data_5J6F
#
_model_server_result.job_id            XVD7a8dxC9MgoqTd7pVNhQ 
_model_server_result.datetime_utc      '2024-11-25 21:35:41' 
_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          5j6f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":404}' 
#
_entry.id    5J6F 
#
_exptl.entry_id    5J6F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              226.183 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PREPHENIC ACID' 
_entity.pdbx_number_of_molecules    2 
_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         120 
_cell.entry_id            5J6F 
_cell.length_a            95.438 
_cell.length_b            95.438 
_cell.length_c            167.452 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J6F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        172 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 64' 
#
_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 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -47.719 82.651732 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 J 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 126 A CYS 126 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? 
metalc ? metalc2 A NE2 HIS 296 A HIS 296 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc3 A OE1 GLU 322 A GLU 322 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc4 A OE2 GLU 322 A GLU 322 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc5 B SG CYS 126 B CYS 126 1_555 G MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc6 B NE2 HIS 296 B HIS 296 1_555 G MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc7 B OE1 GLU 322 B GLU 322 1_555 G MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc8 B OE2 GLU 322 B GLU 322 1_555 G MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc9 B OD2 ASP 333 B ASP 333 1_555 G MN MN . B MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? 
#
_chem_comp.formula           'C10 H10 O6' 
_chem_comp.formula_weight    226.183 
_chem_comp.id                PRE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PREPHENIC 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 PRE sing 258 n n 
C1 C6 PRE sing 259 n n 
C1 C7 PRE sing 260 n n 
C1 C8 PRE sing 261 n n 
C2 C3 PRE doub 262 n n 
C2 H2 PRE sing 263 n n 
C3 C4 PRE sing 264 n n 
C3 H3 PRE sing 265 n n 
C4 O4 PRE sing 266 n n 
C4 C5 PRE sing 267 n n 
C4 H4 PRE sing 268 n n 
O4 HO4 PRE sing 269 n n 
C5 C6 PRE doub 270 n n 
C5 H5 PRE sing 271 n n 
C6 H6 PRE sing 272 n n 
C7 O71 PRE doub 273 n n 
C7 O72 PRE sing 274 n n 
O72 HO72 PRE sing 275 n n 
C8 C1' PRE sing 276 n n 
C8 H81 PRE sing 277 n n 
C8 H82 PRE sing 278 n n 
C1' O1' PRE doub 279 n n 
C1' C2' PRE sing 280 n n 
C2' "O'L" PRE doub 281 n n 
C2' "O'M" PRE sing 282 n n 
"O'M" HO2' PRE sing 283 n n 
#
_atom_sites.entry_id                     5J6F 
_atom_sites.fract_transf_matrix[1][1]    0.010478 
_atom_sites.fract_transf_matrix[1][2]    0.006049 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012099 
_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]    0.005972 
_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
C 2 MN A 1 401 1354 MN MN . 
D 3 SO4 A 1 402 1 SO4 SO4 . 
E 3 SO4 A 1 403 2 SO4 SO4 . 
F 4 PRE A 1 404 2 PRE PRE . 
G 2 MN B 1 401 1355 MN MN . 
H 3 SO4 B 1 402 3 SO4 SO4 . 
I 3 SO4 B 1 403 4 SO4 SO4 . 
J 4 PRE B 1 404 1 PRE PRE . 
#
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 PRE . . . F 4 -48.37 33.251 16.225 1 113.81 ? C1 PRE 404 A 1 
HETATM 2 C C2 PRE . . . F 4 -47.045 32.757 16.102 1 115.06 ? C2 PRE 404 A 1 
HETATM 3 C C3 PRE . . . F 4 -46.018 33.556 15.704 1 107.47 ? C3 PRE 404 A 1 
HETATM 4 C C4 PRE . . . F 4 -46.243 35 15.444 1 108.9 ? C4 PRE 404 A 1 
HETATM 5 O O4 PRE . . . F 4 -45.073 35.718 15.823 1 92.42 ? O4 PRE 404 A 1 
HETATM 6 C C5 PRE . . . F 4 -47.468 35.496 16.124 1 110.53 ? C5 PRE 404 A 1 
HETATM 7 C C6 PRE . . . F 4 -48.382 34.611 16.619 1 113.44 ? C6 PRE 404 A 1 
HETATM 8 C C7 PRE . . . F 4 -49.041 32.532 17.353 1 122.54 ? C7 PRE 404 A 1 
HETATM 9 O O71 PRE . . . F 4 -50.09 33.07 17.241 1 126.49 -1 O71 PRE 404 A 1 
HETATM 10 O O72 PRE . . . F 4 -48.189 31.821 17.754 1 107.86 ? O72 PRE 404 A 1 
HETATM 11 C C8 PRE . . . F 4 -49.286 32.887 15.109 1 103.92 ? C8 PRE 404 A 1 
HETATM 12 C C1' PRE . . . F 4 -49.086 33.633 13.817 1 88.28 ? C1' PRE 404 A 1 
HETATM 13 O O1' PRE . . . F 4 -48.264 33.294 12.977 1 83.47 ? O1' PRE 404 A 1 
HETATM 14 C C2' PRE . . . F 4 -49.967 34.888 13.644 1 75.93 ? C2' PRE 404 A 1 
HETATM 15 O "O'L" PRE . . . F 4 -49.435 35.897 13.123 1 62.63 -1 "O'L" PRE 404 A 1 
HETATM 16 O "O'M" PRE . . . F 4 -51.151 34.837 14.057 1 73.6 ? "O'M" PRE 404 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           16 
#