data_1YF8 # _model_server_result.job_id X2imkxPpkeuTxc5u67Eb-w _model_server_result.datetime_utc '2024-11-05 00:18:05' _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 1yf8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1013}' # _entry.id 1YF8 # _exptl.entry_id 1YF8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 9 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-galactopyranose _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 1YF8 _cell.length_a 109.422 _cell.length_b 109.422 _cell.length_c 309.798 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YF8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 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,I,J,K,L _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 9 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 BMA MAN C1 O1 . O3 HO3 . sing 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 5 3 2 MAN NAG C1 O1 . O4 HO4 . sing 7 ? 6 2 1 GAL BGC C1 O1 . O4 HO4 . 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 3 n C NAG 1 C 1 NAG B 256 NAG 3 n C NAG 2 C 2 NAG B 257 NAG 4 n D NAG 1 D 1 NAG B 258 NAG 4 n D NAG 2 D 2 NAG B 259 NAG 4 n D MAN 3 D 3 MAN B 260 MAN 4 n D BMA 4 D 4 BMA B 261 BMA 5 n E NAG 1 E 1 NAG B 262 NAG 5 n E NAG 2 E 2 NAG B 263 NAG 5 n E MAN 3 E 3 MAN B 264 MAN 6 n F BGC 1 F 1 BGC B 265 BGC 6 n F GAL 2 F 2 GAL B 266 GAL 6 n G BGC 1 G 1 BGC B 1014 BGC 6 n G GAL 2 G 2 GAL B 1015 GAL # 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 240 A CYS 240 1_555 B SG CYS 1 B CYS 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 B SG CYS 60 B CYS 60 1_555 B SG CYS 77 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? disulf ? disulf3 B SG CYS 148 B CYS 148 1_555 B SG CYS 161 B CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? disulf ? disulf4 B SG CYS 186 B CYS 186 1_555 B SG CYS 202 B CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? covale ? covale1 A ND2 ASN 107 A ASN 107 1_555 H C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B ND2 ASN 57 B ASN 57 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B ND2 ASN 92 B ASN 92 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale4 B ND2 ASN 132 B ASN 132 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale8 D O3 MAN . D MAN 3 1_555 D C1 BMA . D BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 E O4 NAG . E NAG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 F O4 BGC . F BGC 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale12 G O4 BGC . G BGC 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id GAL _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-galactopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-galactose;D-galactose;galactose # 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 GAL sing 131 n n C1 O1 GAL sing 132 n n C1 O5 GAL sing 133 n n C1 H1 GAL sing 134 n n C2 C3 GAL sing 135 n n C2 O2 GAL sing 136 n n C2 H2 GAL sing 137 n n C3 C4 GAL sing 138 n n C3 O3 GAL sing 139 n n C3 H3 GAL sing 140 n n C4 C5 GAL sing 141 n n C4 O4 GAL sing 142 n n C4 H4 GAL sing 143 n n C5 C6 GAL sing 144 n n C5 O5 GAL sing 145 n n C5 H5 GAL sing 146 n n C6 O6 GAL sing 147 n n C6 H61 GAL sing 148 n n C6 H62 GAL sing 149 n n O1 HO1 GAL sing 150 n n O2 HO2 GAL sing 151 n n O3 HO3 GAL sing 152 n n O4 HO4 GAL sing 153 n n O6 HO6 GAL sing 154 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 GAL DGalpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 GAL b-D-galactopyranose 'COMMON NAME' GMML 1 GAL b-D-Galp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 GAL Gal 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1YF8 _atom_sites.fract_transf_matrix[1][1] 0.009139 _atom_sites.fract_transf_matrix[1][2] 0.005276 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010553 _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] 0.003228 _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 H 7 NAG A 1 1003 1003 NAG NAG . I 8 P6C A 1 1001 1001 P6C P6C . J 9 GAL B 1 1013 1013 GAL GAL . K 10 HOH A 1 1004 1004 HOH HOH . K 10 HOH A 2 1005 1005 HOH HOH . K 10 HOH A 3 1006 1006 HOH HOH . K 10 HOH A 4 1007 1007 HOH HOH . K 10 HOH A 5 1008 1008 HOH HOH . K 10 HOH A 6 1009 1009 HOH HOH . K 10 HOH A 7 1010 1010 HOH HOH . K 10 HOH A 8 1011 1011 HOH HOH . K 10 HOH A 9 1012 1012 HOH HOH . K 10 HOH A 10 1013 1013 HOH HOH . K 10 HOH A 11 1014 1014 HOH HOH . K 10 HOH A 12 1015 1015 HOH HOH . K 10 HOH A 13 1016 1016 HOH HOH . K 10 HOH A 14 1017 1017 HOH HOH . K 10 HOH A 15 1018 1018 HOH HOH . K 10 HOH A 16 1019 1019 HOH HOH . K 10 HOH A 17 1020 1020 HOH HOH . K 10 HOH A 18 1021 1021 HOH HOH . K 10 HOH A 19 1022 1022 HOH HOH . K 10 HOH A 20 1023 1023 HOH HOH . K 10 HOH A 21 1024 1024 HOH HOH . K 10 HOH A 22 1025 1025 HOH HOH . K 10 HOH A 23 1026 1026 HOH HOH . K 10 HOH A 24 1027 1027 HOH HOH . K 10 HOH A 25 1028 1028 HOH HOH . K 10 HOH A 26 1029 1029 HOH HOH . K 10 HOH A 27 1030 1030 HOH HOH . K 10 HOH A 28 1031 1031 HOH HOH . K 10 HOH A 29 1032 1032 HOH HOH . K 10 HOH A 30 1033 1033 HOH HOH . K 10 HOH A 31 1034 1034 HOH HOH . K 10 HOH A 32 1035 1035 HOH HOH . K 10 HOH A 33 1036 1036 HOH HOH . K 10 HOH A 34 1037 1037 HOH HOH . K 10 HOH A 35 1038 1038 HOH HOH . K 10 HOH A 36 1039 1039 HOH HOH . K 10 HOH A 37 1040 1040 HOH HOH . K 10 HOH A 38 1041 1041 HOH HOH . K 10 HOH A 39 1042 1042 HOH HOH . K 10 HOH A 40 1043 1043 HOH HOH . K 10 HOH A 41 1044 1044 HOH HOH . K 10 HOH A 42 1045 1045 HOH HOH . K 10 HOH A 43 1046 1046 HOH HOH . K 10 HOH A 44 1047 1047 HOH HOH . K 10 HOH A 45 1048 1048 HOH HOH . K 10 HOH A 46 1049 1049 HOH HOH . K 10 HOH A 47 1050 1050 HOH HOH . K 10 HOH A 48 1051 1051 HOH HOH . K 10 HOH A 49 1052 1052 HOH HOH . K 10 HOH A 50 1053 1053 HOH HOH . K 10 HOH A 51 1054 1054 HOH HOH . K 10 HOH A 52 1055 1055 HOH HOH . K 10 HOH A 53 1056 1056 HOH HOH . K 10 HOH A 54 1057 1057 HOH HOH . K 10 HOH A 55 1058 1058 HOH HOH . L 10 HOH B 1 1016 1016 HOH HOH . L 10 HOH B 2 1017 1017 HOH HOH . L 10 HOH B 3 1018 1018 HOH HOH . L 10 HOH B 4 1019 1019 HOH HOH . L 10 HOH B 5 1020 1020 HOH HOH . L 10 HOH B 6 1021 1021 HOH HOH . L 10 HOH B 7 1022 1022 HOH HOH . L 10 HOH B 8 1023 1023 HOH HOH . L 10 HOH B 9 1024 1024 HOH HOH . L 10 HOH B 10 1025 1025 HOH HOH . L 10 HOH B 11 1026 1026 HOH HOH . L 10 HOH B 12 1027 1027 HOH HOH . L 10 HOH B 13 1028 1028 HOH HOH . L 10 HOH B 14 1029 1029 HOH HOH . L 10 HOH B 15 1030 1030 HOH HOH . L 10 HOH B 16 1031 1031 HOH HOH . L 10 HOH B 17 1032 1032 HOH HOH . L 10 HOH B 18 1033 1033 HOH HOH . L 10 HOH B 19 1034 1034 HOH HOH . L 10 HOH B 20 1035 1035 HOH HOH . L 10 HOH B 21 1036 1036 HOH HOH . L 10 HOH B 22 1037 1037 HOH HOH . L 10 HOH B 23 1038 1038 HOH HOH . L 10 HOH B 24 1039 1039 HOH HOH . L 10 HOH B 25 1040 1040 HOH HOH . L 10 HOH B 26 1041 1041 HOH HOH . L 10 HOH B 27 1042 1042 HOH HOH . L 10 HOH B 28 1043 1043 HOH HOH . L 10 HOH B 29 1044 1044 HOH HOH . L 10 HOH B 30 1045 1045 HOH HOH . L 10 HOH B 31 1046 1046 HOH HOH . L 10 HOH B 32 1047 1047 HOH HOH . L 10 HOH B 33 1048 1048 HOH HOH . L 10 HOH B 34 1049 1049 HOH HOH . L 10 HOH B 35 1050 1050 HOH HOH . L 10 HOH B 36 1051 1051 HOH HOH . L 10 HOH B 37 1052 1052 HOH HOH . L 10 HOH B 38 1053 1053 HOH HOH . L 10 HOH B 39 1054 1054 HOH HOH . L 10 HOH B 40 1055 1055 HOH HOH . L 10 HOH B 41 1056 1056 HOH HOH . L 10 HOH B 42 1057 1057 HOH HOH . L 10 HOH B 43 1058 1058 HOH HOH . L 10 HOH B 44 1059 1059 HOH HOH . L 10 HOH B 45 1060 1060 HOH HOH . L 10 HOH B 46 1061 1061 HOH HOH . L 10 HOH B 47 1062 1062 HOH HOH . L 10 HOH B 48 1063 1063 HOH HOH . L 10 HOH B 49 1064 1064 HOH HOH . L 10 HOH B 50 1065 1065 HOH HOH . L 10 HOH B 51 1066 1066 HOH HOH . L 10 HOH B 52 1067 1067 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 GAL . . . J 9 56.56 30.875 -20.763 1 122.47 ? C1 GAL 1013 B 1 HETATM 2 C C2 GAL . . . J 9 57.513 30.248 -19.736 1 112.65 ? C2 GAL 1013 B 1 HETATM 3 C C3 GAL . . . J 9 58.847 30.93 -19.99 1 109.61 ? C3 GAL 1013 B 1 HETATM 4 C C4 GAL . . . J 9 59.293 30.974 -21.469 1 108.85 ? C4 GAL 1013 B 1 HETATM 5 C C5 GAL . . . J 9 58.209 31.133 -22.533 1 125.6 ? C5 GAL 1013 B 1 HETATM 6 C C6 GAL . . . J 9 58.747 30.598 -23.887 1 120.62 ? C6 GAL 1013 B 1 HETATM 7 O O2 GAL . . . J 9 57.088 30.386 -18.382 1 94.31 ? O2 GAL 1013 B 1 HETATM 8 O O3 GAL . . . J 9 59.804 30.548 -19.02 1 113.89 ? O3 GAL 1013 B 1 HETATM 9 O O4 GAL . . . J 9 60.288 30.087 -21.967 1 114.45 ? O4 GAL 1013 B 1 HETATM 10 O O5 GAL . . . J 9 56.962 30.561 -22.101 1 124.94 ? O5 GAL 1013 B 1 HETATM 11 O O6 GAL . . . J 9 59.318 31.636 -24.69 1 119.89 ? O6 GAL 1013 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #