data_8AGC # _model_server_result.job_id d7v16s_MbEUqS4DwjpPXSg _model_server_result.datetime_utc '2024-11-25 14:14:11' _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 8agc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":501}' # _entry.id 8AGC # _exptl.entry_id 8AGC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 17 _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 8AGC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AGC _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? 17 U N N ? 17 V N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 10 oligosaccharide 11 oligosaccharide 12 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 ? 10 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 10 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 10 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 10 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 10 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 10 7 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 11 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 12 2 1 NAG NDG C1 O1 . O4 HO4 . sing 9 ? 12 3 2 BMA NAG C1 O1 . O4 HO4 . sing 10 ? 12 4 3 MAN BMA C1 O1 . O3 HO3 . sing 11 ? 12 5 4 MAN MAN C1 O1 . O2 HO2 . sing 12 ? 12 6 5 MAN MAN C1 O1 . O2 HO2 . sing 13 ? 12 7 6 GLC MAN C1 O1 . O3 HO3 . sing 14 ? 12 8 7 GLC GLC C1 O1 . O3 HO3 . sing 15 ? 12 9 8 GLC GLC C1 O1 . O2 HO2 . sing 16 ? 12 10 3 MAN BMA C1 O1 . O6 HO6 . sing 17 ? 12 11 10 MAN MAN C1 O1 . O3 HO3 . 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 10 n J NAG 1 I 1 NAG A 1002 NAG 10 n J NAG 2 I 2 NAG A 1009 NAG 10 n J BMA 3 I 3 BMA A 1010 BMA 10 n J MAN 4 I 4 MAN A 1011 MAN 10 n J MAN 5 I 5 MAN A 1006 MAN 10 n J MAN 6 I 6 MAN A 1007 MAN 10 n J MAN 7 I 7 MAN A 1008 MAN 11 n K NAG 1 J 1 NAG I 1 NAG 11 n K NAG 2 J 2 NAG I 2 NAG 11 n L NAG 1 K 1 NAG J 1 NAG 11 n L NAG 2 K 2 NAG J 2 NAG 12 n M NDG 1 L 1 NDG K 1 NDG 12 n M NAG 2 L 2 NAG K 2 NAG 12 n M BMA 3 L 3 BMA K 3 BMA 12 n M MAN 4 L 4 MAN K 4 MAN 12 n M MAN 5 L 5 MAN K 5 MAN 12 n M MAN 6 L 6 MAN K 6 MAN 12 n M GLC 7 L 7 GLC K 7 GLC 12 n M GLC 8 L 8 GLC K 8 GLC 12 n M GLC 9 L 9 GLC K 9 GLC 12 n M MAN 10 L 10 MAN K 10 MAN 12 n M MAN 11 L 11 MAN K 11 MAN # 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 covale ? covale1 A ND2 ASN 539 A ASN 539 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 N O1B ELU . A ELU 1001 1_555 M C1 NDG . L NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale3 E ND2 ASN 336 E ASN 336 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 E ND2 ASN 400 E ASN 400 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 G ND2 ASN 60 G ASN 60 1_555 V C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 G ND2 ASN 332 G ASN 332 1_555 U C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 I N TYR 1 P TYR 2 1_555 X C25 323 . P 323 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 I C ALA 2 P ALA 3 1_555 I N DAB 3 P DAB 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 I C DAB 3 P DAB 4 1_555 I N ALA 4 P ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale11 J O4 NAG . I NAG 2 1_555 J C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 J O3 BMA . I BMA 3 1_555 J C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 J O6 BMA . I BMA 3 1_555 J C1 MAN . I MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 J O2 MAN . I MAN 4 1_555 J C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale15 J O2 MAN . I MAN 5 1_555 J C1 MAN . I MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale17 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 M O4 NDG . L NDG 1 1_555 M C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 M O4 NAG . L NAG 2 1_555 M C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale20 M O3 BMA . L BMA 3 1_555 M C1 MAN . L MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale21 M O6 BMA . L BMA 3 1_555 M C1 MAN . L MAN 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale22 M O2 MAN . L MAN 4 1_555 M C1 MAN . L MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale23 M O2 MAN . L MAN 5 1_555 M C1 MAN . L MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale24 M O3 MAN . L MAN 6 1_555 M C1 GLC . L GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale25 M O3 GLC . L GLC 7 1_555 M C1 GLC . L GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale26 M O2 GLC . L GLC 8 1_555 M C1 GLC . L GLC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale27 M O3 MAN . L MAN 10 1_555 M C1 MAN . L MAN 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OD2 ASP 166 A ASP 166 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 N O2B ELU . A ELU 1001 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _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 577 n n C1 O1 NAG sing 578 n n C1 O5 NAG sing 579 n n C1 H1 NAG sing 580 n n C2 C3 NAG sing 581 n n C2 N2 NAG sing 582 n n C2 H2 NAG sing 583 n n C3 C4 NAG sing 584 n n C3 O3 NAG sing 585 n n C3 H3 NAG sing 586 n n C4 C5 NAG sing 587 n n C4 O4 NAG sing 588 n n C4 H4 NAG sing 589 n n C5 C6 NAG sing 590 n n C5 O5 NAG sing 591 n n C5 H5 NAG sing 592 n n C6 O6 NAG sing 593 n n C6 H61 NAG sing 594 n n C6 H62 NAG sing 595 n n C7 C8 NAG sing 596 n n C7 N2 NAG sing 597 n n C7 O7 NAG doub 598 n n C8 H81 NAG sing 599 n n C8 H82 NAG sing 600 n n C8 H83 NAG sing 601 n n N2 HN2 NAG sing 602 n n O1 HO1 NAG sing 603 n n O3 HO3 NAG sing 604 n n O4 HO4 NAG sing 605 n n O6 HO6 NAG sing 606 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 8AGC _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 N 13 ELU A 1 1001 1001 ELU ELU . O 14 CPL A 1 1002 1003 CPL CPL . P 15 PTY A 1 1003 1004 PTY PTY . Q 16 MN A 1 1004 1005 MN MN . R 14 CPL C 1 101 101 CPL CPL . S 14 CPL E 1 501 501 CPL CPL . T 14 CPL F 1 301 301 CPL CPL . U 17 NAG G 1 501 501 NAG NAG . V 17 NAG G 1 502 502 NAG NAG . W 15 PTY H 1 901 901 PTY PTY . X 18 323 P 1 101 1 323 323 . # 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 17 124.335 185.397 112.711 1 70 ? C1 NAG 501 G 1 HETATM 2 C C2 NAG . . . U 17 124.438 185.842 111.244 1 70 ? C2 NAG 501 G 1 HETATM 3 C C3 NAG . . . U 17 123.365 185.166 110.369 1 70 ? C3 NAG 501 G 1 HETATM 4 C C4 NAG . . . U 17 121.979 185.19 111.011 1 70 ? C4 NAG 501 G 1 HETATM 5 C C5 NAG . . . U 17 122.016 184.761 112.474 1 70 ? C5 NAG 501 G 1 HETATM 6 C C6 NAG . . . U 17 122.327 183.299 112.702 1 70 ? C6 NAG 501 G 1 HETATM 7 C C7 NAG . . . U 17 125.394 188.091 111.416 1 70 ? C7 NAG 501 G 1 HETATM 8 C C8 NAG . . . U 17 125.148 189.561 111.252 1 70 ? C8 NAG 501 G 1 HETATM 9 N N2 NAG . . . U 17 124.363 187.289 111.131 1 70 ? N2 NAG 501 G 1 HETATM 10 O O3 NAG . . . U 17 123.759 183.835 110.055 1 70 ? O3 NAG 501 G 1 HETATM 11 O O4 NAG . . . U 17 121.432 186.501 110.929 1 70 ? O4 NAG 501 G 1 HETATM 12 O O5 NAG . . . U 17 122.979 185.557 113.175 1 70 ? O5 NAG 501 G 1 HETATM 13 O O6 NAG . . . U 17 122.086 182.927 114.052 1 70 ? O6 NAG 501 G 1 HETATM 14 O O7 NAG . . . U 17 126.477 187.65 111.788 1 70 ? O7 NAG 501 G 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #