data_1YF8 # _model_server_result.job_id P44I3EC6XkE96sZSsf3Prg _model_server_result.datetime_utc '2024-11-05 00:21:35' _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":"H","auth_seq_id":1003}' # _entry.id 1YF8 # _exptl.entry_id 1YF8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 7 _struct_asym.id H _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 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 333 n n C1 O1 NAG sing 334 n n C1 O5 NAG sing 335 n n C1 H1 NAG sing 336 n n C2 C3 NAG sing 337 n n C2 N2 NAG sing 338 n n C2 H2 NAG sing 339 n n C3 C4 NAG sing 340 n n C3 O3 NAG sing 341 n n C3 H3 NAG sing 342 n n C4 C5 NAG sing 343 n n C4 O4 NAG sing 344 n n C4 H4 NAG sing 345 n n C5 C6 NAG sing 346 n n C5 O5 NAG sing 347 n n C5 H5 NAG sing 348 n n C6 O6 NAG sing 349 n n C6 H61 NAG sing 350 n n C6 H62 NAG sing 351 n n C7 C8 NAG sing 352 n n C7 N2 NAG sing 353 n n C7 O7 NAG doub 354 n n C8 H81 NAG sing 355 n n C8 H82 NAG sing 356 n n C8 H83 NAG sing 357 n n N2 HN2 NAG sing 358 n n O1 HO1 NAG sing 359 n n O3 HO3 NAG sing 360 n n O4 HO4 NAG sing 361 n n O6 HO6 NAG sing 362 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc '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 NAG . . . H 7 49.09 44.472 29.921 1 127.54 ? C1 NAG 1003 A 1 HETATM 2 C C2 NAG . . . H 7 50.309 43.702 29.373 1 134.79 ? C2 NAG 1003 A 1 HETATM 3 C C3 NAG . . . H 7 49.92 42.291 28.89 1 132.68 ? C3 NAG 1003 A 1 HETATM 4 C C4 NAG . . . H 7 49.372 41.538 30.101 1 136.7 ? C4 NAG 1003 A 1 HETATM 5 C C5 NAG . . . H 7 48.226 42.336 30.727 1 137.35 ? C5 NAG 1003 A 1 HETATM 6 C C6 NAG . . . H 7 48.478 42.552 32.218 1 147.58 ? C6 NAG 1003 A 1 HETATM 7 C C7 NAG . . . H 7 51.829 45.559 28.723 1 148.4 ? C7 NAG 1003 A 1 HETATM 8 C C8 NAG . . . H 7 51.305 46.95 28.444 1 143.49 ? C8 NAG 1003 A 1 HETATM 9 N N2 NAG . . . H 7 51.067 44.495 28.405 1 142.99 ? N2 NAG 1003 A 1 HETATM 10 O O3 NAG . . . H 7 50.965 41.561 28.269 1 118.36 ? O3 NAG 1003 A 1 HETATM 11 O O4 NAG . . . H 7 49.018 40.192 29.845 1 136.04 ? O4 NAG 1003 A 1 HETATM 12 O O5 NAG . . . H 7 47.985 43.579 30.074 1 127.88 ? O5 NAG 1003 A 1 HETATM 13 O O6 NAG . . . H 7 47.381 42.058 32.963 1 152.93 ? O6 NAG 1003 A 1 HETATM 14 O O7 NAG . . . H 7 52.982 45.438 29.143 1 145.13 ? O7 NAG 1003 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #