data_1JWL # _model_server_result.job_id 2W7S67ohyABSrRqXOl492g _model_server_result.datetime_utc '2025-03-06 03:56:42' _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 1jwl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":334}' # _entry.id 1JWL # _exptl.entry_id 1JWL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 285.25 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-nitrophenyl beta-D-fucopyranoside' _entity.pdbx_number_of_molecules 3 _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 1JWL _cell.length_a 255.771 _cell.length_b 255.771 _cell.length_c 206.795 _cell.Z_PDB 54 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JWL _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,F,G 1 1 E,H 2 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' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 147.669456 137.863333 # 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 G N N ? 4 H 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 hydrog WATSON-CRICK hydrog1 A N3 DT 6 D DT 6 1_555 B N1 DA 19 E DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 6 D DT 6 1_555 B N6 DA 19 E DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 7 D DG 7 1_555 B N3 DC 18 E DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 7 D DG 7 1_555 B O2 DC 18 E DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 7 D DG 7 1_555 B N4 DC 18 E DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DT 8 D DT 8 1_555 B N1 DA 17 E DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 DT 8 D DT 8 1_555 B N6 DA 17 E DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DG 9 D DG 9 1_555 B N3 DC 16 E DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N2 DG 9 D DG 9 1_555 B O2 DC 16 E DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O6 DG 9 D DG 9 1_555 B N4 DC 16 E DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DA 10 D DA 10 1_555 B N3 DT 15 E DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N6 DA 10 D DA 10 1_555 B O4 DT 15 E DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DG 11 D DG 11 1_555 B N3 DC 14 E DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 DG 11 D DG 11 1_555 B O2 DC 14 E DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 DG 11 D DG 11 1_555 B N4 DC 14 E DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 12 D DC 12 1_555 B N1 DG 13 E DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 12 D DC 12 1_555 B O6 DG 13 E DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 12 D DC 12 1_555 B N2 DG 13 E DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DG 13 D DG 13 1_555 B N3 DC 12 E DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 DG 13 D DG 13 1_555 B O2 DC 12 E DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 DG 13 D DG 13 1_555 B N4 DC 12 E DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog22 A N1 DG 14 D DG 14 1_555 B O4 DT 10 E DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DG 14 D DG 14 1_555 B N3 DC 11 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 DG 14 D DG 14 1_555 B O2 DC 11 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O6 DG 14 D DG 14 1_555 B N4 DC 11 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DA MISPAIR' hydrog26 A N1 DA 15 D DA 15 1_555 B N6 DA 9 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N1 DA 15 D DA 15 1_555 B N3 DT 10 E DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N6 DA 15 D DA 15 1_555 B O4 DT 10 E DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 DT 16 D DT 16 1_555 B N1 DA 9 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O4 DT 16 D DT 16 1_555 B N6 DA 9 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 DA 17 D DA 17 1_555 B N3 DT 8 E DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N6 DA 17 D DA 17 1_555 B O4 DT 8 E DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N1 DA 18 D DA 18 1_555 B N3 DT 7 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N6 DA 18 D DA 18 1_555 B O4 DT 7 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N3 DC 19 D DC 19 1_555 B N1 DG 6 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N4 DC 19 D DC 19 1_555 B O6 DG 6 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A O2 DC 19 D DC 19 1_555 B N2 DG 6 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C12 H15 N O7' _chem_comp.formula_weight 285.25 _chem_comp.id NPF _chem_comp.mon_nstd_flag n _chem_comp.name '2-nitrophenyl beta-D-fucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE;2-nitrophenyl 6-deoxy-beta-D-galactopyranoside;2-nitrophenyl beta-D-fucoside;2-nitrophenyl D-fucoside;2-nitrophenyl fucoside' # 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 C1A C2A NPF doub 384 n y C1A C6A NPF sing 385 n y C1A O1 NPF sing 386 n n C2A C3A NPF sing 387 n y C2A H2A NPF sing 388 n n C3A C4A NPF doub 389 n y C3A H3A NPF sing 390 n n C4A C5A NPF sing 391 n y C4A H4A NPF sing 392 n n C5A C6A NPF doub 393 n y C5A H5A NPF sing 394 n n C6A N6 NPF sing 395 n n N6 O6A NPF sing 396 n n N6 O6B NPF doub 397 n n O1 C1 NPF sing 398 n n C1 C2 NPF sing 399 n n C1 O5 NPF sing 400 n n C1 H1 NPF sing 401 n n C2 O2 NPF sing 402 n n C2 C3 NPF sing 403 n n C2 H2 NPF sing 404 n n O2 HO2 NPF sing 405 n n C3 O3 NPF sing 406 n n C3 C4 NPF sing 407 n n C3 H3 NPF sing 408 n n O3 HO3 NPF sing 409 n n C4 O4 NPF sing 410 n n C4 C5 NPF sing 411 n n C4 H4 NPF sing 412 n n O4 HO4 NPF sing 413 n n C5 C6 NPF sing 414 n n C5 O5 NPF sing 415 n n C5 H5 NPF sing 416 n n C6 H61 NPF sing 417 n n C6 H62 NPF sing 418 n n C6 H63 NPF sing 419 n n # _pdbx_chem_comp_identifier.comp_id NPF _pdbx_chem_comp_identifier.identifier orthonitrophenyl-b-D-fucopyranoside _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1JWL _atom_sites.fract_transf_matrix[1][1] 0.00391 _atom_sites.fract_transf_matrix[1][2] 0.002257 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004515 _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] 0.004836 _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 F 4 NPF A 1 334 1 NPF ONP . G 4 NPF B 1 334 1 NPF ONP . H 4 NPF C 1 334 1 NPF ONP . # 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 C1A NPF . . . F 4 -13.592 89.298 32.961 1 46.31 ? C1A NPF 334 A 1 HETATM 2 C C2A NPF . . . F 4 -12.784 90.469 32.778 1 46.63 ? C2A NPF 334 A 1 HETATM 3 C C3A NPF . . . F 4 -11.509 90.635 33.343 1 46.75 ? C3A NPF 334 A 1 HETATM 4 C C4A NPF . . . F 4 -10.98 89.605 34.146 1 47.03 ? C4A NPF 334 A 1 HETATM 5 C C5A NPF . . . F 4 -11.775 88.487 34.448 1 46.69 ? C5A NPF 334 A 1 HETATM 6 C C6A NPF . . . F 4 -13.085 88.346 33.893 1 47.36 ? C6A NPF 334 A 1 HETATM 7 N N6 NPF . . . F 4 -13.907 87.299 34.363 1 48.85 ? N6 NPF 334 A 1 HETATM 8 O O6A NPF . . . F 4 -14.937 86.931 33.827 1 49.04 ? O6A NPF 334 A 1 HETATM 9 O O6B NPF . . . F 4 -13.515 86.573 35.249 1 50.92 ? O6B NPF 334 A 1 HETATM 10 O O1 NPF . . . F 4 -14.337 88.747 31.821 1 45.67 ? O1 NPF 334 A 1 HETATM 11 C C1 NPF . . . F 4 -15.763 88.9 31.6 1 46.51 ? C1 NPF 334 A 1 HETATM 12 C C2 NPF . . . F 4 -15.956 90.179 30.749 1 48.27 ? C2 NPF 334 A 1 HETATM 13 O O2 NPF . . . F 4 -16.214 91.294 31.61 1 51.51 ? O2 NPF 334 A 1 HETATM 14 C C3 NPF . . . F 4 -17.014 90.175 29.666 1 49.06 ? C3 NPF 334 A 1 HETATM 15 O O3 NPF . . . F 4 -16.722 91.301 28.804 1 49.56 ? O3 NPF 334 A 1 HETATM 16 C C4 NPF . . . F 4 -16.862 88.881 28.9 1 48.99 ? C4 NPF 334 A 1 HETATM 17 O O4 NPF . . . F 4 -15.527 88.961 28.334 1 49.55 ? O4 NPF 334 A 1 HETATM 18 C C5 NPF . . . F 4 -17.141 87.689 29.859 1 47.46 ? C5 NPF 334 A 1 HETATM 19 C C6 NPF . . . F 4 -17.034 86.364 29.133 1 46.64 ? C6 NPF 334 A 1 HETATM 20 O O5 NPF . . . F 4 -16.248 87.659 31.008 1 45.23 ? O5 NPF 334 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #