data_6Q87 # _model_server_result.job_id ObzFdmcBuMstT-fSXbLdew _model_server_result.datetime_utc '2024-10-14 00:21:43' _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 6q87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 6Q87 # _exptl.entry_id 6Q87 _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 120 _cell.entry_id 6Q87 _cell.length_a 130.2 _cell.length_b 130.2 _cell.length_c 49.623 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Q87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 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,H _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.21 ? covale ? covale2 B C DLE 1 B DLE 2 1_555 B N DLE 2 B DLE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C DLE 2 B DLE 3 1_555 B N DLY 3 B DLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C DLY 3 B DLY 4 1_555 B N DAL 4 B DAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 B C DAL 4 B DAL 5 1_555 B N DLE 5 B DLE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C DLE 5 B DLE 6 1_555 B N DLY 6 B DLY 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 B C DLY 6 B DLY 7 1_555 B N DLY 7 B DLY 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B C DLY 7 B DLY 8 1_555 B N DLE 8 B DLE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 B C DLE 8 B DLE 9 1_555 B N DAL 9 B DAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 B C DAL 9 B DAL 10 1_555 B N DLY 10 B DLY 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 B C DLY 10 B DLY 11 1_555 B N DLY 11 B DLY 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 B C DLY 11 B DLY 12 1_555 B N DTY 12 B DTY 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C DTY 12 B DTY 13 1_555 B N DLY 13 B DLY 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 B C DLY 13 B DLY 14 1_555 F N NH2 . B NH2 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A O ASN 21 A ASN 21 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc2 A OE1 GLU 95 A GLU 95 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc3 A OE2 GLU 95 A GLU 95 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc4 A OD1 ASP 99 A ASP 99 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc5 A OD2 ASP 101 A ASP 101 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc6 A OD1 ASP 101 A ASP 101 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 A OD1 ASN 103 A ASN 103 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc8 A OD1 ASP 104 A ASP 104 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc9 A OD2 ASP 104 A ASP 104 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc10 A OD2 ASP 104 A ASP 104 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc11 A O GLY 114 A GLY 114 1_555 D CA CA . A CA 302 12_567 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 C CA CA . A CA 301 1_555 E O3 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc13 C CA CA . A CA 301 1_555 E O4 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc14 D CA CA . A CA 302 1_555 E O3 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc15 D CA CA . A CA 302 1_555 E O2 ZDC . B ZDC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? # _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 405 n n C1M H1M1 ZDC sing 406 n n C1M H1M2 ZDC sing 407 n n C1M H1M3 ZDC sing 408 n n C1 H1 ZDC sing 409 n n C1 O5 ZDC sing 410 n n C1 C2 ZDC sing 411 n n C2 H2 ZDC sing 412 n n C2 O2 ZDC sing 413 n n O2 H2O ZDC sing 414 n n C2 C3 ZDC sing 415 n n C3 H3 ZDC sing 416 n n C3 O3 ZDC sing 417 n n O3 H3O ZDC sing 418 n n C3 C4 ZDC sing 419 n n C4 H4 ZDC sing 420 n n C4 O4 ZDC sing 421 n n O4 H4O ZDC sing 422 n n C4 C5 ZDC sing 423 n n C5 H5 ZDC sing 424 n n C5 O5 ZDC sing 425 n n C5 C6 ZDC sing 426 n n C6 H61 ZDC sing 427 n n C6 H62 ZDC sing 428 n n C6 C7 ZDC sing 429 n n C7 O7A ZDC doub 430 n n C7 O7B ZDC sing 431 n n O7B H7OB ZDC sing 432 n n # _atom_sites.entry_id 6Q87 _atom_sites.fract_transf_matrix[1][1] 0.00768 _atom_sites.fract_transf_matrix[1][2] 0.004434 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008869 _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] 0.020152 _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 NH2 B 1 202 14 NH2 NH2 . G 6 HOH A 1 401 9 HOH HOH . G 6 HOH A 2 402 7 HOH HOH . G 6 HOH A 3 403 3 HOH HOH . G 6 HOH A 4 404 4 HOH HOH . G 6 HOH A 5 405 6 HOH HOH . G 6 HOH A 6 406 10 HOH HOH . G 6 HOH A 7 407 1 HOH HOH . G 6 HOH A 8 408 2 HOH HOH . G 6 HOH A 9 409 5 HOH HOH . G 6 HOH A 10 410 11 HOH HOH . G 6 HOH A 11 411 12 HOH HOH . H 6 HOH B 1 301 8 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 -10.443 51.021 70.769 1 74.52 ? C1 ZDC 1 B 1 HETATM 2 C C1M ZDC . . . E 4 -9.758 52.293 71.271 1 66.21 ? C1M ZDC 1 B 1 HETATM 3 C C2 ZDC . . . E 4 -11.947 51.301 70.479 1 70.69 ? C2 ZDC 1 B 1 HETATM 4 C C3 ZDC . . . E 4 -12.522 50.108 69.756 1 74.13 ? C3 ZDC 1 B 1 HETATM 5 C C4 ZDC . . . E 4 -11.731 49.745 68.535 1 81.23 ? C4 ZDC 1 B 1 HETATM 6 C C5 ZDC . . . E 4 -10.378 49.328 69.07 1 73.07 ? C5 ZDC 1 B 1 HETATM 7 C C6 ZDC . . . E 4 -10.149 47.947 69.549 1 75.68 ? C6 ZDC 1 B 1 HETATM 8 C C7 ZDC . . . E 4 -8.852 47.75 70.32 1 80 ? C7 ZDC 1 B 1 HETATM 9 O O2 ZDC . . . E 4 -12.066 52.381 69.531 1 66.91 ? O2 ZDC 1 B 1 HETATM 10 O O3 ZDC . . . E 4 -13.815 50.54 69.287 1 82.99 ? O3 ZDC 1 B 1 HETATM 11 O O4 ZDC . . . E 4 -12.37 48.629 67.852 1 86.58 ? O4 ZDC 1 B 1 HETATM 12 O O5 ZDC . . . E 4 -9.724 50.481 69.61 1 70.8 ? O5 ZDC 1 B 1 HETATM 13 O O7A ZDC . . . E 4 -8.675 48.33 71.362 1 82.37 ? O7A ZDC 1 B 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 600 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #