data_8QY6 # _model_server_result.job_id 9eI8tdhsw5i7QH2TPtengw _model_server_result.datetime_utc '2024-11-26 11:14:26' _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 8qy6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1001}' # _entry.id 8QY6 # _exptl.entry_id 8QY6 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 8QY6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QY6 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M,N,O,P,Q,R _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 Q N N ? 5 R N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 NAG _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 4 n G NAG 1 G 1 NAG A 608 NAG 4 n G NAG 2 G 2 NAG A 609 NAG 4 n H NAG 1 H 1 NAG A 610 NAG 4 n H NAG 2 H 2 NAG A 611 NAG 4 n I NAG 1 I 1 NAG A 612 NAG 4 n I NAG 2 I 2 NAG A 613 NAG 4 n J NAG 1 J 1 NAG A 614 NAG 4 n J NAG 2 J 2 NAG A 615 NAG 4 n K NAG 1 K 1 NAG A 616 NAG 4 n K NAG 2 K 2 NAG A 617 NAG 4 n L NAG 1 L 1 NAG D 608 NAG 4 n L NAG 2 L 2 NAG D 609 NAG 4 n M NAG 1 M 1 NAG D 610 NAG 4 n M NAG 2 M 2 NAG D 611 NAG 4 n N NAG 1 N 1 NAG D 612 NAG 4 n N NAG 2 N 2 NAG D 613 NAG 4 n O NAG 1 O 1 NAG D 614 NAG 4 n O NAG 2 O 2 NAG D 615 NAG 4 n P NAG 1 P 1 NAG D 616 NAG 4 n P NAG 2 P 2 NAG D 617 NAG # 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 28 A CYS 28 1_555 A SG CYS 54 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 48 A CYS 48 1_555 A SG CYS 103 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 134 A CYS 134 1_555 A SG CYS 144 A CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 172 A CYS 172 1_555 A SG CYS 180 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 456 A CYS 456 1_555 A SG CYS 464 A CYS 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 72 B CYS 44 1_555 B SG CYS 78 B CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf7 B SG CYS 101 B CYS 73 1_555 B SG CYS 111 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 C SG CYS 121 C CYS 102 1_555 C SG CYS 132 C CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 165 C CYS 146 1_555 C SG CYS 176 C CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf10 D SG CYS 72 E CYS 44 1_555 D SG CYS 78 E CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf11 D SG CYS 101 E CYS 73 1_555 D SG CYS 111 E CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 E SG CYS 121 F CYS 102 1_555 E SG CYS 132 F CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 E SG CYS 165 F CYS 146 1_555 E SG CYS 176 F CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf14 F SG CYS 28 D CYS 28 1_555 F SG CYS 54 D CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 F SG CYS 48 D CYS 48 1_555 F SG CYS 103 D CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf16 F SG CYS 134 D CYS 134 1_555 F SG CYS 144 D CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 F SG CYS 172 D CYS 172 1_555 F SG CYS 180 D CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf18 F SG CYS 456 D CYS 456 1_555 F SG CYS 464 D CYS 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 43 A ASN 43 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 61 A ASN 61 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 83 A ASN 83 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 131 A ASN 131 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 157 A ASN 157 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 A ND2 ASN 225 A ASN 225 1_555 Q C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 F ND2 ASN 43 D ASN 43 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 F ND2 ASN 61 D ASN 61 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 F ND2 ASN 83 D ASN 83 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 F ND2 ASN 131 D ASN 131 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 F ND2 ASN 157 D ASN 157 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 F ND2 ASN 225 D ASN 225 1_555 R C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale16 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale17 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale19 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale20 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale21 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale22 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 8QY6 _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 Q 5 NAG A 1 1001 618 NAG NAG . R 5 NAG D 1 1001 618 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 . . . R 5 214.251 227.753 243.19 1 21.03 ? C1 NAG 1001 D 1 HETATM 2 C C2 NAG . . . R 5 213.578 226.707 244.089 1 22.96 ? C2 NAG 1001 D 1 HETATM 3 C C3 NAG . . . R 5 214.618 225.723 244.618 1 22.47 ? C3 NAG 1001 D 1 HETATM 4 C C4 NAG . . . R 5 215.438 225.148 243.47 1 24.54 ? C4 NAG 1001 D 1 HETATM 5 C C5 NAG . . . R 5 216.037 226.298 242.657 1 25.89 ? C5 NAG 1001 D 1 HETATM 6 C C6 NAG . . . R 5 216.869 225.855 241.474 1 24.11 ? C6 NAG 1001 D 1 HETATM 7 C C7 NAG . . . R 5 211.653 227.881 245.093 1 23.98 ? C7 NAG 1001 D 1 HETATM 8 C C8 NAG . . . R 5 211.131 228.49 246.371 1 19.14 ? C8 NAG 1001 D 1 HETATM 9 N N2 NAG . . . R 5 212.883 227.341 245.178 1 25.71 ? N2 NAG 1001 D 1 HETATM 10 O O3 NAG . . . R 5 213.944 224.723 245.334 1 19.23 ? O3 NAG 1001 D 1 HETATM 11 O O4 NAG . . . R 5 216.438 224.33 244.033 1 27.48 ? O4 NAG 1001 D 1 HETATM 12 O O5 NAG . . . R 5 214.985 227.108 242.178 1 23.63 ? O5 NAG 1001 D 1 HETATM 13 O O6 NAG . . . R 5 216.143 226.061 240.285 1 23.33 ? O6 NAG 1001 D 1 HETATM 14 O O7 NAG . . . R 5 210.99 227.889 244.066 1 19.69 ? O7 NAG 1001 D 1 HETATM 15 H H1 NAG . . . R 5 214.856 228.288 243.727 1 19.78 ? H1 NAG 1001 D 1 HETATM 16 H H2 NAG . . . R 5 212.927 226.224 243.556 1 21.3 ? H2 NAG 1001 D 1 HETATM 17 H H3 NAG . . . R 5 215.226 226.21 245.196 1 22.24 ? H3 NAG 1001 D 1 HETATM 18 H H4 NAG . . . R 5 214.843 224.634 242.902 1 22.95 ? H4 NAG 1001 D 1 HETATM 19 H H5 NAG . . . R 5 216.622 226.813 243.234 1 23.85 ? H5 NAG 1001 D 1 HETATM 20 H H61 NAG . . . R 5 217.702 226.352 241.482 1 22.72 ? H61 NAG 1001 D 1 HETATM 21 H H62 NAG . . . R 5 217.102 224.923 241.605 1 22.81 ? H62 NAG 1001 D 1 HETATM 22 H H81 NAG . . . R 5 211.728 229.2 246.655 1 17 ? H81 NAG 1001 D 1 HETATM 23 H H82 NAG . . . R 5 210.265 228.893 246.203 1 16.91 ? H82 NAG 1001 D 1 HETATM 24 H H83 NAG . . . R 5 211.039 227.857 247.1 1 17.92 ? H83 NAG 1001 D 1 HETATM 25 H HN2 NAG . . . R 5 213.29 227.373 245.935 1 23.28 ? HN2 NAG 1001 D 1 HETATM 26 H HO3 NAG . . . R 5 214.526 224.259 245.745 1 20.07 ? HO3 NAG 1001 D 1 HETATM 27 H HO4 NAG . . . R 5 216.739 223.809 243.432 1 25.12 ? HO4 NAG 1001 D 1 HETATM 28 H HO6 NAG . . . R 5 216.626 225.814 239.631 1 22.43 ? HO6 NAG 1001 D 1 # _model_server_stats.io_time_ms 268 _model_server_stats.parse_time_ms 79 _model_server_stats.create_model_time_ms 109 _model_server_stats.query_time_ms 1184 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #