOH . 
I 4 HOH A 13 513 44 HOH HOH . 
I 4 HOH A 14 514 10 HOH HOH . 
I 4 HOH A 15 515 96 HOH HOH . 
I 4 HOH A 16 516 18 HOH HOH . 
I 4 HOH A 17 517 7 HOH HOH . 
I 4 HOH A 18 518 3 HOH HOH . 
I 4 HOH A 19 519 16 HOH HOH . 
I 4 HOH A 20 520 12 HOH HOH . 
I 4 HOH A 21 521 6 HOH HOH . 
I 4 HOH A 22 522 25 HOH HOH . 
I 4 HOH A 23 523 112 HOH HOH . 
I 4 HOH A 24 524 51 HOH HOH . 
I 4 HOH A 25 525 24 HOH HOH . 
I 4 HOH A 26 526 15 HOH HOH . 
J 4 HOH B 1 501 90 HOH HOH . 
J 4 HOH B 2 502 95 HOH HOH . 
J 4 HOH B 3 503 99 HOH HOH . 
J 4 HOH B 4 504 34 HOH HOH . 
J 4 HOH B 5 505 83 HOH HOH . 
J 4 HOH B 6 506 39 HOH HOH . 
J 4 HOH B 7 507 42 HOH HOH . 
J 4 HOH B 8 508 30 HOH HOH . 
J 4 HOH B 9 509 38 HOH HOH . 
J 4 HOH B 10 510 84 HOH HOH . 
J 4 HOH B 11 511 31 HOH HOH . 
J 4 HOH B 12 512 110 HOH HOH . 
J 4 HOH B 13 513 101 HOH HOH . 
J 4 HOH B 14 514 27 HOH HOH . 
J 4 HOH B 15 515 32 HOH HOH . 
J 4 HOH B 16 516 36 HOH HOH . 
J 4 HOH B 17 517 70 HOH HOH . 
J 4 HOH B 18 518 5 HOH HOH . 
J 4 HOH B 19 519 92 HOH HOH . 
J 4 HOH B 20 520 102 HOH HOH . 
J 4 HOH B 21 521 35 HOH HOH . 
J 4 HOH B 22 522 43 HOH HOH . 
J 4 HOH B 23 523 40 HOH HOH . 
J 4 HOH B 24 524 41 HOH HOH . 
J 4 HOH B 25 525 93 HOH HOH . 
K 4 HOH C 1 501 94 HOH HOH . 
K 4 HOH C 2 502 52 HOH HOH . 
K 4 HOH C 3 503 58 HOH HOH . 
K 4 HOH C 4 504 61 HOH HOH . 
K 4 HOH C 5 505 80 HOH HOH . 
K 4 HOH C 6 506 100 HOH HOH . 
K 4 HOH C 7 507 56 HOH HOH . 
K 4 HOH C 8 508 45 HOH HOH . 
K 4 HOH C 9 509 79 HOH HOH . 
K 4 HOH C 10 510 106 HOH HOH . 
K 4 HOH C 11 511 108 HOH HOH . 
K 4 HOH C 12 512 88 HOH HOH . 
K 4 HOH C 13 513 60 HOH HOH . 
K 4 HOH C 14 514 54 HOH HOH . 
K 4 HOH C 15 515 1 HOH HOH . 
K 4 HOH C 16 516 53 HOH HOH . 
K 4 HOH C 17 517 86 HOH HOH . 
K 4 HOH C 18 518 28 HOH HOH . 
K 4 HOH C 19 519 17 HOH HOH . 
K 4 HOH C 20 520 33 HOH HOH . 
K 4 HOH C 21 521 46 HOH HOH . 
K 4 HOH C 22 522 57 HOH HOH . 
K 4 HOH C 23 523 48 HOH HOH . 
K 4 HOH C 24 524 63 HOH HOH . 
K 4 HOH C 25 525 11 HOH HOH . 
K 4 HOH C 26 526 47 HOH HOH . 
K 4 HOH C 27 527 49 HOH HOH . 
K 4 HOH C 28 528 50 HOH HOH . 
K 4 HOH C 29 529 77 HOH HOH . 
K 4 HOH C 30 530 59 HOH HOH . 
L 4 HOH D 1 501 87 HOH HOH . 
L 4 HOH D 2 502 89 HOH HOH . 
L 4 HOH D 3 503 85 HOH HOH . 
L 4 HOH D 4 504 76 HOH HOH . 
L 4 HOH D 5 505 75 HOH HOH . 
L 4 HOH D 6 506 72 HOH HOH . 
L 4 HOH D 7 507 68 HOH HOH . 
L 4 HOH D 8 508 67 HOH HOH . 
L 4 HOH D 9 509 29 HOH HOH . 
L 4 HOH D 10 510 66 HOH HOH . 
L 4 HOH D 11 511 109 HOH HOH . 
L 4 HOH D 12 512 69 HOH HOH . 
L 4 HOH D 13 513 81 HOH HOH . 
L 4 HOH D 14 514 104 HOH HOH . 
L 4 HOH D 15 515 111 HOH HOH . 
L 4 HOH D 16 516 37 HOH HOH . 
L 4 HOH D 17 517 2 HOH HOH . 
L 4 HOH D 18 518 65 HOH HOH . 
L 4 HOH D 19 519 21 HOH HOH . 
L 4 HOH D 20 520 71 HOH HOH . 
L 4 HOH D 21 521 82 HOH HOH . 
L 4 HOH D 22 522 98 HOH HOH . 
L 4 HOH D 23 523 74 HOH HOH . 
L 4 HOH D 24 524 78 HOH HOH . 
L 4 HOH D 25 525 8 HOH HOH . 
L 4 HOH D 26 526 22 HOH HOH . 
L 4 HOH D 27 527 64 HOH HOH . 
L 4 HOH D 28 528 73 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 . . . F 3 16.164 -1.256 53.095 1 71.08 ? C1 AKG 401 B 1 
HETATM 2 O O1 AKG . . . F 3 16.799 -1.693 52.076 1 63.62 ? O1 AKG 401 B 1 
HETATM 3 O O2 AKG . . . F 3 15.992 -0.061 53.606 1 69.8 ? O2 AKG 401 B 1 
HETATM 4 C C2 AKG . . . F 3 15.421 -2.322 53.639 1 61.68 ? C2 AKG 401 B 1 
HETATM 5 O O5 AKG . . . F 3 15.051 -3.097 52.754 1 78.78 ? O5 AKG 401 B 1 
HETATM 6 C C3 AKG . . . F 3 15.06 -2.377 55.1 1 58.9 ? C3 AKG 401 B 1 
HETATM 7 C C4 AKG . . . F 3 16.332 -2.034 55.829 1 55.06 ? C4 AKG 401 B 1 
HETATM 8 C C5 AKG . . . F 3 16.463 -2.874 57.01 1 63.25 ? C5 AKG 401 B 1 
HETATM 9 O O3 AKG . . . F 3 17.003 -4.023 56.792 1 58.39 ? O3 AKG 401 B 1 
HETATM 10 O O4 AKG . . . F 3 15.972 -2.32 58.028 1 63.61 ? O4 AKG 401 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           10 
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