data_8QY4 # _model_server_result.job_id YF96imP1dip2kU9R5LwDYQ _model_server_result.datetime_utc '2024-12-26 16:15:01' _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 8qy4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1004}' # _entry.id 8QY4 # _exptl.entry_id 8QY4 _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 10 _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 8QY4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QY4 _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,S,T,U,V _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 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 V 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 C 608 NAG 4 n G NAG 2 G 2 NAG C 609 NAG 4 n H NAG 1 H 1 NAG F 608 NAG 4 n H NAG 2 H 2 NAG F 609 NAG 4 n I NAG 1 I 1 NAG B 318 NAG 4 n I NAG 2 I 2 NAG B 319 NAG 4 n J NAG 1 J 1 NAG B 320 NAG 4 n J NAG 2 J 2 NAG B 321 NAG 4 n K NAG 1 K 1 NAG E 318 NAG 4 n K NAG 2 K 2 NAG E 319 NAG 4 n L NAG 1 L 1 NAG E 320 NAG 4 n L NAG 2 L 2 NAG E 321 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 B SG CYS 28 C CYS 28 1_555 B SG CYS 54 C CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 48 C CYS 48 1_555 B SG CYS 103 C CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 134 C CYS 134 1_555 B SG CYS 144 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 B SG CYS 172 C CYS 172 1_555 B SG CYS 180 C CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 B SG CYS 456 C CYS 456 1_555 B SG CYS 464 C CYS 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 D SG CYS 28 F CYS 28 1_555 D SG CYS 54 F CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 48 F CYS 48 1_555 D SG CYS 103 F CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 D SG CYS 134 F CYS 134 1_555 D SG CYS 144 F CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 D SG CYS 172 F CYS 172 1_555 D SG CYS 180 F CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf10 D SG CYS 456 F CYS 456 1_555 D SG CYS 464 F CYS 464 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 E SG CYS 120 B CYS 120 1_555 E SG CYS 130 B CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 E SG CYS 170 B CYS 170 1_555 E SG CYS 180 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 F SG CYS 120 E CYS 120 1_555 F SG CYS 130 E CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 F SG CYS 170 E CYS 170 1_555 F SG CYS 180 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 B ND2 ASN 43 C ASN 43 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 B ND2 ASN 61 C ASN 61 1_555 M C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B ND2 ASN 83 C ASN 83 1_555 N C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 131 C ASN 131 1_555 O C1 NAG . C NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 157 C ASN 157 1_555 P C1 NAG . C NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 B ND2 ASN 225 C ASN 225 1_555 Q C1 NAG . C NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 D ND2 ASN 43 F ASN 43 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 D ND2 ASN 61 F ASN 61 1_555 R C1 NAG . F NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 D ND2 ASN 83 F ASN 83 1_555 S C1 NAG . F NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D ND2 ASN 131 F ASN 131 1_555 T C1 NAG . F NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D ND2 ASN 157 F ASN 157 1_555 U C1 NAG . F NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 D ND2 ASN 225 F ASN 225 1_555 V C1 NAG . F NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 E ND2 ASN 127 B ASN 127 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 E ND2 ASN 194 B ASN 194 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 F ND2 ASN 127 E ASN 127 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 F ND2 ASN 194 E ASN 194 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale20 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale22 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 8QY4 _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 M 5 NAG C 1 1001 610 NAG NAG . N 5 NAG C 1 1002 611 NAG NAG . O 5 NAG C 1 1003 612 NAG NAG . P 5 NAG C 1 1004 613 NAG NAG . Q 5 NAG C 1 1005 614 NAG NAG . R 5 NAG F 1 1001 610 NAG NAG . S 5 NAG F 1 1002 611 NAG NAG . T 5 NAG F 1 1003 612 NAG NAG . U 5 NAG F 1 1004 613 NAG NAG . V 5 NAG F 1 1005 614 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 . . . U 5 256.904 237.738 213.543 1 24.68 ? C1 NAG 1004 F 1 HETATM 2 C C2 NAG . . . U 5 257.955 238.415 212.651 1 26.25 ? C2 NAG 1004 F 1 HETATM 3 C C3 NAG . . . U 5 257.416 239.707 212.04 1 26.86 ? C3 NAG 1004 F 1 HETATM 4 C C4 NAG . . . U 5 256.054 239.474 211.402 1 26.08 ? C4 NAG 1004 F 1 HETATM 5 C C5 NAG . . . U 5 255.129 238.874 212.461 1 25.24 ? C5 NAG 1004 F 1 HETATM 6 C C6 NAG . . . U 5 253.709 238.644 211.991 1 30.24 ? C6 NAG 1004 F 1 HETATM 7 C C7 NAG . . . U 5 260.376 238.25 213.119 1 20.48 ? C7 NAG 1004 F 1 HETATM 8 C C8 NAG . . . U 5 261.449 238.704 214.076 1 18.01 ? C8 NAG 1004 F 1 HETATM 9 N N2 NAG . . . U 5 259.142 238.703 213.409 1 23.47 ? N2 NAG 1004 F 1 HETATM 10 O O3 NAG . . . U 5 258.358 240.169 211.108 1 27.35 ? O3 NAG 1004 F 1 HETATM 11 O O4 NAG . . . U 5 255.584 240.715 210.93 1 24.68 ? O4 NAG 1004 F 1 HETATM 12 O O5 NAG . . . U 5 255.675 237.639 212.864 1 25.57 ? O5 NAG 1004 F 1 HETATM 13 O O6 NAG . . . U 5 253.706 237.727 210.922 1 32.25 ? O6 NAG 1004 F 1 HETATM 14 O O7 NAG . . . U 5 260.63 237.529 212.166 1 17.1 ? O7 NAG 1004 F 1 HETATM 15 H H1 NAG . . . U 5 256.777 238.283 214.334 1 22.48 ? H1 NAG 1004 F 1 HETATM 16 H H2 NAG . . . U 5 258.188 237.8 211.938 1 23.72 ? H2 NAG 1004 F 1 HETATM 17 H H3 NAG . . . U 5 257.296 240.349 212.756 1 24.58 ? H3 NAG 1004 F 1 HETATM 18 H H4 NAG . . . U 5 256.164 238.838 210.678 1 25.66 ? H4 NAG 1004 F 1 HETATM 19 H H5 NAG . . . U 5 255.081 239.483 213.214 1 24.99 ? H5 NAG 1004 F 1 HETATM 20 H H61 NAG . . . U 5 253.187 238.324 212.743 1 28.08 ? H61 NAG 1004 F 1 HETATM 21 H H62 NAG . . . U 5 253.334 239.502 211.74 1 28.51 ? H62 NAG 1004 F 1 HETATM 22 H H81 NAG . . . U 5 261.51 238.077 214.813 1 15.86 ? H81 NAG 1004 F 1 HETATM 23 H H82 NAG . . . U 5 262.306 238.699 213.621 1 15.91 ? H82 NAG 1004 F 1 HETATM 24 H H83 NAG . . . U 5 261.302 239.591 214.441 1 18.23 ? H83 NAG 1004 F 1 HETATM 25 H HN2 NAG . . . U 5 259.049 239.207 214.099 1 21.94 ? HN2 NAG 1004 F 1 HETATM 26 H HO3 NAG . . . U 5 257.948 240.333 210.382 1 24.93 ? HO3 NAG 1004 F 1 HETATM 27 H HO4 NAG . . . U 5 255.28 240.615 210.142 1 26.04 ? HO4 NAG 1004 F 1 HETATM 28 H HO6 NAG . . . U 5 253.881 236.955 211.231 1 29.06 ? HO6 NAG 1004 F 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #