data_6A87 # _model_server_result.job_id VZ4YZqLPL6ijclliZHtRDQ _model_server_result.datetime_utc '2024-12-02 22:51:10' _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 6a87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":101}' # _entry.id 6A87 # _exptl.entry_id 6A87 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 3 _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 120 _cell.entry_id 6A87 _cell.length_a 145.778 _cell.length_b 145.778 _cell.length_c 39.531 _cell.Z_PDB 54 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 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,J,N,O,P 1 1 D,E,F,G,H,I,K,L,M,Q,R,S 2 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 3 _struct_asym.id J _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 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 FUC _pdbx_entity_branch_link.comp_id_2 NAG _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 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _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 G NAG 1 G 1 NAG F 101 NAG 2 n G FUC 2 G 2 FUC F 102 FUC 2 n H NAG 1 H 1 NAG D 101 NAG 2 n H FUC 2 H 2 FUC D 102 FUC 2 n I NAG 1 I 1 NAG E 101 NAG 2 n I FUC 2 I 2 FUC E 102 FUC # 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 10 A CYS 10 1_555 A SG CYS 17 A CYS 17 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 E SG CYS 10 E CYS 10 1_555 E SG CYS 17 E CYS 17 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.056 ? disulf ? disulf3 F SG CYS 10 F CYS 10 1_555 F SG CYS 17 F CYS 17 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 F SG CYS 10 F CYS 10 1_555 F SG CYS 17 F CYS 17 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.036 ? covale ? covale1 K S MEE . E MEE 101 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? covale ? covale2 L S MEE . E MEE 104 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? covale ? covale3 M S MEE . F MEE 103 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? covale ? covale4 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 I O6 NAG . I NAG 1 1_555 I C1 FUC . I FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _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 41 n n C1 O1 FUC sing 42 n n C1 O5 FUC sing 43 n n C1 H1 FUC sing 44 n n C2 C3 FUC sing 45 n n C2 O2 FUC sing 46 n n C2 H2 FUC sing 47 n n C3 C4 FUC sing 48 n n C3 O3 FUC sing 49 n n C3 H3 FUC sing 50 n n C4 C5 FUC sing 51 n n C4 O4 FUC sing 52 n n C4 H4 FUC sing 53 n n C5 C6 FUC sing 54 n n C5 O5 FUC sing 55 n n C5 H5 FUC sing 56 n n C6 H61 FUC sing 57 n n C6 H62 FUC sing 58 n n C6 H63 FUC sing 59 n n O1 HO1 FUC sing 60 n n O2 HO2 FUC sing 61 n n O3 HO3 FUC sing 62 n n O4 HO4 FUC sing 63 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 6A87 _atom_sites.fract_transf_matrix[1][1] 0.00686 _atom_sites.fract_transf_matrix[1][2] 0.00396 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007921 _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] 0.025297 _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 J 3 FUC A 1 101 102 FUC FUC . K 4 MEE E 1 101 100 MEE MEE . L 4 MEE E 1 104 100 MEE MEE . M 4 MEE F 1 103 100 MEE MEE . N 5 HOH A 1 201 14 HOH HOH . N 5 HOH A 2 202 11 HOH HOH . N 5 HOH A 3 203 4 HOH HOH . N 5 HOH A 4 204 15 HOH HOH . N 5 HOH A 5 205 9 HOH HOH . N 5 HOH A 6 206 23 HOH HOH . N 5 HOH A 7 207 15 HOH HOH . N 5 HOH A 8 208 25 HOH HOH . N 5 HOH A 9 209 28 HOH HOH . N 5 HOH A 10 210 32 HOH HOH . N 5 HOH A 11 211 60 HOH HOH . N 5 HOH A 12 212 24 HOH HOH . O 5 HOH B 1 101 6 HOH HOH . O 5 HOH B 2 102 4 HOH HOH . O 5 HOH B 3 103 32 HOH HOH . O 5 HOH B 4 104 40 HOH HOH . O 5 HOH B 5 105 20 HOH HOH . O 5 HOH B 6 106 65 HOH HOH . O 5 HOH B 7 107 13 HOH HOH . O 5 HOH B 8 108 44 HOH HOH . O 5 HOH B 9 109 7 HOH HOH . O 5 HOH B 10 110 17 HOH HOH . O 5 HOH B 11 111 20 HOH HOH . O 5 HOH B 12 112 14 HOH HOH . O 5 HOH B 13 113 72 HOH HOH . P 5 HOH C 1 101 38 HOH HOH . P 5 HOH C 2 102 46 HOH HOH . P 5 HOH C 3 103 11 HOH HOH . P 5 HOH C 4 104 50 HOH HOH . P 5 HOH C 5 105 24 HOH HOH . P 5 HOH C 6 106 80 HOH HOH . Q 5 HOH D 1 201 33 HOH HOH . Q 5 HOH D 2 202 5 HOH HOH . Q 5 HOH D 3 203 22 HOH HOH . Q 5 HOH D 4 204 40 HOH HOH . Q 5 HOH D 5 205 21 HOH HOH . Q 5 HOH D 6 206 10 HOH HOH . Q 5 HOH D 7 207 8 HOH HOH . Q 5 HOH D 8 208 24 HOH HOH . Q 5 HOH D 9 209 1 HOH HOH . Q 5 HOH D 10 210 18 HOH HOH . Q 5 HOH D 11 211 14 HOH HOH . Q 5 HOH D 12 212 2 HOH HOH . Q 5 HOH D 13 213 48 HOH HOH . Q 5 HOH D 14 214 25 HOH HOH . Q 5 HOH D 15 215 35 HOH HOH . Q 5 HOH D 16 216 38 HOH HOH . Q 5 HOH D 17 217 7 HOH HOH . R 5 HOH E 1 201 8 HOH HOH . R 5 HOH E 2 202 12 HOH HOH . R 5 HOH E 3 203 22 HOH HOH . R 5 HOH E 4 204 22 HOH HOH . R 5 HOH E 5 205 5 HOH HOH . R 5 HOH E 6 206 10 HOH HOH . R 5 HOH E 7 207 54 HOH HOH . R 5 HOH E 8 208 27 HOH HOH . R 5 HOH E 9 209 16 HOH HOH . R 5 HOH E 10 210 31 HOH HOH . R 5 HOH E 11 211 51 HOH HOH . R 5 HOH E 12 212 47 HOH HOH . S 5 HOH F 1 201 36 HOH HOH . S 5 HOH F 2 202 30 HOH HOH . S 5 HOH F 3 203 1 HOH HOH . S 5 HOH F 4 204 19 HOH HOH . S 5 HOH F 5 205 34 HOH HOH . S 5 HOH F 6 206 33 HOH HOH . S 5 HOH F 7 207 53 HOH HOH . S 5 HOH F 8 208 37 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 FUC . . . J 3 22.64 23.213 10.17 1 55.08 ? C1 FUC 101 A 1 HETATM 2 C C2 FUC . . . J 3 23.447 23.865 11.328 1 50.8 ? C2 FUC 101 A 1 HETATM 3 C C3 FUC . . . J 3 24.476 24.959 10.917 1 47.75 ? C3 FUC 101 A 1 HETATM 4 C C4 FUC . . . J 3 23.85 25.949 9.926 1 46.05 ? C4 FUC 101 A 1 HETATM 5 C C5 FUC . . . J 3 23.174 25.143 8.808 1 46.96 ? C5 FUC 101 A 1 HETATM 6 C C6 FUC . . . J 3 22.535 26.066 7.781 1 45.88 ? C6 FUC 101 A 1 HETATM 7 O O1 FUC . . . J 3 23.433 22.271 9.397 1 51.76 ? O1 FUC 101 A 1 HETATM 8 O O2 FUC . . . J 3 24.055 22.757 12.038 1 51.83 ? O2 FUC 101 A 1 HETATM 9 O O3 FUC . . . J 3 24.942 25.719 12.078 1 48.05 ? O3 FUC 101 A 1 HETATM 10 O O4 FUC . . . J 3 22.876 26.724 10.688 1 42.88 ? O4 FUC 101 A 1 HETATM 11 O O5 FUC . . . J 3 22.114 24.307 9.366 1 52.3 ? O5 FUC 101 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 454 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 11 #