data_4L04
#
_model_server_result.job_id            9c50k0Rn8dtNQwQPpXROQg 
_model_server_result.datetime_utc      '2024-10-10 15:16:18' 
_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          4l04 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":501}' 
#
_entry.id    4L04 
#
_exptl.entry_id    4L04 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              146.098 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-OXOGLUTARIC ACID' 
_entity.pdbx_number_of_molecules    6 
_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            4L04 
_cell.length_a            96.41 
_cell.length_b            116.622 
_cell.length_c            275.729 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4L04 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,J,K,L,Y,Z 1 1 
C,D,M,N,O,P,Q,R,AA,BA 2 1 
E,F,S,T,U,V,W,X,CA,DA 3 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
? 2 G N N 
? 2 K N N 
? 2 M N N 
? 2 P N N 
? 2 S N N 
? 2 V 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 OD2 ASP 252 A ASP 252 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc2 A OD1 ASP 275 A ASP 275 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? 
metalc ? metalc3 A OD2 ASP 279 A ASP 279 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc4 G O2 AKG . A AKG 501 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc5 G O5 AKG . A AKG 501 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc6 H CA CA . A CA 502 1_555 B OD2 ASP 252 B ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc7 I CA CA . A CA 503 1_555 B OD1 ASP 275 B ASP 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc8 I CA CA . A CA 503 1_555 B OD2 ASP 279 B ASP 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? 
metalc ? metalc9 I CA CA . A CA 503 1_555 K O2 AKG . B AKG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc10 I CA CA . A CA 503 1_555 K O5 AKG . B AKG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc11 I CA CA . A CA 503 1_555 Z O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc12 C OD2 ASP 252 C ASP 252 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.191 ? 
metalc ? metalc13 C OD1 ASP 275 C ASP 275 1_555 N CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc14 C OD2 ASP 279 C ASP 279 1_555 N CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? 
metalc ? metalc15 M O2 AKG . C AKG 501 1_555 N CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc16 M O5 AKG . C AKG 501 1_555 N CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? 
metalc ? metalc17 N CA CA . C CA 502 1_555 AA O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? 
metalc ? metalc18 N CA CA . C CA 502 1_555 D OD2 ASP 252 D ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc19 D OD1 ASP 275 D ASP 275 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc20 D O ASP 275 D ASP 275 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? 
metalc ? metalc21 D OD1 ASP 279 D ASP 279 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? 
metalc ? metalc22 P O2 AKG . D AKG 501 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc23 P O5 AKG . D AKG 501 1_555 Q CA CA . D CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
metalc ? metalc24 E OD2 ASP 252 E ASP 252 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc25 E OD1 ASP 275 E ASP 275 1_555 T CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc26 E OD2 ASP 279 E ASP 279 1_555 T CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? 
metalc ? metalc27 S O5 AKG . E AKG 501 1_555 T CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? 
metalc ? metalc28 S O2 AKG . E AKG 501 1_555 T CA CA . E CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? 
metalc ? metalc29 T CA CA . E CA 502 1_555 F OD2 ASP 252 F ASP 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc30 F OD1 ASP 275 F ASP 275 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? 
metalc ? metalc31 F O ASP 275 F ASP 275 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? 
metalc ? metalc32 F OD1 ASP 279 F ASP 279 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc33 V O2 AKG . F AKG 501 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc34 V O5 AKG . F AKG 501 1_555 W CA CA . F CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? 
#
_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                     4L04 
_atom_sites.fract_transf_matrix[1][1]    0.010372 
_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]    0.008575 
_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]    0.003627 
_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
G 2 AKG A 1 501 1 AKG AKG . 
H 3 CA A 1 502 1 CA CA . 
I 3 CA A 1 503 2 CA CA . 
J 4 NAP A 1 504 1 NAP NAP . 
K 2 AKG B 1 501 2 AKG AKG . 
L 4 NAP B 1 502 2 NAP NAP . 
M 2 AKG C 1 501 3 AKG AKG . 
N 3 CA C 1 502 3 CA CA . 
O 4 NAP C 1 503 3 NAP NAP . 
P 2 AKG D 1 501 4 AKG AKG . 
Q 3 CA D 1 502 4 CA CA . 
R 4 NAP D 1 503 4 NAP NAP . 
S 2 AKG E 1 501 5 AKG AKG . 
T 3 CA E 1 502 5 CA CA . 
U 4 NAP E 1 503 5 NAP NAP . 
V 2 AKG F 1 501 6 AKG AKG . 
W 3 CA F 1 502 6 CA CA . 
X 4 NAP F 1 503 6 NAP NAP . 
Y 5 HOH A 1 601 4 HOH HOH . 
Y 5 HOH A 2 602 6 HOH HOH . 
Y 5 HOH A 3 603 15 HOH HOH . 
Y 5 HOH A 4 604 16 HOH HOH . 
Y 5 HOH A 5 605 26 HOH HOH . 
Y 5 HOH A 6 606 27 HOH HOH . 
Y 5 HOH A 7 607 29 HOH HOH . 
Y 5 HOH A 8 608 30 HOH HOH . 
Y 5 HOH A 9 609 37 HOH HOH . 
Y 5 HOH A 10 610 42 HOH HOH . 
Y 5 HOH A 11 611 44 HOH HOH . 
Y 5 HOH A 12 612 45 HOH HOH . 
Y 5 HOH A 13 613 52 HOH HOH . 
Y 5 HOH A 14 614 54 HOH HOH . 
Y 5 HOH A 15 615 55 HOH HOH . 
Y 5 HOH A 16 616 58 HOH HOH . 
Y 5 HOH A 17 617 62 HOH HOH . 
Y 5 HOH A 18 618 65 HOH HOH . 
Z 5 HOH B 1 601 1 HOH HOH . 
Z 5 HOH B 2 602 3 HOH HOH . 
Z 5 HOH B 3 603 8 HOH HOH . 
Z 5 HOH B 4 604 13 HOH HOH . 
Z 5 HOH B 5 605 19 HOH HOH . 
Z 5 HOH B 6 606 28 HOH HOH . 
Z 5 HOH B 7 607 33 HOH HOH . 
Z 5 HOH B 8 608 34 HOH HOH . 
Z 5 HOH B 9 609 35 HOH HOH . 
Z 5 HOH B 10 610 49 HOH HOH . 
Z 5 HOH B 11 611 53 HOH HOH . 
Z 5 HOH B 12 612 57 HOH HOH . 
Z 5 HOH B 13 613 68 HOH HOH . 
AA 5 HOH C 1 601 14 HOH HOH . 
AA 5 HOH C 2 602 18 HOH HOH . 
AA 5 HOH C 3 603 20 HOH HOH . 
AA 5 HOH C 4 604 22 HOH HOH . 
AA 5 HOH C 5 605 24 HOH HOH . 
AA 5 HOH C 6 606 31 HOH HOH . 
AA 5 HOH C 7 607 32 HOH HOH . 
AA 5 HOH C 8 608 43 HOH HOH . 
AA 5 HOH C 9 609 46 HOH HOH . 
AA 5 HOH C 10 610 47 HOH HOH . 
AA 5 HOH C 11 611 48 HOH HOH . 
AA 5 HOH C 12 612 50 HOH HOH . 
AA 5 HOH C 13 613 61 HOH HOH . 
AA 5 HOH C 14 614 63 HOH HOH . 
AA 5 HOH C 15 615 66 HOH HOH . 
AA 5 HOH C 16 616 69 HOH HOH . 
BA 5 HOH D 1 601 2 HOH HOH . 
BA 5 HOH D 2 602 10 HOH HOH . 
BA 5 HOH D 3 603 12 HOH HOH . 
BA 5 HOH D 4 604 25 HOH HOH . 
BA 5 HOH D 5 605 36 HOH HOH . 
BA 5 HOH D 6 606 41 HOH HOH . 
BA 5 HOH D 7 607 67 HOH HOH . 
BA 5 HOH D 8 608 70 HOH HOH . 
CA 5 HOH E 1 601 9 HOH HOH . 
CA 5 HOH E 2 602 21 HOH HOH . 
CA 5 HOH E 3 603 38 HOH HOH . 
CA 5 HOH E 4 604 51 HOH HOH . 
CA 5 HOH E 5 605 56 HOH HOH . 
CA 5 HOH E 6 606 60 HOH HOH . 
CA 5 HOH E 7 607 64 HOH HOH . 
DA 5 HOH F 1 601 5 HOH HOH . 
DA 5 HOH F 2 602 7 HOH HOH . 
DA 5 HOH F 3 603 11 HOH HOH . 
DA 5 HOH F 4 604 23 HOH HOH . 
DA 5 HOH F 5 605 39 HOH HOH . 
DA 5 HOH F 6 606 40 HOH HOH . 
DA 5 HOH F 7 607 59 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 . . . S 2 29.2 -71.281 -108.546 1 96.83 ? C1 AKG 501 E 1 
HETATM 2 O O1 AKG . . . S 2 28.181 -71.242 -107.826 1 96.9 ? O1 AKG 501 E 1 
HETATM 3 O O2 AKG . . . S 2 29.175 -71.11 -109.782 1 95.35 ? O2 AKG 501 E 1 
HETATM 4 C C2 AKG . . . S 2 30.473 -71.537 -107.9 1 98.09 ? C2 AKG 501 E 1 
HETATM 5 O O5 AKG . . . S 2 31.19 -72.421 -108.333 1 98.1 ? O5 AKG 501 E 1 
HETATM 6 C C3 AKG . . . S 2 30.876 -70.675 -106.722 1 98.83 ? C3 AKG 501 E 1 
HETATM 7 C C4 AKG . . . S 2 31.738 -71.44 -105.722 1 97.8 ? C4 AKG 501 E 1 
HETATM 8 C C5 AKG . . . S 2 32.592 -70.471 -104.947 1 93.43 ? C5 AKG 501 E 1 
HETATM 9 O O3 AKG . . . S 2 32.026 -69.566 -104.306 1 91.58 ? O3 AKG 501 E 1 
HETATM 10 O O4 AKG . . . S 2 33.83 -70.616 -104.98 1 91.77 ? O4 AKG 501 E 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           10 
#