data_2PAF # _model_server_result.job_id -DiMZRV8zHu5OaOfU63C1w _model_server_result.datetime_utc '2024-11-26 12:54:47' _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 2paf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":902}' # _entry.id 2PAF # _exptl.entry_id 2PAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 285.25 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-nitrophenyl beta-D-fucopyranoside' _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 90 _cell.entry_id 2PAF _cell.length_a 77.541 _cell.length_b 77.541 _cell.length_c 212.456 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PAF _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id ND2 _struct_conn.ptnr1_label_comp_id ASN _struct_conn.ptnr1_label_seq_id 64 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id ASN _struct_conn.ptnr1_auth_seq_id 125 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id O6B _struct_conn.ptnr2_label_comp_id NPF _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id NPF _struct_conn.ptnr2_auth_seq_id 901 _struct_conn.ptnr2_symmetry 1_555 _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 1.871 _struct_conn.pdbx_value_order ? # _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 235 n y C1A C6A NPF sing 236 n y C1A O1 NPF sing 237 n n C2A C3A NPF sing 238 n y C2A H2A NPF sing 239 n n C3A C4A NPF doub 240 n y C3A H3A NPF sing 241 n n C4A C5A NPF sing 242 n y C4A H4A NPF sing 243 n n C5A C6A NPF doub 244 n y C5A H5A NPF sing 245 n n C6A N6 NPF sing 246 n n N6 O6A NPF sing 247 n n N6 O6B NPF doub 248 n n O1 C1 NPF sing 249 n n C1 C2 NPF sing 250 n n C1 O5 NPF sing 251 n n C1 H1 NPF sing 252 n n C2 O2 NPF sing 253 n n C2 C3 NPF sing 254 n n C2 H2 NPF sing 255 n n O2 HO2 NPF sing 256 n n C3 O3 NPF sing 257 n n C3 C4 NPF sing 258 n n C3 H3 NPF sing 259 n n O3 HO3 NPF sing 260 n n C4 O4 NPF sing 261 n n C4 C5 NPF sing 262 n n C4 H4 NPF sing 263 n n O4 HO4 NPF sing 264 n n C5 C6 NPF sing 265 n n C5 O5 NPF sing 266 n n C5 H5 NPF sing 267 n n C6 H61 NPF sing 268 n n C6 H62 NPF sing 269 n n C6 H63 NPF sing 270 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 2PAF _atom_sites.fract_transf_matrix[1][1] 0.012896 _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] 0.012896 _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] 0.004707 _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 NPF A 1 902 902 NPF NPF . D 2 NPF B 1 901 901 NPF NPF . # 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 . . . C 2 -10.245 16.168 -0.892 1 56.45 ? C1A NPF 902 A 1 HETATM 2 C C2A NPF . . . C 2 -9.007 15.853 -0.291 1 58.28 ? C2A NPF 902 A 1 HETATM 3 C C3A NPF . . . C 2 -8.495 14.555 -0.077 1 59.62 ? C3A NPF 902 A 1 HETATM 4 C C4A NPF . . . C 2 -9.213 13.432 -0.485 1 61.1 ? C4A NPF 902 A 1 HETATM 5 C C5A NPF . . . C 2 -10.459 13.625 -1.106 1 61.72 ? C5A NPF 902 A 1 HETATM 6 C C6A NPF . . . C 2 -11.015 14.908 -1.337 1 60.18 ? C6A NPF 902 A 1 HETATM 7 N N6 NPF . . . C 2 -12.219 15.018 -1.94 1 61.96 ? N6 NPF 902 A 1 HETATM 8 O O6A NPF . . . C 2 -12.858 16.299 -2.215 1 60.82 ? O6A NPF 902 A 1 HETATM 9 O O6B NPF . . . C 2 -12.89 13.795 -2.324 1 63.65 ? O6B NPF 902 A 1 HETATM 10 O O1 NPF . . . C 2 -10.183 17.142 -1.981 1 50.26 ? O1 NPF 902 A 1 HETATM 11 C C1 NPF . . . C 2 -10.521 18.365 -1.334 1 46.47 ? C1 NPF 902 A 1 HETATM 12 C C2 NPF . . . C 2 -9.743 19.531 -1.938 1 43.71 ? C2 NPF 902 A 1 HETATM 13 O O2 NPF . . . C 2 -8.383 19.412 -1.516 1 38.9 ? O2 NPF 902 A 1 HETATM 14 C C3 NPF . . . C 2 -10.33 20.913 -1.525 1 43.45 ? C3 NPF 902 A 1 HETATM 15 O O3 NPF . . . C 2 -10.221 21.826 -2.628 1 42.74 ? O3 NPF 902 A 1 HETATM 16 C C4 NPF . . . C 2 -11.813 20.922 -1.016 1 43.76 ? C4 NPF 902 A 1 HETATM 17 O O4 NPF . . . C 2 -12.726 21.184 -2.071 1 42.61 ? O4 NPF 902 A 1 HETATM 18 C C5 NPF . . . C 2 -12.27 19.628 -0.347 1 44.83 ? C5 NPF 902 A 1 HETATM 19 C C6 NPF . . . C 2 -13.746 19.722 0.128 1 45.07 ? C6 NPF 902 A 1 HETATM 20 O O5 NPF . . . C 2 -11.97 18.575 -1.302 1 46.33 ? O5 NPF 902 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #