data_2YGQ # _model_server_result.job_id uVetqu-GBa8zUsGp9Hrx9g _model_server_result.datetime_utc '2024-11-22 17:39:56' _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 2ygq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1278}' # _entry.id 2YGQ # _exptl.entry_id 2YGQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-L-fucopyranose _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 2YGQ _cell.length_a 178.007 _cell.length_b 178.007 _cell.length_c 178.007 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 3 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GU4 _pdbx_entity_branch_link.comp_id_2 YYJ _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GU4 1 B 1 GU4 A 1279 SCR 2 n B YYJ 2 B 2 YYJ A 1279 SCR # 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 disulf ? disulf1 A SG CYS 109 A CYS 140 1_555 A SG CYS 146 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 151 A CYS 182 1_555 A SG CYS 161 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 155 A CYS 186 1_555 A SG CYS 167 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 169 A CYS 200 1_555 A SG CYS 178 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 183 A CYS 214 1_555 A SG CYS 193 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 A SG CYS 187 A CYS 218 1_555 A SG CYS 199 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 201 A CYS 232 1_555 A SG CYS 210 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 215 A CYS 246 1_555 A SG CYS 225 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 219 A CYS 250 1_555 A SG CYS 231 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 A SG CYS 233 A CYS 264 1_555 A SG CYS 242 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 57 A ASN 88 1_555 D C1 NAG . A NAG 1276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 214 A ASN 245 1_555 E C1 NAG . A NAG 1277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A OG1 THR 224 A THR 255 1_555 F C1 FUC . A FUC 1278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B C1 GU4 . B GU4 1 1_555 B O2 YYJ . B YYJ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing # _chem_comp.formula 'C6 H12 O5' _chem_comp.formula_weight 164.156 _chem_comp.id FUC _chem_comp.mon_nstd_flag . _chem_comp.name alpha-L-fucopyranose _chem_comp.type 'l-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-L-fucose;6-deoxy-alpha-L-galactopyranose;L-fucose;fucose # 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 FUC sing 83 n n C1 O1 FUC sing 84 n n C1 O5 FUC sing 85 n n C1 H1 FUC sing 86 n n C2 C3 FUC sing 87 n n C2 O2 FUC sing 88 n n C2 H2 FUC sing 89 n n C3 C4 FUC sing 90 n n C3 O3 FUC sing 91 n n C3 H3 FUC sing 92 n n C4 C5 FUC sing 93 n n C4 O4 FUC sing 94 n n C4 H4 FUC sing 95 n n C5 C6 FUC sing 96 n n C5 O5 FUC sing 97 n n C5 H5 FUC sing 98 n n C6 H61 FUC sing 99 n n C6 H62 FUC sing 100 n n C6 H63 FUC sing 101 n n O1 HO1 FUC sing 102 n n O2 HO2 FUC sing 103 n n O3 HO3 FUC sing 104 n n O4 HO4 FUC sing 105 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version FUC LFucpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 FUC a-L-fucopyranose 'COMMON NAME' GMML 1 FUC a-L-Fucp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 FUC Fuc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2YGQ _atom_sites.fract_transf_matrix[1][1] 0.005618 _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] 0.005618 _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] 0.005618 _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 PCF A 1 1275 1275 PCF PCF . D 4 NAG A 1 1276 1276 NAG NAG . E 4 NAG A 1 1277 1277 NAG NAG . F 5 FUC A 1 1278 1278 FUC FUC . # 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 FUC . . . F 5 27.259 -13.474 8.172 1 295.55 ? C1 FUC 1278 A 1 HETATM 2 C C2 FUC . . . F 5 28.469 -14.395 8.358 1 305.07 ? C2 FUC 1278 A 1 HETATM 3 C C3 FUC . . . F 5 28.141 -15.743 7.725 1 305.59 ? C3 FUC 1278 A 1 HETATM 4 C C4 FUC . . . F 5 27.831 -15.504 6.245 1 299.21 ? C4 FUC 1278 A 1 HETATM 5 C C5 FUC . . . F 5 26.642 -14.533 6.154 1 290.77 ? C5 FUC 1278 A 1 HETATM 6 C C6 FUC . . . F 5 26.318 -14.287 4.678 1 287.48 ? C6 FUC 1278 A 1 HETATM 7 O O2 FUC . . . F 5 28.751 -14.571 9.747 1 315.07 ? O2 FUC 1278 A 1 HETATM 8 O O3 FUC . . . F 5 29.248 -16.636 7.863 1 315.26 ? O3 FUC 1278 A 1 HETATM 9 O O4 FUC . . . F 5 28.973 -14.937 5.598 1 301.82 ? O4 FUC 1278 A 1 HETATM 10 O O5 FUC . . . F 5 26.969 -13.28 6.777 1 288.93 ? O5 FUC 1278 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #