data_8DPN
#
_model_server_result.job_id            9tB3E8K_H58seDE7p8KHKg 
_model_server_result.datetime_utc      '2025-07-10 04:58:13' 
_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          8dpn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":501}' 
#
_entry.id    8DPN 
#
_exptl.entry_id    8DPN 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              206.15 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-HYDROXY-3-CARBOXY-ADIPIC ACID' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 
_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    ? 
_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 E N N 
? 3 I 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 SG CYS 62 A CYS 62 1_555 G FE3 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc2 A SG CYS 88 A CYS 88 1_555 G FE4 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc3 A SG CYS 88 A CYS 88 1_555 G FE5 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc4 A SG CYS 154 A CYS 154 1_555 G FE1 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc5 A SG CYS 275 A CYS 275 1_555 F FE1 ICS . A ICS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc6 B SG CYS 70 B CYS 70 1_555 G FE7 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc7 B SG CYS 95 B CYS 95 1_555 G FE2 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc8 B SG CYS 95 B CYS 95 1_555 G FE8 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc9 B O ARG 108 B ARG 108 1_555 K FE FE . D FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc10 B SG CYS 153 B CYS 153 1_555 G FE6 CLF . B CLF 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc11 B OD1 ASP 353 B ASP 353 1_555 H FE FE . B FE 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
metalc ? metalc12 B OD2 ASP 353 B ASP 353 1_555 H FE FE . B FE 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc13 B OD2 ASP 357 B ASP 357 1_555 H FE FE . B FE 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc14 H FE FE . B FE 602 1_555 D O ARG 108 D ARG 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc15 H FE FE . B FE 602 1_555 D OE1 GLU 109 D GLU 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc16 C SG CYS 62 C CYS 62 1_555 L FE3 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc17 C SG CYS 88 C CYS 88 1_555 L FE4 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc18 C SG CYS 88 C CYS 88 1_555 L FE5 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc19 C SG CYS 154 C CYS 154 1_555 L FE1 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc20 C SG CYS 275 C CYS 275 1_555 J FE1 ICS . C ICS 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc21 D SG CYS 70 D CYS 70 1_555 L FE7 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc22 D SG CYS 95 D CYS 95 1_555 L FE2 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc23 D SG CYS 95 D CYS 95 1_555 L FE8 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc24 D SG CYS 153 D CYS 153 1_555 L FE6 CLF . D CLF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc25 D OD1 ASP 353 D ASP 353 1_555 K FE FE . D FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc26 D OD2 ASP 353 D ASP 353 1_555 K FE FE . D FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
metalc ? metalc27 D OD2 ASP 357 D ASP 357 1_555 K FE FE . D FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
#
_chem_comp.formula           'C7 H10 O7' 
_chem_comp.formula_weight    206.15 
_chem_comp.id                HCA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-HYDROXY-3-CARBOXY-ADIPIC 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 C2 HCA sing 153 n n 
C1 O1 HCA doub 154 n n 
C1 O2 HCA sing 155 n n 
C2 C3 HCA sing 156 n n 
C2 H21 HCA sing 157 n n 
C2 H22 HCA sing 158 n n 
C3 C4 HCA sing 159 n n 
C3 C7 HCA sing 160 n n 
C3 O7 HCA sing 161 n n 
C4 C5 HCA sing 162 n n 
C4 H41 HCA sing 163 n n 
C4 H42 HCA sing 164 n n 
C5 C6 HCA sing 165 n n 
C5 H51 HCA sing 166 n n 
C5 H52 HCA sing 167 n n 
C6 O3 HCA doub 168 n n 
C6 O4 HCA sing 169 n n 
C7 O5 HCA doub 170 n n 
C7 O6 HCA sing 171 n n 
O2 HO2 HCA sing 172 n n 
O4 HO4 HCA sing 173 n n 
O6 HO6 HCA sing 174 n n 
O7 HO7 HCA sing 175 n n 
#
_atom_sites.entry_id                     8DPN 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 HCA A 1 501 1494 HCA HCA . 
F 4 ICS A 1 502 1496 ICS ICS . 
G 5 CLF B 1 601 1498 CLF CLF . 
H 6 FE B 1 602 1492 FE FE . 
I 3 HCA C 1 501 1494 HCA HCA . 
J 4 ICS C 1 502 1496 ICS ICS . 
K 6 FE D 1 601 1492 FE FE . 
L 5 CLF D 1 602 1498 CLF CLF . 
M 7 HOH A 1 601 7 HOH HOH . 
M 7 HOH A 2 602 30 HOH HOH . 
M 7 HOH A 3 603 39 HOH HOH . 
M 7 HOH A 4 604 38 HOH HOH . 
M 7 HOH A 5 605 32 HOH HOH . 
M 7 HOH A 6 606 1 HOH HOH . 
M 7 HOH A 7 607 11 HOH HOH . 
N 7 HOH B 1 701 20 HOH HOH . 
N 7 HOH B 2 702 22 HOH HOH . 
N 7 HOH B 3 703 2 HOH HOH . 
N 7 HOH B 4 704 34 HOH HOH . 
N 7 HOH B 5 705 33 HOH HOH . 
N 7 HOH B 6 706 31 HOH HOH . 
N 7 HOH B 7 707 4 HOH HOH . 
N 7 HOH B 8 708 3 HOH HOH . 
N 7 HOH B 9 709 37 HOH HOH . 
N 7 HOH B 10 710 23 HOH HOH . 
O 7 HOH C 1 601 15 HOH HOH . 
O 7 HOH C 2 602 10 HOH HOH . 
O 7 HOH C 3 603 19 HOH HOH . 
O 7 HOH C 4 604 17 HOH HOH . 
O 7 HOH C 5 605 35 HOH HOH . 
O 7 HOH C 6 606 25 HOH HOH . 
O 7 HOH C 7 607 9 HOH HOH . 
O 7 HOH C 8 608 16 HOH HOH . 
O 7 HOH C 9 609 28 HOH HOH . 
O 7 HOH C 10 610 24 HOH HOH . 
O 7 HOH C 11 611 26 HOH HOH . 
P 7 HOH D 1 701 8 HOH HOH . 
P 7 HOH D 2 702 29 HOH HOH . 
P 7 HOH D 3 703 27 HOH HOH . 
P 7 HOH D 4 704 36 HOH HOH . 
P 7 HOH D 5 705 6 HOH HOH . 
P 7 HOH D 6 706 40 HOH HOH . 
P 7 HOH D 7 707 5 HOH HOH . 
P 7 HOH D 8 708 18 HOH HOH . 
P 7 HOH D 9 709 13 HOH HOH . 
P 7 HOH D 10 710 21 HOH HOH . 
P 7 HOH D 11 711 12 HOH HOH . 
P 7 HOH D 12 712 14 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 HCA . . . E 3 133.501 143.033 158.907 1 49.06 ? C1 HCA 501 A 1 
HETATM 2 C C2 HCA . . . E 3 134.885 143.6 158.701 1 49.06 ? C2 HCA 501 A 1 
HETATM 3 C C3 HCA . . . E 3 135.952 142.555 158.997 1 49.06 ? C3 HCA 501 A 1 
HETATM 4 C C4 HCA . . . E 3 136.577 142.777 160.367 1 49.06 ? C4 HCA 501 A 1 
HETATM 5 C C5 HCA . . . E 3 137.552 141.652 160.688 1 49.06 ? C5 HCA 501 A 1 
HETATM 6 C C6 HCA . . . E 3 138.325 141.977 161.941 1 49.06 ? C6 HCA 501 A 1 
HETATM 7 C C7 HCA . . . E 3 137.022 142.647 157.941 1 49.06 ? C7 HCA 501 A 1 
HETATM 8 O O1 HCA . . . E 3 133.343 141.795 158.915 1 49.06 ? O1 HCA 501 A 1 
HETATM 9 O O2 HCA . . . E 3 132.555 143.834 159.053 1 49.06 ? O2 HCA 501 A 1 
HETATM 10 O O3 HCA . . . E 3 139.566 142.098 161.858 1 49.06 ? O3 HCA 501 A 1 
HETATM 11 O O4 HCA . . . E 3 137.699 142.115 163.012 1 49.06 ? O4 HCA 501 A 1 
HETATM 12 O O5 HCA . . . E 3 137.462 141.593 157.441 1 49.06 ? O5 HCA 501 A 1 
HETATM 13 O O6 HCA . . . E 3 137.432 143.779 157.607 1 49.06 ? O6 HCA 501 A 1 
HETATM 14 O O7 HCA . . . E 3 135.37 141.251 158.97 1 49.06 ? O7 HCA 501 A 1 
#
_model_server_stats.io_time_ms              80 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#