data_6Q8D
#
_model_server_result.job_id            RUvKQKLu2QKyYOqkqwFmyw 
_model_server_result.datetime_utc      '2024-12-03 04:35:55' 
_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          6q8d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1}' 
#
_entry.id    6Q8D 
#
_exptl.entry_id    6Q8D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              206.193 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            '3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid' 
_entity.pdbx_number_of_molecules    1 
_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            6Q8D 
_cell.length_a            51.445 
_cell.length_b            51.445 
_cell.length_c            98.006 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Q8D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        93 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 42 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                      4 
_struct_asym.id                             E 
_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
covale ? covale1 E C7 ZDC . B ZDC 1 1_555 B N DLE 1 B DLE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.254 ? 
covale ? covale2 B C DLE 1 B DLE 2 1_555 B N DLY 2 B DLY 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 B C DLY 2 B DLY 3 1_555 B N DAL 3 B DAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C DAL 3 B DAL 4 1_555 B N DLE 4 B DLE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale5 B C DLE 4 B DLE 5 1_555 B N DLY 5 B DLY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 B C DLY 5 B DLY 6 1_555 B N DLY 6 B DLY 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale7 B C DLY 6 B DLY 7 1_555 B N DLE 7 B DLE 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale8 B C DLE 7 B DLE 8 1_555 B N DAL 8 B DAL 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
metalc ? metalc1 A O ASN 21 A ASN 21 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc2 A OE1 GLU 95 A GLU 95 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc3 A OE2 GLU 95 A GLU 95 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc4 A OD1 ASP 99 A ASP 99 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc5 A OD1 ASP 101 A ASP 101 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc6 A OD1 ASP 101 A ASP 101 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? 
metalc ? metalc7 A OD2 ASP 101 A ASP 101 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc8 A OD1 ASN 103 A ASN 103 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc9 A OD1 ASP 104 A ASP 104 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc10 A OD2 ASP 104 A ASP 104 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc11 A OD1 ASP 104 A ASP 104 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc12 A O GLY 114 A GLY 114 1_555 D CA CA . A CA 302 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
metalc ? metalc13 C CA CA . A CA 301 1_555 E O3 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc14 C CA CA . A CA 301 1_555 E O4 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc15 D CA CA . A CA 302 1_555 E O2 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc16 D CA CA . A CA 302 1_555 E O3 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? 
#
_chem_comp.formula           'C8 H14 O6' 
_chem_comp.formula_weight    206.193 
_chem_comp.id                ZDC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid' 
_chem_comp.type              d-saccharide 
_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 C1M ZDC sing 403 n n 
C1M H1M1 ZDC sing 404 n n 
C1M H1M2 ZDC sing 405 n n 
C1M H1M3 ZDC sing 406 n n 
C1 H1 ZDC sing 407 n n 
C1 O5 ZDC sing 408 n n 
C1 C2 ZDC sing 409 n n 
C2 H2 ZDC sing 410 n n 
C2 O2 ZDC sing 411 n n 
O2 H2O ZDC sing 412 n n 
C2 C3 ZDC sing 413 n n 
C3 H3 ZDC sing 414 n n 
C3 O3 ZDC sing 415 n n 
O3 H3O ZDC sing 416 n n 
C3 C4 ZDC sing 417 n n 
C4 H4 ZDC sing 418 n n 
C4 O4 ZDC sing 419 n n 
O4 H4O ZDC sing 420 n n 
C4 C5 ZDC sing 421 n n 
C5 H5 ZDC sing 422 n n 
C5 O5 ZDC sing 423 n n 
C5 C6 ZDC sing 424 n n 
C6 H61 ZDC sing 425 n n 
C6 H62 ZDC sing 426 n n 
C6 C7 ZDC sing 427 n n 
C7 O7A ZDC doub 428 n n 
C7 O7B ZDC sing 429 n n 
O7B H7OB ZDC sing 430 n n 
#
_atom_sites.entry_id                     6Q8D 
_atom_sites.fract_transf_matrix[1][1]    0.019438 
_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]    0.019438 
_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]    0.010203 
_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 3 CA A 1 301 301 CA CA . 
D 3 CA A 1 302 302 CA CA . 
E 4 ZDC B 1 1 201 ZDC FUD . 
F 5 HOH A 1 401 18 HOH HOH . 
F 5 HOH A 2 402 17 HOH HOH . 
F 5 HOH A 3 403 30 HOH HOH . 
F 5 HOH A 4 404 14 HOH HOH . 
F 5 HOH A 5 405 52 HOH HOH . 
F 5 HOH A 6 406 43 HOH HOH . 
F 5 HOH A 7 407 5 HOH HOH . 
F 5 HOH A 8 408 24 HOH HOH . 
F 5 HOH A 9 409 27 HOH HOH . 
F 5 HOH A 10 410 33 HOH HOH . 
F 5 HOH A 11 411 48 HOH HOH . 
F 5 HOH A 12 412 1 HOH HOH . 
F 5 HOH A 13 413 8 HOH HOH . 
F 5 HOH A 14 414 58 HOH HOH . 
F 5 HOH A 15 415 28 HOH HOH . 
F 5 HOH A 16 416 41 HOH HOH . 
F 5 HOH A 17 417 15 HOH HOH . 
F 5 HOH A 18 418 37 HOH HOH . 
F 5 HOH A 19 419 11 HOH HOH . 
F 5 HOH A 20 420 2 HOH HOH . 
F 5 HOH A 21 421 12 HOH HOH . 
F 5 HOH A 22 422 3 HOH HOH . 
F 5 HOH A 23 423 6 HOH HOH . 
F 5 HOH A 24 424 47 HOH HOH . 
F 5 HOH A 25 425 62 HOH HOH . 
F 5 HOH A 26 426 36 HOH HOH . 
F 5 HOH A 27 427 4 HOH HOH . 
F 5 HOH A 28 428 50 HOH HOH . 
F 5 HOH A 29 429 46 HOH HOH . 
F 5 HOH A 30 430 16 HOH HOH . 
F 5 HOH A 31 431 10 HOH HOH . 
F 5 HOH A 32 432 31 HOH HOH . 
F 5 HOH A 33 433 68 HOH HOH . 
F 5 HOH A 34 434 7 HOH HOH . 
F 5 HOH A 35 435 32 HOH HOH . 
F 5 HOH A 36 436 61 HOH HOH . 
F 5 HOH A 37 437 29 HOH HOH . 
F 5 HOH A 38 438 49 HOH HOH . 
F 5 HOH A 39 439 25 HOH HOH . 
F 5 HOH A 40 440 67 HOH HOH . 
F 5 HOH A 41 441 22 HOH HOH . 
F 5 HOH A 42 442 59 HOH HOH . 
F 5 HOH A 43 443 13 HOH HOH . 
F 5 HOH A 44 444 19 HOH HOH . 
F 5 HOH A 45 445 21 HOH HOH . 
F 5 HOH A 46 446 9 HOH HOH . 
F 5 HOH A 47 447 57 HOH HOH . 
F 5 HOH A 48 448 34 HOH HOH . 
F 5 HOH A 49 449 63 HOH HOH . 
F 5 HOH A 50 450 42 HOH HOH . 
F 5 HOH A 51 451 56 HOH HOH . 
F 5 HOH A 52 452 26 HOH HOH . 
F 5 HOH A 53 453 51 HOH HOH . 
F 5 HOH A 54 454 44 HOH HOH . 
F 5 HOH A 55 455 20 HOH HOH . 
F 5 HOH A 56 456 45 HOH HOH . 
F 5 HOH A 57 457 60 HOH HOH . 
F 5 HOH A 58 458 39 HOH HOH . 
F 5 HOH A 59 459 35 HOH HOH . 
F 5 HOH A 60 460 38 HOH HOH . 
F 5 HOH A 61 461 65 HOH HOH . 
F 5 HOH A 62 462 55 HOH HOH . 
F 5 HOH A 63 463 64 HOH HOH . 
F 5 HOH A 64 464 54 HOH HOH . 
F 5 HOH A 65 465 53 HOH HOH . 
F 5 HOH A 66 466 40 HOH HOH . 
F 5 HOH A 67 467 66 HOH HOH . 
G 5 HOH B 1 301 23 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 ZDC . . . E 4 39.14 15.411 16.724 1 33.47 ? C1 ZDC 1 B 1 
HETATM 2 C C1M ZDC . . . E 4 39.691 14.664 17.947 1 32.73 ? C1M ZDC 1 B 1 
HETATM 3 C C2 ZDC . . . E 4 38.885 14.461 15.512 1 32.66 ? C2 ZDC 1 B 1 
HETATM 4 C C3 ZDC . . . E 4 38.221 15.278 14.416 1 32.98 ? C3 ZDC 1 B 1 
HETATM 5 C C4 ZDC . . . E 4 36.982 16.001 14.887 1 34.19 ? C4 ZDC 1 B 1 
HETATM 6 C C5 ZDC . . . E 4 37.433 16.942 16.003 1 35.6 ? C5 ZDC 1 B 1 
HETATM 7 C C6 ZDC . . . E 4 37.878 18.345 15.771 1 35.64 ? C6 ZDC 1 B 1 
HETATM 8 C C7 ZDC . . . E 4 38.224 19.111 17.058 1 37.91 ? C7 ZDC 1 B 1 
HETATM 9 O O2 ZDC . . . E 4 37.939 13.444 15.887 1 33.59 ? O2 ZDC 1 B 1 
HETATM 10 O O3 ZDC . . . E 4 37.847 14.396 13.313 1 33.69 ? O3 ZDC 1 B 1 
HETATM 11 O O4 ZDC . . . E 4 36.428 16.736 13.753 1 36.92 ? O4 ZDC 1 B 1 
HETATM 12 O O5 ZDC . . . E 4 37.942 16.16 17.098 1 35.57 ? O5 ZDC 1 B 1 
HETATM 13 O O7A ZDC . . . E 4 39.334 19.028 17.527 1 37.54 ? O7A ZDC 1 B 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           13 
#