data_8Y6A # _model_server_result.job_id 6XlB-WAh1OjRcse55npSnA _model_server_result.datetime_utc '2025-03-04 07:58:52' _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 8y6a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":803}' # _entry.id 8Y6A # _exptl.entry_id 8Y6A _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 8Y6A _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y6A _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 ? _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 ? 8 I N N ? 8 K N N ? 8 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide 7 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 7 2 1 NAG NAG 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 5 n E NAG 1 E 1 NAG E 1 NAG 5 n E NAG 2 E 2 NAG E 2 NAG 5 n E BMA 3 E 3 BMA E 3 BMA 5 n E MAN 4 E 4 MAN E 4 MAN 6 n F NAG 1 F 1 NAG F 1 NAG 6 n F NAG 2 F 2 NAG F 2 NAG 6 n F BMA 3 F 3 BMA F 3 BMA 7 n G NAG 1 G 1 NAG G 1 NAG 7 n G NAG 2 G 2 NAG G 2 NAG 6 n H NAG 1 H 1 NAG H 1 NAG 6 n H NAG 2 H 2 NAG H 2 NAG 6 n H BMA 3 H 3 BMA H 3 BMA # 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 18 B CYS 336 1_555 B SG CYS 43 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 B SG CYS 61 B CYS 379 1_555 B SG CYS 114 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 162 B CYS 480 1_555 B SG CYS 169 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 C SG CYS 22 C CYS 22 1_555 C SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 C SG CYS 154 C CYS 154 1_555 C SG CYS 210 C CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 D SG CYS 23 D CYS 23 1_555 D SG CYS 89 D CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 134 D CYS 134 1_555 D SG CYS 194 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 35 A ASN 53 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A ND2 ASN 72 A ASN 90 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 A ND2 ASN 85 A ASN 103 1_555 I C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 304 A ASN 322 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 A ND2 ASN 528 A ASN 546 1_555 K C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 B ND2 ASN 25 B ASN 343 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 36 B ASN 354 1_555 L C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale9 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale10 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale12 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale15 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? metalc ? metalc1 A NE2 HIS 356 A HIS 374 1_555 J ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc2 A NE2 HIS 360 A HIS 378 1_555 J ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 A OE1 GLU 384 A GLU 402 1_555 J ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc4 A OE2 GLU 384 A GLU 402 1_555 J ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8Y6A _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 8 NAG A 1 801 801 NAG NAG . J 9 ZN A 1 802 805 ZN ZN . K 8 NAG A 1 803 808 NAG NAG . L 8 NAG B 1 601 521 NAG NAG . # 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 . . . K 8 156.512 117.894 119.586 1 162.54 ? C1 NAG 803 A 1 HETATM 2 C C2 NAG . . . K 8 156.976 116.567 118.99 1 164.03 ? C2 NAG 803 A 1 HETATM 3 C C3 NAG . . . K 8 157.172 115.542 120.098 1 165 ? C3 NAG 803 A 1 HETATM 4 C C4 NAG . . . K 8 158.114 116.067 121.169 1 166.49 ? C4 NAG 803 A 1 HETATM 5 C C5 NAG . . . K 8 157.6 117.405 121.689 1 166.26 ? C5 NAG 803 A 1 HETATM 6 C C6 NAG . . . K 8 158.552 118.064 122.661 1 166.15 ? C6 NAG 803 A 1 HETATM 7 C C7 NAG . . . K 8 156.132 115.973 116.74 1 164.4 ? C7 NAG 803 A 1 HETATM 8 C C8 NAG . . . K 8 157.467 116.378 116.195 1 164.64 ? C8 NAG 803 A 1 HETATM 9 N N2 NAG . . . K 8 155.982 116.077 118.061 1 163.69 ? N2 NAG 803 A 1 HETATM 10 O O3 NAG . . . K 8 157.665 114.334 119.535 1 164.41 ? O3 NAG 803 A 1 HETATM 11 O O4 NAG . . . K 8 158.157 115.139 122.249 1 166.8 ? O4 NAG 803 A 1 HETATM 12 O O5 NAG . . . K 8 157.41 118.327 120.598 1 165.46 ? O5 NAG 803 A 1 HETATM 13 O O6 NAG . . . K 8 159.818 118.316 122.057 1 166.24 ? O6 NAG 803 A 1 HETATM 14 O O7 NAG . . . K 8 155.229 115.564 116.017 1 162.16 ? O7 NAG 803 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #